4V4G | pdb_00004v4g

Crystal structure of five 70s ribosomes from Escherichia Coli in complex with protein Y.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 11.50 Å
  • R-Value Free: 
    0.401 (Depositor), 0.406 (DCC) 
  • R-Value Work: 
    0.395 (Depositor), 0.405 (DCC) 
  • R-Value Observed: 
    0.395 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history. 

Literature

Structural basis for the control of translation initiation during stress.

Vila-Sanjurjo, A., Schuwirth, B.S., Hau, C.W., Cate, J.H.

(2004) Nat Struct Mol Biol 11: 1054-1059

  • DOI: https://doi.org/10.1038/nsmb850
  • Primary Citation Related Structures: 
    4V4G

  • PubMed Abstract: 

    During environmental stress, organisms limit protein synthesis by storing inactive ribosomes that are rapidly reactivated when conditions improve. Here we present structural and biochemical data showing that protein Y, an Escherichia coli stress protein, fills the tRNA- and mRNA-binding channel of the small ribosomal subunit to stabilize intact ribosomes. Protein Y inhibits translation initiation during cold shock but not at normal temperatures. Furthermore, protein Y competes with conserved translation initiation factors that, in bacteria, are required for ribosomal subunit dissociation. The mechanism used by protein Y to reduce translation initiation during stress and quickly release ribosomes for renewed translation initiation may therefore occur widely in nature.

    • Organizational Affiliation: 
    • Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.

Macromolecule Content 

  • Total Structure Weight: 10,637.75 kDa 
  • Atom Count: 717,805 
  • Modeled Residue Count: 52,600 
  • Deposited Residue Count: 52,610 
  • Unique protein chains: 50
  • Unique nucleic acid chains: 3

