9NL7 | pdb_00009nl7

E. coli initiation complex with EQ2-YbiT in Non-hydrolytic 2/PtIM(b) conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

E. coli initiation complex with EQ2-YbiT in Non-hydrolytic 2/PtIM(b) conformation

Hunt, J.F.Singh, S.

To be published.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL1A [auth 1]220Escherichia coliMutation(s): 0 
Gene Names: rplAb3984JW3947
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13B [auth 13]142Escherichia coliMutation(s): 0 
Gene Names: rplMb3231JW3200
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14C [auth 14]122Escherichia coliMutation(s): 0 
Gene Names: rplNA13A_03633
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15D [auth 15]144Escherichia coliMutation(s): 0 
Gene Names: rplOb3301JW3263
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16E [auth 16]136Escherichia coliMutation(s): 0 
Gene Names: rplPb3313JW3275
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL17F [auth 17]120Escherichia coliMutation(s): 0 
Gene Names: rplQb3294JW3256
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18G [auth 18]116Escherichia coliMutation(s): 0 
Gene Names: rplRb3304JW3266
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19H [auth 19]114Escherichia coliMutation(s): 0 
Gene Names: rplSA13A_02795
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2I [auth 2]271Escherichia coliMutation(s): 0 
Gene Names: rplBb3317JW3279
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL20J [auth 20]117Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL21K [auth 21]103Escherichia coliMutation(s): 0 
Gene Names: rplUUTI89_C3620
UniProt
Find proteins for Q1R6F0 (Escherichia coli (strain UTI89 / UPEC))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22L [auth 22]110Escherichia coliMutation(s): 0 
Gene Names: rplVUTI89_C3767
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23M [auth 23]93Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24N [auth 24]102Escherichia coliMutation(s): 0 
Gene Names: rplX
UniProt
Find proteins for A0A7U9LWC1 (Escherichia coli O145:H28)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL25O [auth 25]94Escherichia coliMutation(s): 0 
Gene Names: rplY
UniProt
Find proteins for P68919 (Escherichia coli (strain K12))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27P [auth 27]75Escherichia coliMutation(s): 0 
Gene Names: rpmAECVG_02038
UniProt
Find proteins for A0A1X3JCC7 (Escherichia coli H386)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28Q [auth 28]77Escherichia coliMutation(s): 0 
Gene Names: rpmBG925_03874
UniProt
Find proteins for A0A0E2KZD0 (Escherichia coli (strain UMEA 3162-1))
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29R [auth 29]63Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3S [auth 3]209Escherichia coliMutation(s): 0 
Gene Names: rplCb3320JW3282
UniProt
Find proteins for P60438 (Escherichia coli (strain K12))
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30T [auth 30]58Escherichia coliMutation(s): 0 
Gene Names: rpmDb3302JW3264
UniProt
Find proteins for P0AG51 (Escherichia coli (strain K12))
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL31U [auth 31]66Escherichia coliMutation(s): 0 
Gene Names: rpmEb3936JW3907
UniProt
Find proteins for P0A7M9 (Escherichia coli (strain K12))
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32V [auth 32]56Escherichia coliMutation(s): 0 
Gene Names: rpmFECDEC2D_1303
UniProt
