4BTS

THE CRYSTAL STRUCTURE OF THE EUKARYOTIC 40S RIBOSOMAL SUBUNIT IN COMPLEX WITH EIF1 AND EIF1A

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

The crystal structure of the eukaryotic 40S ribosomal subunit in complex with eIF1 and eIF1A.

Weisser, M., Voigts-Hoffmann, F., Rabl, J., Leibundgut, M., Ban, N.

(2013) Nat Struct Mol Biol 20: 1015-1017

  • DOI: https://doi.org/10.1038/nsmb.2622
  • Primary Citation of Related Structures:  
    4BTS

  • PubMed Abstract: 

    Eukaryotic translation initiation factors (eIFs) 1A and 1 are central players in the complex process of start-codon recognition. To improve mechanistic understanding of this process, we determined the crystal structure of the 40S ribosomal subunit in complex with eIF1A and eIF1 from Tetrahymena thermophila at a resolution of 3.7 Å. It reveals the positions of the two factors on the 40S and the conformational changes that accompany their binding.

    • Organizational Affiliation: 

    Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRANSLATION INITIATION FACTOR EIF-1A FAMILY PROTEINA [auth A0],
ED [auth D0],
KA [auth B0],
UB [auth C0]		211Tetrahymena thermophila SB210Mutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS28EB [auth A1],
FD [auth D1],
LA [auth B1],
VB [auth C1]		68Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S8C [auth A2],
GD [auth D2],
MA [auth B2],
WB [auth C2]		208Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS7ED [auth A3],
HD [auth D3],
NA [auth B3],
XB [auth C3]		197Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S3AE [auth A4],
ID [auth D4],
OA [auth B4],
YB [auth C4]		265Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS26EF [auth A5],
JD [auth D5],
PA [auth B5],
ZB [auth C5]		119Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S27AC [auth C6],
G [auth A6],
KD [auth D6],
QA [auth B6]		81Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS10EBC [auth C7],
H [auth A7],
LD [auth D7],
RA [auth B7]		162Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS25ECC [auth C8],
I [auth A8],
MD [auth D8],
SA [auth B8]		143Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS31EDC [auth C9],
J [auth A9],
ND [auth D9],
TA [auth B9]		189Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN SAFC [auth CB],
L [auth AB],
PD [auth DB],
VA [auth BB]		241Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS3EGC [auth CC],
M [auth AC],
QD [auth DC],
WA [auth BC]		243Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS9EHC [auth CD],
N [auth AD],
RD [auth DD],
XA [auth BD]		181Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS2EIC [auth CE],
O [auth AE],
SD [auth DE],
YA [auth BE]		296Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
EIF1JC [auth CF],
P [auth AF],
TD [auth DF],
ZA [auth BF]		101Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS5EAB [auth BG],
KC [auth CG],
Q [auth AG],
UD [auth DG]		200Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS22EBB [auth BH],
LC [auth CH],
R [auth AH],
VD [auth DH]		130Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS16ECB [auth BI],
MC [auth CI],
S [auth AI],
WD [auth DI]		145Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS20EDB [auth BJ],
NC [auth CJ],
T [auth AJ],
XD [auth DJ]		120Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS14EEB [auth BK],
OC [auth CK],
U [auth AK],
YD [auth DK]		151Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S12FB [auth BL],
PC [auth CL],
V [auth AL],
ZD [auth DL]		142Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS18EAE [auth DM],
GB [auth BM],
QC [auth CM],
W [auth AM]		155Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS29EBE [auth DN],
