4V4G

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 11.5 Å
  • R-Value Free: 0.401 
  • R-Value Work: 0.395 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/nsmb850
  • Primary Citation of Related Structures:  1VOQ, 1VOR, 1VOS, 1VOU, 1VOV, 1VOW, 1VOX, 1VOY, 1VOZ, 1VP0

  • 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 prot ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
AB, CB, EB, GB, IB
234N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
AC, CC, EC, GC, IC
206N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
AD, CD, ED, GD, ID
208N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
AE, CE, EE, GE, IE
150N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
AF, CF, EF, GF, IF
101N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
AG, CG, EG, GG, IG
155N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
AH, CH, EH, GH, IH
138N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
AI, CI, EI, GI, II
127N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
AJ, CJ, EJ, GJ, IJ
98N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
AK, CK, EK, GK, IK
119N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
AL, CL, EL, GL, IL
124N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
AM, CM, EM, GM, IM
125N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14
AN, CN, EN, GN, IN
60N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
AO, CO, EO, GO, IO
88N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
AP, CP, EP, GP, IP
83N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
AQ, CQ, EQ, GQ, IQ
104N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
AR, CR, ER, GR, IR
73N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
AS, CS, ES, GS, IS
80N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
AT, CT, ET, GT, IT
99N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
protein Y
Aa, Ca, Ea, Ga, Ia
90N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
BD, DD, FD, HD, JD
270N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
BE, DE, FE, HE, JE
205N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
BF, DF, FF, HF, JF
198N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
BG, DG, FG, HG, JG
178N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
BH, DH, FH, HH, JH
177N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
BI, DI, FI, HI, JI
52N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L11
BJ, DJ, FJ, HJ, JJ
143N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
BK, DK, FK, HK, JK
143N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
BL, DL, FL, HL, JL
132N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
BM, DM, FM, HM, JM
141N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
BN, DN, FN, HN, JN
124N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
BO, DO, FO, HO, JO
114N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
BP, DP, FP, HP, JP
111N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
BQ, DQ, FQ, HQ, JQ
125N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
BR, DR, FR, HR, JR
117N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
BS, DS, FS, HS, JS
100N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
BT, DT, FT, HT, JT
130N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
BU, DU, FU, HU, JU
93N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
BV, DV, FV, HV, JV
113N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
general stress protein Ctc
BW, DW, FW, HW, JW
173N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
BX, DX, FX, HX, JX
86N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
BY, DY, FY, HY, JY
65N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
BZ, DZ, FZ, HZ, JZ
55N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
B1, D1, F1, H1, J1
73N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
B2, D2, F2, H2, J2
58N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
B3, D3, F3, H3, J3
53N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
B4, D4, F4, H4, J4
46N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
B5, D5, F5, H5, J5
63N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
B6, D6, F6, H6, J6
35N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L1P
B7, D7, F7, H7, J7
217N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 1
MoleculeChainsLengthOrganism
16S ribosomal RNAAA,CA,EA,GA,IA1526Escherichia coli
Entity ID: 22
MoleculeChainsLengthOrganism
23S RIBOSOMAL RNABB,DB,FB,HB,JB2825Escherichia coli
Entity ID: 23
MoleculeChainsLengthOrganism
5S RIBOSOMAL RNABA,DA,FA,HA,JA119Escherichia coli
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
B7, D7, F7, H7, J7
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 11.5 Å
  • R-Value Free: 0.401 
  • R-Value Work: 0.395 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 687.900α = 90.00
b = 687.900β = 90.00
c = 1933.300γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-12-10
    Type: Other