Find proteins for A0A828UBL8 (Escherichia coli DEC2D)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL33W [auth 33]50Escherichia coliMutation(s): 0 
Gene Names: rpmGb3636JW3611
UniProt
Find proteins for P0A7N9 (Escherichia coli (strain K12))
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34X [auth 34]46Escherichia coliMutation(s): 0 
Gene Names: rpmH
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL35Y [auth 35]64Escherichia coliMutation(s): 0 
Gene Names: rpmI
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36Z [auth 36]38Escherichia coliMutation(s): 0 
Gene Names: rpmJ
UniProt
Find proteins for A0A0E2L017 (Escherichia coli (strain UMEA 3162-1))
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4AA [auth 4]201Escherichia coliMutation(s): 0 
Gene Names: rplDeryAb3319JW3281
UniProt
Find proteins for P60723 (Escherichia coli (strain K12))
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5BA [auth 5]177Escherichia coliMutation(s): 0 
Gene Names: rplECCU01_002520
UniProt
Find proteins for A0A4P8BX24 (Escherichia coli O145:NM)
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6CA [auth 6]176Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein bL9DA [auth 9]149Escherichia coliMutation(s): 0 
Gene Names: rplIb4203JW4161
UniProt
Find proteins for P0A7R1 (Escherichia coli (strain K12))
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ATP-binding protein YbiTJA [auth Y]530Escherichia coliMutation(s): 0 
Gene Names: ybiTb0820JW0804
UniProt
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS2KA [auth sb]218Escherichia coliMutation(s): 0 
Gene Names: rpsBb0169JW0164
UniProt
Find proteins for P0A7V0 (Escherichia coli (strain K12))
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS3LA [auth sc]206Escherichia coliMutation(s): 0 
Gene Names: rpsCZ4685ECs4179
UniProt
Find proteins for P0A7V5 (Escherichia coli O157:H7)
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4MA [auth sd]205Escherichia coliMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS5NA [auth se]157Escherichia coliMutation(s): 0 
Gene Names: rpsEspcb3303JW3265
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6, non-modified isoformOA [auth sf]100Escherichia coliMutation(s): 0 
Gene Names: rpsFb4200JW4158
UniProt
Find proteins for P02358 (Escherichia coli (strain K12))
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7PA [auth sg]151Escherichia coliMutation(s): 0 
Gene Names: rpsGb3341JW3303
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8QA [auth sh]129Escherichia coliMutation(s): 0 
Gene Names: rpsHECDEC2D_3910
UniProt
Find proteins for A0A828U358 (Escherichia coli DEC2D)
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS9RA [auth si]127Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10SA [auth sj]98Escherichia coliMutation(s): 0 
Gene Names: rpsJNRG857_16455
UniProt
Find proteins for A0A0H3EQD3 (Escherichia coli O83:H1 (strain NRG 857C / AIEC))
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS11TA [auth sk]116Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS12UA [auth sl]123Escherichia coliMutation(s): 0 
UniProt
Find proteins for C3SQR7 (Escherichia coli)
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13VA [auth sm]114Escherichia coliMutation(s): 0 
Gene Names: rpsMA13A_03621
UniProt
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS14WA [auth sn]100Escherichia coliMutation(s): 0 
Gene Names: rpsNEIMP300_17810
UniProt
Find proteins for A0A8S0FJJ0 (Escherichia coli)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS15XA [auth so]88Escherichia coliMutation(s): 0 
