1IW7

Crystal structure of the RNA polymerase holoenzyme from Thermus thermophilus at 2.6A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 ?
  • R-Value Free: 0.274 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.232 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution

Vassylyev, D.G., Sekine, S., Laptenko, O., Lee, J., Vassylyeva, M.N., Borukhov, S., Yokoyama, S.

(2002) Nature 417: 712-719

  • DOI: https://doi.org/10.1038/nature752
  • Primary Citation of Related Structures:  
    1IW7

  • PubMed Abstract: 

    In bacteria, the binding of a single protein, the initiation factor sigma, to a multi-subunit RNA polymerase core enzyme results in the formation of a holoenzyme, the active form of RNA polymerase essential for transcription initiation. Here we report the crystal structure of a bacterial RNA polymerase holoenzyme from Thermus thermophilus at 2.6 A resolution. In the structure, two amino-terminal domains of the sigma subunit form a V-shaped structure near the opening of the upstream DNA-binding channel of the active site cleft. The carboxy-terminal domain of sigma is near the outlet of the RNA-exit channel, about 57 A from the N-terminal domains. The extended linker domain forms a hairpin protruding into the active site cleft, then stretching through the RNA-exit channel to connect the N- and C-terminal domains. The holoenzyme structure provides insight into the structural organization of transcription intermediate complexes and into the mechanism of transcription initiation.

    • Organizational Affiliation: 

    Cellular Signaling Laboratory, RIKEN Harima Institute at Spring-8, 1-1-1 Kouto, Mikazuki-cho, Sayo, Hyogo 679-5148, Japan. dmitry@yumiyoshi.harima.riken.go.jp