HB [auth BN],
RC [auth CN],
X [auth AN]		55Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS13ECE [auth DO],
IB [auth BO],
SC [auth CO],
Y [auth AO]		153Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S24DE [auth DP],
JB [auth BP],
TC [auth CP],
Z [auth AP]		149Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS11EAA [auth AQ],
EE [auth DQ],
KB [auth BQ],
UC [auth CQ]		157Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RACK1BA [auth AR],
FE [auth DR],
LB [auth BR],
VC [auth CR]		343Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS15ECA [auth AS],
GE [auth DS],
MB [auth BS],
WC [auth CS]		144Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS19EDA [auth AT],
HE [auth DT],
NB [auth BT],
XC [auth CT]		155Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS12EEA [auth AU],
IE [auth DU],
OB [auth BU],
YC [auth CU]		126Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS17EFA [auth AV],
JE [auth DV],
PB [auth BV],
ZC [auth CV]		130Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS4EAD [auth CW],
GA [auth AW],
KE [auth DW],
QB [auth BW]		259Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS30EBD [auth CX],
HA [auth AX],
LE [auth DX],
RB [auth BX]		80Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN S6CD [auth CY],
IA [auth AY],
ME [auth DY],
SB [auth BY]		293Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
40S RIBOSOMAL PROTEIN RPS21EDD [auth CZ],
JA [auth AZ],
NE [auth DZ],
TB [auth BZ]		97Tetrahymena thermophilaMutation(s): 0 
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Entity ID: 11
MoleculeChains LengthOrganismImage
18S ribosomal RNAEC [auth CA],
K [auth AA],
OD [auth DA],
UA [auth BA]		1,753Tetrahymena thermophila
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
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AL [auth C9]
CO [auth CN]
DO [auth D5]
EO [auth D6]
FO [auth D9]
AL [auth C9],
CO [auth CN],
DO [auth D5],
EO [auth D6],
FO [auth D9],
HR [auth DN],
OE [auth A5],
PE [auth A6],
QE [auth A9],
SH [auth AN],
TH [auth B5],
UH [auth B6],
VH [auth B9],
XK [auth BN],
YK [auth C5],
ZK [auth C6]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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AF [auth AA]
AG [auth AA]
AH [auth AA]
AI [auth BA]
AJ [auth BA]
AF [auth AA],
AG [auth AA],
AH [auth AA],
AI [auth BA],
AJ [auth BA],
AK [auth BA],
AM [auth CA],
AN [auth CA],
AO [auth CA],
AP [auth DA],
AQ [auth DA],
AR [auth DA],
BF [auth AA],
BG [auth AA],
BH [auth AA],
BI [auth BA],
BJ [auth BA],
BK [auth BA],
BL [auth CA],
BM [auth CA],
BN [auth CA],
BO [auth CA],
BP [auth DA],
BQ [auth DA],
BR [auth DA],
CF [auth AA],
CG [auth AA],
CH [auth AA],
CI [auth BA],
CJ [auth BA],
CK [auth BA],
CL [auth CA],
CM [auth CA],
CN [auth CA],
CP [auth DA],
CQ [auth DA],
CR [auth DA],
DF [auth AA],
DG [auth AA],
DH [auth AA],
DI [auth BA],
DJ [auth BA],
DK [auth BA],
DL [auth CA],
DM [auth CA],
DN [auth CA],
DP [auth DA],
DQ [auth DA],
DR [auth DA],
EF [auth AA],
EG [auth AA],
EH [auth AA],
EI [auth BA],
EJ [auth BA],
EK [auth BA],
EL [auth CA],
EM [auth CA],
EN [auth CA],
EP [auth DA],
EQ [auth DA],
ER [auth DA],
FF [auth AA],
FG [auth AA],
FH [auth AA],
FI [auth BA],
FJ [auth BA],
FK [auth BA],
FL [auth CA],
FM [auth CA],
FN [auth CA],
FP [auth DA],
FQ [auth DA],
FR [auth DA],
GF [auth AA],
GG [auth AA],
GH [auth AA],
GI [auth BA],
GJ [auth BA],
GK [auth BA],
GL [auth CA],
GM [auth CA],
GN [auth CA],
GO [auth DA],
GP [auth DA],
GQ [auth DA],
GR [auth DA],
HF [auth AA],
HG [auth AA],
HH [auth AA],
HI [auth BA],
HJ [auth BA],
HK [auth BA],
HL [auth CA],
HM [auth CA],
HN [auth CA],
HO [auth DA],
HP [auth DA],