Macromolecules


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|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S2B [auth AB],
CB,
DD [auth EB],
EF [auth GB],
FH [auth IB]		234Escherichia coliMutation(s): 0 
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S3C [auth AC],
DB [auth CC],
ED [auth EC],
FF [auth GC],
GH [auth IC]		206Escherichia coliMutation(s): 0 
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S4D [auth AD],
EB [auth CD],
FD [auth ED],
GF [auth GD],
HH [auth ID]		208Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S5E [auth AE],
FB [auth CE],
GD [auth EE],
HF [auth GE],
IH [auth IE]		150Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S6F [auth AF],
GB [auth CF],
HD [auth EF],
IF [auth GF],
JH [auth IF]		101Escherichia coliMutation(s): 0 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S7G [auth AG],
HB [auth CG],
ID [auth EG],
JF [auth GG],
KH [auth IG]		155Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S8H [auth AH],
IB [auth CH],
JD [auth EH],
KF [auth GH],
LH [auth IH]		138Escherichia coliMutation(s): 0 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S9I [auth AI],
JB [auth CI],
KD [auth EI],
LF [auth GI],
MH [auth II]		127Escherichia coliMutation(s): 0 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S10J [auth AJ],
KB [auth CJ],
LD [auth EJ],
MF [auth GJ],
NH [auth IJ]		98Escherichia coliMutation(s): 0 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S11K [auth AK],
LB [auth CK],
MD [auth EK],
NF [auth GK],
OH [auth IK]		119Escherichia coliMutation(s): 0 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S12L [auth AL],
MB [auth CL],
ND [auth EL],
OF [auth GL],
PH [auth IL]		124Escherichia coliMutation(s): 0 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S13M [auth AM],
NB [auth CM],
OD [auth EM],
PF [auth GM],
QH [auth IM]		125Escherichia coliMutation(s): 0 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S14N [auth AN],
OB [auth CN],
PD [auth EN],
QF [auth GN],
RH [auth IN]		60Escherichia coliMutation(s): 0 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S15O [auth AO],
PB [auth CO],
QD [auth EO],
RF [auth GO],
SH [auth IO]		88Escherichia coliMutation(s): 0 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S16P [auth AP],
QB [auth CP],
RD [auth EP],
SF [auth GP],
TH [auth IP]		83Escherichia coliMutation(s): 0 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S17Q [auth AQ],
RB [auth CQ],
SD [auth EQ],
TF [auth GQ],
UH [auth IQ]		104Escherichia coliMutation(s): 0 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S18R [auth AR],
SB [auth CR],
TD [auth ER],
UF [auth GR],
VH [auth IR]		73Escherichia coliMutation(s): 0 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S19S [auth AS],
TB [auth CS],
UD [auth ES],
VF [auth GS],
WH [auth IS]		80Escherichia coliMutation(s): 0 
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Entity ID: 20
MoleculeChains  Sequence LengthOrganismDetailsImage
30S ribosomal protein S20T [auth AT],
UB [auth CT],
VD [auth ET],
WF [auth GT],
XH [auth IT]		99Escherichia coliMutation(s): 0 
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Entity ID: 21
MoleculeChains  Sequence LengthOrganismDetailsImage
protein YU [auth Aa],
VB [auth Ca],
WD [auth Ea],
XF [auth Ga],
YH [auth Ia]		90Escherichia coliMutation(s): 0 
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Entity ID: 24
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L2AG [auth HD],
BI [auth JD],
X [auth BD],
YB [auth DD],
ZD [auth FD]		270Escherichia coliMutation(s): 0 
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Entity ID: 25
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L3AE [auth FE],
BG [auth HE],
CI [auth JE],
Y [auth BE],
ZB [auth DE]		205Escherichia coliMutation(s): 0 
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Entity ID: 26
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L4AC [auth DF],
BE [auth FF],
CG [auth HF],
DI [auth JF],
Z [auth BF]		198Escherichia coliMutation(s): 0 
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Entity ID: 27
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L5AA [auth BG],
BC [auth DG],
CE [auth FG],
DG [auth HG],
EI [auth JG]		178Escherichia coliMutation(s): 0 
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Entity ID: 28
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L6BA [auth BH],
CC [auth DH],
DE [auth FH],
EG [auth HH],
FI [auth JH]		177Escherichia coliMutation(s): 0 
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Entity ID: 29
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L9CA [auth BI],
DC [auth DI],
EE [auth FI],
FG [auth HI],
GI [auth JI]		52Escherichia coliMutation(s): 0 
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Entity ID: 30
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L11DA [auth BJ],
EC [auth DJ],
FE [auth FJ],
GG [auth HJ],
HI [auth JJ]		143Escherichia coliMutation(s): 0 
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Entity ID: 31
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L13EA [auth BK],
FC [auth DK],
GE [auth FK],
HG [auth HK],
II [auth JK]		143Escherichia coliMutation(s): 0 
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Entity ID: 32
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L14FA [auth BL],
GC [auth DL],
HE [auth FL],
IG [auth HL],
JI [auth JL]		132Escherichia coliMutation(s): 0 
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Entity ID: 33
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L15GA [auth BM],
HC [auth DM],
IE [auth FM],
JG [auth HM],
KI [auth JM]		141Escherichia coliMutation(s): 0 
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Entity ID: 34
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L16HA [auth BN],
IC [auth DN],
JE [auth FN],
