9E6Q

Cryo-EM structure of the Pyrobaculum calidifontis 50S ribosomal subunit in complex with Dri

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.95 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

Structure of an Archaeal Ribosome with a Divergent Active Site

Nissley, A.J., Shulgina, Y., Kivimae, R.W., Downing, B.E., Penev, P.I., Banfield, J.F., Nayak, D.D., Cate, J.H.D.

To be published.

Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Putative signal-transduction protein with CBS domainsC [auth 3]655Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MX58 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL2D [auth AA]244Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL3E [auth AB]338Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL4F [auth AC]285Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL5G [auth AD]178Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL6H [auth AE]196Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL8I [auth AF]149Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL13J [auth AG]186Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL13K [auth AH]157Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL14L [auth AI]144Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
eL14M [auth AJ],
N [auth AK]		103Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL15O [auth AL]156Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15eP [auth AM]189Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL16Q [auth AN]178Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL18R [auth AO]205Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL18S [auth AP]122Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL19T [auth AQ]147Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL20U [auth AR]78Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL21V [auth AS]99Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL22W [auth AT]184Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
Find proteins for A3MTL6 (Pyrobaculum calidifontis (strain DSM 21063 / JCM 11548 / VA1))
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL23X [auth AU]81Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL24Y [auth AV]128Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL24Z [auth AW]62Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL29AA [auth AX]79Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein uL30BA [auth AY]179Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL30CA [auth AZ]101Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL31DA [auth Aa]91Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL32EA [auth Ab]153Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL34FA [auth Ac]84Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL37GA [auth Ad]52Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
LSU ribosomal protein L38EHA [auth Ae]67Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL39IA [auth Af]51Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL40JA [auth Ag]53Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
eL42KA [auth Ah]91Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
Large ribosomal subunit protein eL43LA [auth Ai]102Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
DJ-1/PfpI domain-containing proteinMA [auth Aj]184Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
PaREP1 domain containing proteinNA [auth Ak]93Pyrobaculum calidifontis JCM 11548Mutation(s): 0 
UniProt
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Entity ID: 1
MoleculeChains LengthOrganismImage
23S rRNAA [auth 1]3,024Pyrobaculum calidifontis JCM 11548