HQ [auth DA],
IF [auth AA],
IG [auth AA],
IH [auth AA],
II [auth BA],
IJ [auth BA],
IK [auth BA],
IL [auth CA],
IM [auth CA],
IN [auth CA],
IO [auth DA],
IP [auth DA],
IQ [auth DA],
JF [auth AA],
JG [auth AA],
JH [auth AA],
JI [auth BA],
JJ [auth BA],
JK [auth BA],
JL [auth CA],
JM [auth CA],
JN [auth CA],
JO [auth DA],
JP [auth DA],
JQ [auth DA],
KF [auth AA],
KG [auth AA],
KH [auth AA],
KI [auth BA],
KJ [auth BA],
KK [auth BA],
KL [auth CA],
KM [auth CA],
KN [auth CA],
KO [auth DA],
KP [auth DA],
KQ [auth DA],
LF [auth AA],
LG [auth AA],
LH [auth AA],
LI [auth BA],
LJ [auth BA],
LK [auth BA],
LL [auth CA],
LM [auth CA],
LN [auth CA],
LO [auth DA],
LP [auth DA],
LQ [auth DA],
MF [auth AA],
MG [auth AA],
MH [auth AA],
MI [auth BA],
MJ [auth BA],
MK [auth BA],
ML [auth CA],
MM [auth CA],
MN [auth CA],
MO [auth DA],
MP [auth DA],
MQ [auth DA],
NF [auth AA],
NG [auth AA],
NH [auth AA],
NI [auth BA],
NJ [auth BA],
NK [auth BA],
NL [auth CA],
NM [auth CA],
NN [auth CA],
NO [auth DA],
NP [auth DA],
NQ [auth DA],
OF [auth AA],
OG [auth AA],
OH [auth AA],
OI [auth BA],
OJ [auth BA],
OK [auth BA],
OL [auth CA],
OM [auth CA],
ON [auth CA],
OO [auth DA],
OP [auth DA],
OQ [auth DA],
PF [auth AA],
PG [auth AA],
PH [auth AA],
PI [auth BA],
PJ [auth BA],
PK [auth BA],
PL [auth CA],
PM [auth CA],
PN [auth CA],
PO [auth DA],
PP [auth DA],
PQ [auth DA],
QF [auth AA],
QG [auth AA],
QH [auth AA],
QI [auth BA],
QJ [auth BA],
QK [auth BA],
QL [auth CA],
QM [auth CA],
QN [auth CA],
QO [auth DA],
QP [auth DA],
QQ [auth DA],
RE [auth AA],
RF [auth AA],
RG [auth AA],
RH [auth AA],
RI [auth BA],
RJ [auth BA],
RK [auth BA],
RL [auth CA],
RM [auth CA],
RN [auth CA],
RO [auth DA],
RP [auth DA],
RQ [auth DA],
SE [auth AA],
SF [auth AA],
SG [auth AA],
SI [auth BA],
SJ [auth BA],
SK [auth BA],
SL [auth CA],
SM [auth CA],
SN [auth CA],
SO [auth DA],
SP [auth DA],
SQ [auth DA],
TE [auth AA],
TF [auth AA],
TG [auth AA],
TI [auth BA],
TJ [auth BA],
TK [auth BA],
TL [auth CA],
TM [auth CA],
TN [auth CA],
TO [auth DA],
TP [auth DA],
TQ [auth DA],
UE [auth AA],
UF [auth AA],
UG [auth AA],
UI [auth BA],
UJ [auth BA],
UK [auth BA],
UL [auth CA],
UM [auth CA],
UN [auth CA],
UO [auth DA],
UP [auth DA],
UQ [auth DA],
VE [auth AA],
VF [auth AA],
VG [auth AA],
VI [auth BA],
VJ [auth BA],
VK [auth BA],
VL [auth CA],
VM [auth CA],
VN [auth CA],
VO [auth DA],
VP [auth DA],
VQ [auth DA],
WE [auth AA],
WF [auth AA],
WG [auth AA],
WH [auth BA],
WI [auth BA],
WJ [auth BA],
WK [auth BA],
WL [auth CA],
WM [auth CA],
WN [auth CA],
WO [auth DA],
WP [auth DA],
WQ [auth DA],
XE [auth AA],
XF [auth AA],
XG [auth AA],
XH [auth BA],
XI [auth BA],
XJ [auth BA],
XL [auth CA],
XM [auth CA],
XN [auth CA],
XO [auth DA],
XP [auth DA],
XQ [auth DA],
YE [auth AA],
YF [auth AA],
YG [auth AA],
YH [auth BA],
YI [auth BA],
YJ [auth BA],
YL [auth CA],
YM [auth CA],
YN [auth CA],
YO [auth DA],
YP [auth DA],
YQ [auth DA],
ZE [auth AA],
ZF [auth AA],
ZG [auth AA],
ZH [auth BA],
ZI [auth BA],
ZJ [auth BA],
ZL [auth CA],
ZM [auth CA],
ZN [auth CA],
ZO [auth DA],
ZP [auth DA],
ZQ [auth DA]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 209.99α = 90
b = 471.55β = 91.02
c = 298.54γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

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: 2013-07-17
    Type: Initial release
  • Version 1.1: 2013-07-24
    Changes: Database references
  • Version 1.2: 2014-06-25
    Changes: Database references
  • Version 1.3: 2014-12-10
    Changes: Other
  • Version 1.4: 2018-03-07
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.5: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description