8A3L

Structural insights into the binding of bS1 to the ribosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 2.0 of the entry. See complete history


Literature

Structural insights into the binding of bS1 to the ribosome.

D'Urso, G.Chat, S.Gillet, R.Giudice, E.

(2023) Nucleic Acids Res 51: 3410-3419

  • DOI: https://doi.org/10.1093/nar/gkad126
  • Primary Citation of Related Structures:  
    8A3L

  • PubMed Abstract: 

    The multidomain ribosomal protein bS1 is the biggest and the most flexible and dynamic protein in the 30S small subunit. Despite being essential for mRNA recruitment and its primary role in the accommodation of the start codon within the decoding centre, there has not yet been a high-resolution description of its structure. Here, we present a 3D atomic model of OB1 and OB2, bS1's first two N-terminal domains, bound to an elongation-competent 70S ribosome. Our structure reveals that, as previously reported, bS1 is anchored both by a π-stacking to the 30S subunit and via a salt bridge with the Zn2+ pocket of bS1. These contacts are further stabilized by other interactions with additional residues on OB1. Our model also shows a new conformation of OB2, interacting with the Shine-Dalgarno portion of the mRNA. This study confirms that OB1 plays an anchoring role, but also highlights a novel function for OB2, which is directly involved in the modulation and support of mRNA binding and accommodation on the ribosome.