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S rRNAB [auth 2]129Pyrobaculum calidifontis JCM 11548
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPM
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AB [auth 1]
AC [auth 1]
BB [auth 1]
BC [auth 1]
CB [auth 1]
AB [auth 1],
AC [auth 1],
BB [auth 1],
BC [auth 1],
CB [auth 1],
CC [auth 1],
DB [auth 1],
DC [auth 1],
EB [auth 1],
EC [auth 1],
FB [auth 1],
FC [auth 1],
GB [auth 1],
HB [auth 1],
IB [auth 1],
JB [auth 1],
KB [auth 1],
LB [auth 1],
MB [auth 1],
NB [auth 1],
OA [auth 1],
OB [auth 1],
PA [auth 1],
PB [auth 1],
QA [auth 1],
QB [auth 1],
RA [auth 1],
RB [auth 1],
SA [auth 1],
SB [auth 1],
TA [auth 1],
TB [auth 1],
TI [auth AL],
UA [auth 1],
UB [auth 1],
VA [auth 1],
VB [auth 1],
WA [auth 1],
WB [auth 1],
WI [auth AM],
XA [auth 1],
XB [auth 1],
YA [auth 1],
YB [auth 1],
ZA [auth 1],
ZB [auth 1]
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
ZN
Query on ZN
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AJ [auth Ad],
BJ [auth Ag],
CJ [auth Ah],
DJ [auth Ai],
ZI [auth AW]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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AD [auth 1]
AE [auth 1]
AF [auth 1]
AG [auth 1]
AH [auth 1]
AD [auth 1],
AE [auth 1],
AF [auth 1],
AG [auth 1],
AH [auth 1],
AI [auth 1],
BD [auth 1],
BE [auth 1],
BF [auth 1],
BG [auth 1],
BH [auth 1],
BI [auth 1],
CD [auth 1],
CE [auth 1],
CF [auth 1],
CG [auth 1],
CH [auth 1],
CI [auth 1],
DD [auth 1],
DE [auth 1],
DF [auth 1],
DG [auth 1],
DH [auth 1],
DI [auth 1],
ED [auth 1],
EE [auth 1],
EF [auth 1],
EG [auth 1],
EH [auth 1],
EI [auth 1],
FD [auth 1],
FE [auth 1],
FF [auth 1],
FG [auth 1],
FH [auth 1],
FI [auth 1],
GC [auth 1],
GD [auth 1],
GE [auth 1],
GF [auth 1],
GG [auth 1],
GH [auth 1],
GI [auth 1],
HC [auth 1],
HD [auth 1],
HE [auth 1],
HF [auth 1],
HG [auth 1],
HH [auth 1],
HI [auth 1],
IC [auth 1],
ID [auth 1],
IE [auth 1],
IF [auth 1],
IG [auth 1],
IH [auth 1],
II [auth 1],
JC [auth 1],
JD [auth 1],
JE [auth 1],
JF [auth 1],
JG [auth 1],
JH [auth 1],
JI [auth 1],
KC [auth 1],
KD [auth 1],
KE [auth 1],
KF [auth 1],
KG [auth 1],
KH [auth 1],
KI [auth 1],
LC [auth 1],
LD [auth 1],
LE [auth 1],
LF [auth 1],
LG [auth 1],
LH [auth 1],
LI [auth 1],
MC [auth 1],
MD [auth 1],
ME [auth 1],
MF [auth 1],
MG [auth 1],
MH [auth 1],
MI [auth 1],
NC [auth 1],
ND [auth 1],
NE [auth 1],
NF [auth 1],
NG [auth 1],
NH [auth 1],
NI [auth 1],
OC [auth 1],
OD [auth 1],
OE [auth 1],
OF [auth 1],
OG [auth 1],
OH [auth 1],
OI [auth 1],
PC [auth 1],
PD [auth 1],
PE [auth 1],
PF [auth 1],
PG [auth 1],
PH [auth 1],
PI [auth 1],
QC [auth 1],
QD [auth 1],
QE [auth 1],
QF [auth 1],
QG [auth 1],
QH [auth 1],
QI [auth 1],
RC [auth 1],
RD [auth 1],
RE [auth 1],
RF [auth 1],
RG [auth 1],
RH [auth 1],
RI [auth 1],
SC [auth 1],
SD [auth 1],
SE [auth 1],
SF [auth 1],
SG [auth 1],
SH [auth 1],
SI [auth AA],
TC [auth 1],
TD [auth 1],
TE [auth 1],
TF [auth 1],
TG [auth 1],
TH [auth 1],
UC [auth 1],
UD [auth 1],
UE [auth 1],
UF [auth 1],
UG [auth 1],
UH [auth 1],
UI [auth AL],
VC [auth 1],
VD [auth 1],
VE [auth 1],
VF [auth 1],
VG [auth 1],
VH [auth 1],
VI [auth AL],
WC [auth 1],
WD [auth 1],
WE [auth 1],
WF [auth 1],
WG [auth 1],
WH [auth 1],
XC [auth 1],
XD [auth 1],
XE [auth 1],
XF [auth 1],
XG [auth 1],
XH [auth 1],
XI [auth AN],
YC [auth 1],
YD [auth 1],
YE [auth 1],
YF [auth 1],
YG [auth 1],
YH [auth 1],
YI [auth AT],
ZC [auth 1],
ZD [auth 1],
ZE [auth 1],
ZF [auth 1],
ZG [auth 1],
ZH [auth 1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesCHE-2002182

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-20
    Type: Initial release
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