KG [auth HN],
LI [auth JN]		124Escherichia coliMutation(s): 0 
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Entity ID: 35
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L17IA [auth BO],
JC [auth DO],
KE [auth FO],
LG [auth HO],
MI [auth JO]		114Escherichia coliMutation(s): 0 
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Entity ID: 36
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L18JA [auth BP],
KC [auth DP],
LE [auth FP],
MG [auth HP],
NI [auth JP]		111Escherichia coliMutation(s): 0 
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Entity ID: 37
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L19KA [auth BQ],
LC [auth DQ],
ME [auth FQ],
NG [auth HQ],
OI [auth JQ]		125Escherichia coliMutation(s): 0 
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Entity ID: 38
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L20LA [auth BR],
MC [auth DR],
NE [auth FR],
OG [auth HR],
PI [auth JR]		117Escherichia coliMutation(s): 0 
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Entity ID: 39
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L21MA [auth BS],
NC [auth DS],
OE [auth FS],
PG [auth HS],
QI [auth JS]		100Escherichia coliMutation(s): 0 
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Entity ID: 40
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L22NA [auth BT],
OC [auth DT],
PE [auth FT],
QG [auth HT],
RI [auth JT]		130Escherichia coliMutation(s): 0 
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Entity ID: 41
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L23OA [auth BU],
PC [auth DU],
QE [auth FU],
RG [auth HU],
SI [auth JU]		93Escherichia coliMutation(s): 0 
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Entity ID: 42
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L24PA [auth BV],
QC [auth DV],
RE [auth FV],
SG [auth HV],
TI [auth JV]		113Escherichia coliMutation(s): 0 
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Entity ID: 43
MoleculeChains  Sequence LengthOrganismDetailsImage
general stress protein CtcQA [auth BW],
RC [auth DW],
SE [auth FW],
TG [auth HW],
UI [auth JW]		173Escherichia coliMutation(s): 0 
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Entity ID: 44
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L27RA [auth BX],
SC [auth DX],
TE [auth FX],
UG [auth HX],
VI [auth JX]		86Escherichia coliMutation(s): 0 
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Entity ID: 45
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L29SA [auth BY],
TC [auth DY],
UE [auth FY],
VG [auth HY],
WI [auth JY]		65Escherichia coliMutation(s): 0 
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Entity ID: 46
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L30TA [auth BZ],
UC [auth DZ],
VE [auth FZ],
WG [auth HZ],
XI [auth JZ]		55Escherichia coliMutation(s): 0 
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Entity ID: 47
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L31UA [auth B1],
VC [auth D1],
WE [auth F1],
XG [auth H1],
YI [auth J1]		73Escherichia coliMutation(s): 0 
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Entity ID: 48
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L32VA [auth B2],
WC [auth D2],
XE [auth F2],
YG [auth H2],
ZI [auth J2]		58Escherichia coliMutation(s): 0 
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Entity ID: 49
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L33AJ [auth J3],
WA [auth B3],
XC [auth D3],
YE [auth F3],
ZG [auth H3]		53Escherichia coliMutation(s): 0 
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Entity ID: 50
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L34AH [auth H4],
BJ [auth J4],
XA [auth B4],
YC [auth D4],
ZE [auth F4]		46Escherichia coliMutation(s): 0 
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Entity ID: 51
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L35AF [auth F5],
BH [auth H5],
CJ [auth J5],
YA [auth B5],
ZC [auth D5]		63Escherichia coliMutation(s): 0 
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Entity ID: 52
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L36AD [auth D6],
BF [auth F6],
CH [auth H6],
DJ [auth J6],
ZA [auth B6]		35Escherichia coliMutation(s): 0 
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Entity ID: 53
MoleculeChains  Sequence LengthOrganismDetailsImage
50S ribosomal protein L1PAB [auth B7],
BD [auth D7],
CF [auth F7],
DH [auth H7],
EJ [auth J7]		217Escherichia coliMutation(s): 0 
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNAA [auth AA],
BB [auth CA],
CD [auth EA],
DF [auth GA],
EH [auth IA]		1,526Escherichia coli
Sequence Annotations
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Reference Sequence
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Entity ID: 22
MoleculeChains LengthOrganismImage
23S RIBOSOMAL RNAV [auth BB],
WB [auth DB],
XD [auth FB],
YF [auth HB],
ZH [auth JB]		2,825Escherichia coli
Sequence Annotations
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Reference Sequence
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Entity ID: 23
MoleculeChains LengthOrganismImage
5S RIBOSOMAL RNAAI [auth JA],
W [auth BA],
XB [auth DA],
YD [auth FA],
ZF [auth HA]		119Escherichia coli
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE		AB [auth B7],
BD [auth D7],
CF [auth F7],
DH [auth H7],
EJ [auth J7]		L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 11.50 Å
  • R-Value Free:  0.401 (Depositor), 0.406 (DCC) 
  • R-Value Work:  0.395 (Depositor), 0.405 (DCC) 
  • R-Value Observed: 0.395 (Depositor) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 687.9α = 90
b = 687.9β = 90
c = 1933.3γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-06
    Changes: Data collection
  • Version 1.4: 2024-11-20
    Changes: Structure summary