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase alpha subunitA,
B,
G [auth K],
H [auth L]		315Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q9Z9H6 (Thermus thermophilus)
Explore Q9Z9H6 
Go to UniProtKB:  Q9Z9H6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Z9H6
Sequence Annotations
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase beta subunitC,
I [auth M]		1,119Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q8RQE9 
Go to UniProtKB:  Q8RQE9
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UniProt GroupQ8RQE9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase beta subunitD,
J [auth N]		1,524Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q8RQE8 
Go to UniProtKB:  Q8RQE8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8RQE8
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase omega subunitE,
K [auth O]		99Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
Explore Q8RQE7 
Go to UniProtKB:  Q8RQE7
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UniProt GroupQ8RQE7
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma-70 subunitF,
L [auth P]		423Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q72L95 (Thermus thermophilus (strain ATCC BAA-163 / DSM 7039 / HB27))
Explore Q72L95 
Go to UniProtKB:  Q72L95
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UniProt GroupQ72L95
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PB
Query on PB
Download Ideal Coordinates CCD File 
ND [auth D],
NN [auth N],
OD [auth D],
ON [auth N]		LEAD (II) ION
Pb
RVPVRDXYQKGNMQ-UHFFFAOYSA-N
MG
Query on MG
Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth B]
AC [auth C]
AD [auth C]
AE [auth D]
AA [auth A],
AB [auth B],
AC [auth C],
AD [auth C],
AE [auth D],
AF [auth D],
AG [auth D],
AH [auth D],
AI [auth D],
AJ [auth F],
AK [auth K],
AL [auth L],
AM [auth M],
AN [auth M],
AO [auth N],
AP [auth N],
AQ [auth N],
AR [auth N],
AS [auth P],
BA [auth A],
BB [auth B],
BC [auth C],
BD [auth C],
BE [auth D],
BF [auth D],
BG [auth D],
BH [auth D],
BI [auth D],
BJ [auth F],
BK [auth K],
BL [auth M],
BM [auth M],
BN [auth M],
BO [auth N],
BP [auth N],
BQ [auth N],
BR [auth N],
BS [auth P],
CA [auth A],
CB [auth C],
CC [auth C],
CD [auth C],
CE [auth D],
CF [auth D],
CG [auth D],
CH [auth D],
CI [auth D],
CJ [auth F],
CK [auth K],
CL [auth M],
CM [auth M],
CN [auth M],
CO [auth N],
CP [auth N],
CQ [auth N],
CR [auth N],
CS [auth P],
DA [auth A],
DB [auth C],
DC [auth C],
DD [auth C],
DE [auth D],
DF [auth D],
DG [auth D],
DH [auth D],
DI [auth E],
DJ [auth F],
DK [auth K],
DL [auth M],
DM [auth M],
DN [auth M],
DO [auth N],
DP [auth N],
DQ [auth N],
DR [auth O],
DS [auth P],
EA [auth B],
EB [auth C],
EC [auth C],
ED [auth C],
EE [auth D],
EF [auth D],
EG [auth D],
EH [auth D],
EI [auth E],
EJ [auth F],
EK [auth K],
EL [auth M],
EM [auth M],
EN [auth M],
EO [auth N],
EP [auth N],
EQ [auth N],
ER [auth O],
ES [auth P],
FA [auth B],
FB [auth C],
FC [auth C],
FD [auth C],
FE [auth D],
FF [auth D],
FG [auth D],
FH [auth D],
FI [auth E],
FJ [auth F],
FK [auth K],
FL [auth M],
FM [auth M],
FN [auth M],
FO [auth N],
FP [auth N],
FQ [auth N],
FR [auth O],
FS [auth P],
GA [auth B],
GB [auth C],
GC [auth C],
GD [auth C],
GE [auth D],
GF [auth D],
GG [auth D],
GH [auth D],
GI [auth E],
GJ [auth F],
GK [auth K],
GL [auth M],
GM [auth M],
GN [auth M],
GO [auth N],
GP [auth N],
GQ [auth N],
GR [auth O],
GS [auth P],
HA [auth B],
HB [auth C],
HC [auth C],
HD [auth C],
HE [auth D],
HF [auth D],
HG [auth D],
HH [auth D],
HI [auth E],
HJ [auth F],
HK [auth K],
HL [auth M],
HM [auth M],
HN [auth M],
HO [auth N],
HP [auth N],
HQ [auth N],
HR [auth O],
IA [auth B],
IB [auth C],
IC [auth C],
ID [auth C],
IE [auth D],
IF [auth D],
IG [auth D],
IH [auth D],
II [auth E],
IJ [auth F],
IK [auth L],
IL [auth M],
IM [auth M],
IN [auth M],
IO [auth N],
IP [auth N],
IQ [auth N],
IR [auth O],
JA [auth B],
JB [auth C],
JC [auth C],
JD [auth C],
JE [auth D],
JF [auth D],
JG [auth D],
JH [auth D],
JI [auth F],
JJ [auth F],
JK [auth L],
JL [auth M],
JM [auth M],
JN [auth M],
JO [auth N],
JP [auth N],
JQ [auth N],
JR [auth O],
KA [auth B],
KB [auth C],
KC [auth C],
KD [auth C],
KE [auth D],
KF [auth D],
KG [auth D],
KH [auth D],
KI [auth F],