Gene Names: rpsOsecCb3165JW3134
UniProt
Find proteins for P0ADZ4 (Escherichia coli (strain K12))
Explore P0ADZ4 
Go to UniProtKB:  P0ADZ4
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UniProt GroupP0ADZ4
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS16YA [auth sp]82Escherichia coliMutation(s): 0 
Gene Names: rpsP
UniProt
Find proteins for C3SYP2 (Escherichia coli)
Explore C3SYP2 
Go to UniProtKB:  C3SYP2
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UniProt GroupC3SYP2
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS17ZA [auth sq]80Escherichia coliMutation(s): 0 
Gene Names: rpsQneaAb3311JW3273
UniProt
Find proteins for P0AG63 (Escherichia coli (strain K12))
Explore P0AG63 
Go to UniProtKB:  P0AG63
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UniProt GroupP0AG63
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S18AB [auth sr]65Escherichia coliMutation(s): 0 
Gene Names: rpsRECW_m4565
UniProt
Find proteins for E0J6I2 (Escherichia coli (strain ATCC 9637 / CCM 2024 / DSM 1116 / LMG 11080 / NBRC 13500 / NCIMB 8666 / NRRL B-766 / W))
Explore E0J6I2 
Go to UniProtKB:  E0J6I2
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UniProt GroupE0J6I2
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein uS19BB [auth ss]80Escherichia coliMutation(s): 0 
Gene Names: rpsSb3316JW3278
UniProt
Find proteins for P0A7U3 (Escherichia coli (strain K12))
Explore P0A7U3 
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UniProt GroupP0A7U3
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S20CB [auth st]85Escherichia coliMutation(s): 0 
Gene Names: rpsT
UniProt
Find proteins for C3TRH7 (Escherichia coli)
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UniProt GroupC3TRH7
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
Small ribosomal subunit protein bS21DB [auth su]70Escherichia coliMutation(s): 0 
Gene Names: rpsUb3065JW3037
UniProt
Find proteins for P68679 (Escherichia coli (strain K12))
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Go to UniProtKB:  P68679
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68679
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Entity ID: 31
MoleculeChains LengthOrganismImage
mRNAEA [auth M]9Escherichia coli
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Entity ID: 32
MoleculeChains LengthOrganismImage
23S ribosomal RNAFA [auth R1]2,903Escherichia coli
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Entity ID: 33
MoleculeChains LengthOrganismImage
5S ribosomal RNAGA [auth R2]119Escherichia coli
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Entity ID: 34
MoleculeChains LengthOrganismImage
16S ribosomal RNAHA [auth R3]1,539Escherichia coli
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Entity ID: 35
MoleculeChains LengthOrganismImage
tRNAIA [auth T]77Escherichia coli
Sequence Annotations
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Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
VK [auth Y],
WK [auth Y]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
FME
Query on FME

Download Ideal Coordinates CCD File 
UK [auth T]N-FORMYLMETHIONINE
C6 H11 N O3 S
PYUSHNKNPOHWEZ-YFKPBYRVSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth R1]
AD [auth R1]
AE [auth R1]
AF [auth R1]
AG [auth R1]
AC [auth R1],
AD [auth R1],
AE [auth R1],
AF [auth R1],
AG [auth R1],
AH [auth R1],
AI [auth R1],
AJ [auth R3],
AK [auth R3],
BC [auth R1],
BD [auth R1],
BE [auth R1],
BF [auth R1],
BG [auth R1],
BH [auth R1],