  • Organizational Affiliation

    Univ. Rennes, CNRS, Institut de Génétique et Développement de Rennes (IGDR) UMR6290, 35000 Rennes, France.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2224Escherichia coli K-12Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S3206Escherichia coli K-12Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S4206Escherichia coli K-12Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S5167Escherichia coli K-12Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S6135Escherichia coli K-12Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S7179Escherichia coli K-12Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S8130Escherichia coli K-12Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S9130Escherichia coli K-12Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S10103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S11129Escherichia coli K-12Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S12124Escherichia coli K-12Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S13118Escherichia coli K-12Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S14101Escherichia coli K-12Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1589Escherichia coli K-12Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1682Escherichia coli K-12Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1784Escherichia coli K-12Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1875Escherichia coli K-12Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1992Escherichia coli K-12Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2087Escherichia coli K-12Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S2171Escherichia coli K-12Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
30S ribosomal protein S1557Escherichia coli K-12Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2BA [auth c]273Escherichia coli K-12Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3CA [auth d]209Escherichia coli K-12Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4DA [auth e]201Escherichia coli K-12Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5EA [auth f]179Escherichia coli K-12Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6FA [auth g]177Escherichia coli K-12Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L9GA [auth h]149Escherichia coli K-12Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13HA [auth i]142Escherichia coli K-12Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14IA [auth j]123Escherichia coli K-12Mutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15JA [auth k]144Escherichia coli K-12Mutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16KA [auth l]136Escherichia coli K-12Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17LA [auth m]127Escherichia coli K-12Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18MA [auth n]117Escherichia coli K-12Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19NA [auth o]115Escherichia coli K-12Mutation(s): 0 
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20OA [auth p]118Escherichia coli K-12Mutation(s): 0 
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21PA [auth q]103Escherichia coli K-12Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22QA [auth r]110Escherichia coli K-12Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23RA [auth s]100Escherichia coli K-12Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24SA [auth t]104Escherichia coli K-12Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25TA [auth u]94Escherichia coli K-12Mutation(s): 0 
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27UA [auth v]85Escherichia coli K-12Mutation(s): 0 
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28VA [auth w]78Escherichia coli K-12Mutation(s): 0 
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29WA [auth x]63Escherichia coli K-12Mutation(s): 0 
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30XA [auth y]59Escherichia coli K-12Mutation(s): 0 
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32YA [auth z]57Escherichia coli K-12Mutation(s): 0 
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L33ZA [auth 0]55Escherichia coli K-12Mutation(s): 0 
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Find proteins for P0A7N9 (Escherichia coli (strain K12))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34AB [auth 1]46Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7P5 (Escherichia coli (strain K12))
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UniProt GroupP0A7P5
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35BB [auth 2]65Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7Q1 (Escherichia coli (strain K12))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36CB [auth 3]38Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7Q6 (Escherichia coli (strain K12))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31DB [auth 4]70Escherichia coli K-12Mutation(s): 0 
UniProt
Find proteins for P0A7M9 (Escherichia coli (strain K12))
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S ribosomal RNA1,539Escherichia coli K-12
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Entity ID: 22
MoleculeChains LengthOrganismImage
P-site fMet-tRNA(fMet)77Escherichia coli K-12
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Entity ID: 23
MoleculeChains LengthOrganismImage
E-site tRNA77Escherichia coli K-12
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Entity ID: 24
MoleculeChains LengthOrganismImage
mRNA38Escherichia coli K-12
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Entity ID: 26
MoleculeChains LengthOrganismImage
23S ribosomal RNAZ [auth a]2,903Escherichia coli K-12
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Entity ID: 27
MoleculeChains LengthOrganismImage
5S ribosomal RNAAA [auth b]120Escherichia coli K-12
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
FN [auth 3],
GN [auth 4]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AC [auth A]
AD [auth A]
AE [auth a]
AF [auth a]
AG [auth a]
AC [auth A],
AD [auth A],
AE [auth a],
AF [auth a],
AG [auth a],
AH [auth a],
AI [auth a],
AJ [auth a],
AK [auth a],
AL [auth a],
AM [auth a],
AN [auth c],
BC [auth A],
BD [auth A],
BE [auth a],
BF [auth a],
BG [auth a],
BH [auth a],
BI [auth a],
BJ [auth a],
BK [auth a],
BL [auth a],
BM [auth a],
BN [auth c],
CC [auth A],
CD [auth A],
CE [auth a],
CF [auth a],
CG [auth a],
CH [auth a],
CI [auth a],
CJ [auth a],
CK [auth a],
CL [auth a],
CM [auth a],
CN [auth d],
DC [auth A],
DD [auth A],
DE [auth a],
DF [auth a],
DG [auth a],
DH [auth a],
DI [auth a],
DJ [auth a],
DK [auth a],
DL [auth a],
DM [auth a],
DN [auth m],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth a],
EF [auth a],
EG [auth a],
EH [auth a],
EI [auth a],
EJ [auth a],
EK [auth a],
EL [auth a],
EM [auth a],
EN [auth z],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth a],
FF [auth a],
FG [auth a],
FH [auth a],
FI [auth a],
FJ [auth a],
FK [auth a],
FL [auth a],
FM [auth a],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth a],
GF [auth a],
GG [auth a],
GH [auth a],
GI [auth a],
GJ [auth a],
GK [auth a],
GL [auth a],
GM [auth a],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth a],
HF [auth a],
HG [auth a],
HH [auth a],
HI [auth a],
HJ [auth a],
HK [auth a],
HL [auth a],
HM [auth a],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth a],
IF [auth a],
IG [auth a],
IH [auth a],
II [auth a],
IJ [auth a],
IK [auth a],
IL [auth a],
IM [auth a],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth a],
JF [auth a],
JG [auth a],
JH [auth a],
JI [auth a],
JJ [auth a],
JK [auth a],
JL [auth a],
JM [auth a],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth a],
KF [auth a],
KG [auth a],
KH [auth a],
KI [auth a],
KJ [auth a],
KK [auth a],
KL [auth a],
KM [auth a],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth a],
LF [auth a],
LG [auth a],
LH [auth a],
LI [auth a],
LJ [auth a],
LK [auth a],
LL [auth a],
LM [auth a],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth a],
MF [auth a],
MG [auth a],
MH [auth a],
MI [auth a],
MJ [auth a],
MK [auth a],
ML [auth a],
MM [auth a],
NB [auth A],
NC [auth A],
ND [auth A],
NE [auth a],
NF [auth a],
NG [auth a],
NH [auth a],
NI [auth a],
NJ [auth a],
NK [auth a],
NL [auth a],
NM [auth a],
OB [auth A],
OC [auth A],
OD [auth A],
OE [auth a],
OF [auth a],
OG [auth a],
OH [auth a],
OI [auth a],
OJ [auth a],
OK [auth a],
OL [auth a],
OM [auth a],
PB [auth A],
PC [auth A],
PD [auth A],
PE [auth a],
PF [auth a],
PG [auth a],
PH [auth a],
PI [auth a],
PJ [auth a],
PK [auth a],
PL [auth a],
PM [auth a],
QB [auth A],
QC [auth A],
QD [auth A],
QE [auth a],
QF [auth a],
QG [auth a],
QH [auth a],
QI [auth a],
QJ [auth a],
QK [auth a],
QL [auth a],
QM [auth a],
RB [auth A],
RC [auth A],
RD [auth A],
RE [auth a],
RF [auth a],
RG [auth a],
RH [auth a],
RI [auth a],
RJ [auth a],
RK [auth a],
RL [auth a],
RM [auth a],
SB [auth A],
SC [auth A],
SD [auth A],
SE [auth a],
SF [auth a],
SG [auth a],
SH [auth a],
SI [auth a],
SJ [auth a],
SK [auth a],
SL [auth a],
SM [auth a],
TB [auth A],
TC [auth A],
TD [auth A],
TE [auth a],
TF [auth a],
TG [auth a],
TH [auth a],
TI [auth a],
TJ [auth a],
TK [auth a],
TL [auth a],
TM [auth a],
UB [auth A],
UC [auth A],
UD [auth A],
UE [auth a],
UF [auth a],
UG [auth a],
UH [auth a],
UI [auth a],
UJ [auth a],
UK [auth a],
UL [auth a],
UM [auth a],
VB [auth A],
VC [auth A],
VD [auth A],
VE [auth a],
VF [auth a],
VG [auth a],
VH [auth a],
VI [auth a],
VJ [auth a],
VK [auth a],
VL [auth a],
VM [auth a],
WB [auth A],
WC [auth A],
WD [auth A],
WE [auth a],
WF [auth a],
WG [auth a],
WH [auth a],
WI [auth a],
WJ [auth a],
WK [auth a],
WL [auth a],
WM [auth a],
XB [auth A],
XC [auth A],
XD [auth a],
XE [auth a],
XF [auth a],
XG [auth a],
XH [auth a],
XI [auth a],
XJ [auth a],
XK [auth a],
XL [auth a],
XM [auth b],
YB [auth A],
YC [auth A],
YD [auth a],
YE [auth a],
YF [auth a],
YG [auth a],
YH [auth a],
YI [auth a],
YJ [auth a],
YK [auth a],
YL [auth a],
YM [auth b],
ZB [auth A],
ZC [auth A],
ZD [auth a],
ZE [auth a],
ZF [auth a],
ZG [auth a],
ZH [auth a],
ZI [auth a],
ZJ [auth a],
ZK [auth a],
ZL [auth a],
ZM [auth c]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
D2T
Query on D2T
L
L-PEPTIDE LINKINGC5 H9 N O4 SASP
MEQ
Query on MEQ
CA [auth d]L-PEPTIDE LINKINGC6 H12 N2 O3GLN
4D4
Query on 4D4
KA [auth l]L-PEPTIDE LINKINGC6 H14 N4 O3ARG
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1 beta
RECONSTRUCTIONCCP4 package
MODEL REFINEMENTPHENIX1.18.2

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Centre National de la Recherche Scientifique (CNRS)France--

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations, Refinement description