KJ [auth F],
KK [auth L],
KL [auth M],
KM [auth M],
KN [auth M],
KO [auth N],
KP [auth N],
KQ [auth N],
KR [auth O],
LA [auth B],
LB [auth C],
LC [auth C],
LD [auth C],
LE [auth D],
LF [auth D],
LG [auth D],
LH [auth D],
LI [auth F],
LJ [auth F],
LK [auth L],
LL [auth M],
LM [auth M],
LN [auth M],
LO [auth N],
LP [auth N],
LQ [auth N],
LR [auth P],
M [auth A],
MA [auth B],
MB [auth C],
MC [auth C],
MD [auth C],
ME [auth D],
MF [auth D],
MG [auth D],
MH [auth D],
MI [auth F],
MJ [auth F],
MK [auth L],
ML [auth M],
MM [auth M],
MN [auth M],
MO [auth N],
MP [auth N],
MQ [auth N],
MR [auth P],
N [auth A],
NA [auth B],
NB [auth C],
NC [auth C],
NE [auth D],
NF [auth D],
NG [auth D],
NH [auth D],
NI [auth F],
NJ [auth F],
NK [auth L],
NL [auth M],
NM [auth M],
NO [auth N],
NP [auth N],
NQ [auth N],
NR [auth P],
O [auth A],
OA [auth B],
OB [auth C],
OC [auth C],
OE [auth D],
OF [auth D],
OG [auth D],
OH [auth D],
OI [auth F],
OJ [auth K],
OK [auth L],
OL [auth M],
OM [auth M],
OO [auth N],
OP [auth N],
OQ [auth N],
OR [auth P],
P [auth A],
PA [auth B],
PB [auth C],
PC [auth C],
PD [auth D],
PE [auth D],
PF [auth D],
PG [auth D],
PH [auth D],
PI [auth F],
PJ [auth K],
PK [auth L],
PL [auth M],
PM [auth M],
PN [auth N],
PO [auth N],
PP [auth N],
PQ [auth N],
PR [auth P],
Q [auth A],
QA [auth B],
QB [auth C],
QC [auth C],
QD [auth D],
QE [auth D],
QF [auth D],
QG [auth D],
QH [auth D],
QI [auth F],
QJ [auth K],
QK [auth L],
QL [auth M],
QM [auth M],
QN [auth N],
QO [auth N],
QP [auth N],
QQ [auth N],
QR [auth P],
R [auth A],
RA [auth B],
RB [auth C],
RC [auth C],
RD [auth D],
RE [auth D],
RF [auth D],
RG [auth D],
RH [auth D],
RI [auth F],
RJ [auth K],
RK [auth L],
RL [auth M],
RM [auth M],
RN [auth N],
RO [auth N],
RP [auth N],
RQ [auth N],
RR [auth P],
S [auth A],
SA [auth B],
SB [auth C],
SC [auth C],
SD [auth D],
SE [auth D],
SF [auth D],
SG [auth D],
SH [auth D],
SI [auth F],
SJ [auth K],
SK [auth L],
SL [auth M],
SM [auth M],
SN [auth N],
SO [auth N],
SP [auth N],
SQ [auth N],
SR [auth P],
T [auth A],
TA [auth B],
TB [auth C],
TC [auth C],
TD [auth D],
TE [auth D],
TF [auth D],
TG [auth D],
TH [auth D],
TI [auth F],
TJ [auth K],
TK [auth L],
TL [auth M],
TM [auth M],
TN [auth N],
TO [auth N],
TP [auth N],
TQ [auth N],
TR [auth P],
U [auth A],
UA [auth B],
UB [auth C],
UC [auth C],
UD [auth D],
UE [auth D],
UF [auth D],
UG [auth D],
UH [auth D],
UI [auth F],
UJ [auth K],
UK [auth L],
UL [auth M],
UM [auth M],
UN [auth N],
UO [auth N],
UP [auth N],
UQ [auth N],
UR [auth P],
V [auth A],
VA [auth B],
VB [auth C],
VC [auth C],
VD [auth D],
VE [auth D],
VF [auth D],
VG [auth D],
VH [auth D],
VI [auth F],
VJ [auth K],
VK [auth L],
VL [auth M],
VM [auth M],
VN [auth N],
VO [auth N],
VP [auth N],
VQ [auth N],
VR [auth P],
W [auth A],
WA [auth B],
WB [auth C],
WC [auth C],
WD [auth D],
WE [auth D],
WF [auth D],
WG [auth D],
WH [auth D],
WI [auth F],
WJ [auth K],
WK [auth L],
WL [auth M],
WM [auth M],
WN [auth N],
WO [auth N],
WP [auth N],
WQ [auth N],
WR [auth P],
X [auth A],
XA [auth B],
XB [auth C],
XC [auth C],
XD [auth D],
XE [auth D],
XF [auth D],
XG [auth D],
XH [auth D],
XI [auth F],
XJ [auth K],
XK [auth L],
XL [auth M],
XM [auth M],
XN [auth N],
XO [auth N],
XP [auth N],
XQ [auth N],
XR [auth P],
Y [auth A],
YA [auth B],
YB [auth C],
YC [auth C],
YD [auth D],
YE [auth D],
YF [auth D],
YG [auth D],
YH [auth D],
YI [auth F],
YJ [auth K],
YK [auth L],
YL [auth M],
YM [auth M],
YN [auth N],
YO [auth N],
YP [auth N],
YQ [auth N],
YR [auth P],
Z [auth A],
ZA [auth B],
ZB [auth C],
ZC [auth C],
ZD [auth D],
ZE [auth D],
ZF [auth D],
ZG [auth D],
ZH [auth D],
ZI [auth F],
ZJ [auth K],
ZK [auth L],
ZL [auth M],
ZM [auth M],
ZN [auth N],
ZO [auth N],
ZP [auth N],
ZQ [auth N],
ZR [auth P]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 ?
  • R-Value Free: 0.274 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.232 
  • Space Group: P 32
Unit Cell:
Length ( ? )Angle ( ? )
a = 236.35¦Á = 90
b = 236.35¦Â = 90
c = 249.04¦Ã = 120
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-26
    Type: Initial release
  • Version 1.1: 2008-04-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description
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