BI [auth R1],
BJ [auth R3],
BK [auth R3],
CC [auth R1],
CD [auth R1],
CE [auth R1],
CF [auth R1],
CG [auth R1],
CH [auth R1],
CI [auth R1],
CJ [auth R3],
CK [auth R3],
DC [auth R1],
DD [auth R1],
DE [auth R1],
DF [auth R1],
DG [auth R1],
DH [auth R1],
DI [auth R1],
DJ [auth R3],
DK [auth R3],
EB [auth 17],
EC [auth R1],
ED [auth R1],
EE [auth R1],
EF [auth R1],
EG [auth R1],
EH [auth R1],
EI [auth R3],
EJ [auth R3],
EK [auth R3],
FB [auth 32],
FC [auth R1],
FD [auth R1],
FE [auth R1],
FF [auth R1],
FG [auth R1],
FH [auth R1],
FI [auth R3],
FJ [auth R3],
FK [auth R3],
GB [auth 4],
GC [auth R1],
GD [auth R1],
GE [auth R1],
GF [auth R1],
GG [auth R1],
GH [auth R1],
GI [auth R3],
GJ [auth R3],
GK [auth R3],
HB [auth R1],
HC [auth R1],
HD [auth R1],
HE [auth R1],
HF [auth R1],
HG [auth R1],
HH [auth R1],
HI [auth R3],
HJ [auth R3],
HK [auth R3],
IB [auth R1],
IC [auth R1],
ID [auth R1],
IE [auth R1],
IF [auth R1],
IG [auth R1],
IH [auth R1],
II [auth R3],
IJ [auth R3],
IK [auth R3],
JB [auth R1],
JC [auth R1],
JD [auth R1],
JE [auth R1],
JF [auth R1],
JG [auth R1],
JH [auth R1],
JI [auth R3],
JJ [auth R3],
JK [auth R3],
KB [auth R1],
KC [auth R1],
KD [auth R1],
KE [auth R1],
KF [auth R1],
KG [auth R1],
KH [auth R1],
KI [auth R3],
KJ [auth R3],
KK [auth R3],
LB [auth R1],
LC [auth R1],
LD [auth R1],
LE [auth R1],
LF [auth R1],
LG [auth R1],
LH [auth R1],
LI [auth R3],
LJ [auth R3],
LK [auth R3],
MB [auth R1],
MC [auth R1],
MD [auth R1],
ME [auth R1],
MF [auth R1],
MG [auth R1],
MH [auth R1],
MI [auth R3],
MJ [auth R3],
MK [auth R3],
NB [auth R1],
NC [auth R1],
ND [auth R1],
NE [auth R1],
NF [auth R1],
NG [auth R1],
NH [auth R1],
NI [auth R3],
NJ [auth R3],
NK [auth R3],
OB [auth R1],
OC [auth R1],
OD [auth R1],
OE [auth R1],
OF [auth R1],
OG [auth R1],
OH [auth R1],
OI [auth R3],
OJ [auth R3],
OK [auth R3],
PB [auth R1],
PC [auth R1],
PD [auth R1],
PE [auth R1],
PF [auth R1],
PG [auth R1],
PH [auth R1],
PI [auth R3],
PJ [auth R3],
PK [auth R3],
QB [auth R1],
QC [auth R1],
QD [auth R1],
QE [auth R1],
QF [auth R1],
QG [auth R1],
QH [auth R1],
QI [auth R3],
QJ [auth R3],
QK [auth R3],
RB [auth R1],
RC [auth R1],
RD [auth R1],
RE [auth R1],
RF [auth R1],
RG [auth R1],
RH [auth R1],
RI [auth R3],
RJ [auth R3],
RK [auth R3],
SB [auth R1],
SC [auth R1],
SD [auth R1],
SE [auth R1],
SF [auth R1],
SG [auth R1],
SH [auth R1],
SI [auth R3],
SJ [auth R3],
SK [auth R3],
TB [auth R1],
TC [auth R1],
TD [auth R1],
TE [auth R1],
TF [auth R1],
TG [auth R1],
TH [auth R1],
TI [auth R3],
TJ [auth R3],
TK [auth R3],
UB [auth R1],
UC [auth R1],
UD [auth R1],
UE [auth R1],
UF [auth R1],
UG [auth R1],
UH [auth R1],
UI [auth R3],
UJ [auth R3],
VB [auth R1],
VC [auth R1],
VD [auth R1],
VE [auth R1],
VF [auth R1],
VG [auth R1],
VH [auth R1],
VI [auth R3],
VJ [auth R3],
WB [auth R1],
WC [auth R1],
WD [auth R1],
WE [auth R1],
WF [auth R1],
WG [auth R1],
WH [auth R1],
WI [auth R3],
WJ [auth R3],
XB [auth R1],
XC [auth R1],
XD [auth R1],
XE [auth R1],
XF [auth R1],
XG [auth R1],
XH [auth R1],
XI [auth R3],
XJ [auth R3],
YB [auth R1],
YC [auth R1],
YD [auth R1],
YE [auth R1],
YF [auth R1],
YG [auth R1],
YH [auth R1],
YI [auth R3],
YJ [auth R3],
ZB [auth R1],
ZC [auth R1],
ZD [auth R1],
ZE [auth R1],
ZF [auth R1],
ZG [auth R1],
ZH [auth R1],
ZI [auth R3],
ZJ [auth R3]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
XK [auth Y],
YK [auth Y]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-02
    Type: Initial release
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