4V5G

The crystal structure of the 70S ribosome bound to EF-Tu and tRNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.281 

Starting Models: experimental
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This is version 1.4 of the entry. See complete history. 


Literature

The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA.

Schmeing, T.M., Voorhees, R.M., Kelley, A.C., Gao, Y.G., Murphy, F.V., Weir, J.R., Ramakrishnan, V.

(2009) Science 326: 688-694

  • DOI: https://doi.org/10.1126/science.1179700
  • Primary Citation of Related Structures:  
    4V5G

  • PubMed Abstract: 

    The ribosome selects a correct transfer RNA (tRNA) for each amino acid added to the polypeptide chain, as directed by messenger RNA. Aminoacyl-tRNA is delivered to the ribosome by elongation factor Tu (EF-Tu), which hydrolyzes guanosine triphosphate (GTP) and releases tRNA in response to codon recognition. The signaling pathway that leads to GTP hydrolysis upon codon recognition is critical to accurate decoding. Here we present the crystal structure of the ribosome complexed with EF-Tu and aminoacyl-tRNA, refined to 3.6 angstrom resolution. The structure reveals details of the tRNA distortion that allows aminoacyl-tRNA to interact simultaneously with the decoding center of the 30S subunit and EF-Tu at the factor binding site. A series of conformational changes in EF-Tu and aminoacyl-tRNA suggests a communication pathway between the decoding center and the guanosine triphosphatase center of EF-Tu.

    • Organizational Affiliation: 

    MRC Laboratory of Molecular Biology, Cambridge, UK, CB2 0QH.


Macromolecules

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S2B [auth AB],
IB [auth CB]		256Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S3C [auth AC],
JB [auth CC]		239Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S4D [auth AD],
KB [auth CD]		209Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S5E [auth AE],
LB [auth CE]		162Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S6F [auth AF],
MB [auth CF]		101Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S7G [auth AG],
NB [auth CG]		156Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S8H [auth AH],
OB [auth CH]		138Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S9I [auth AI],
PB [auth CI]		128Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S10J [auth AJ],
QB [auth CJ]		105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S11K [auth AK],
RB [auth CK]		129Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S12L [auth AL],
SB [auth CL]		135Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S13M [auth AM],
TB [auth CM]		126Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S14 TYPE ZN [auth AN],
UB [auth CN]		61Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S15O [auth AO],
VB [auth CO]		89Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S16P [auth AP],
WB [auth CP]		88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S17Q [auth AQ],
XB [auth CQ]		105Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S18R [auth AR],
YB [auth CR]		88Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S19S [auth AS],
ZB [auth CS]		93Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN S20AC [auth CT],
T [auth AT]		106Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
30S RIBOSOMAL PROTEIN THXBC [auth CU],
U [auth AU]		27Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
ELONGATION FACTOR TU-AGC [auth CZ],
Z [auth AZ]		406Thermus thermophilus HB8Mutation(s): 0 
EC: 3.6.5.3
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L27AA [auth B0],
HC [auth D0]		85Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L28BA [auth B1],
IC [auth D1]		98Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L29CA [auth B2],
JC [auth D2]		72Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L30DA [auth B3],
KC [auth D3]		60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L31EA [auth B4],
LC [auth D4]		71Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L32FA [auth B5],
MC [auth D5]		60Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L33GA [auth B6],
NC [auth D6]		54Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L34HA [auth B7],
OC [auth D7]		49Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 34
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L35IA [auth B8],
PC [auth D8]		65Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L36JA [auth B9],
QC [auth D9]		37Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L1MA [auth BC],
TC [auth DC]		229Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L2NA [auth BD],
UC [auth DD]		276Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L3OA [auth BE],
VC [auth DE]		206Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L4PA [auth BF],
WC [auth DF]		210Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L5QA [auth BG],
XC [auth DG]		182Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L6RA [auth BH],
YC [auth DH]		180Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L10SA [auth BJ],
ZC [auth DJ]		173Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L11AD [auth DK],
TA [auth BK]		147Thermus thermophilus HB8Mutation(s): 0 
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L13BD [auth DN],
UA [auth BN]		140Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L14CD [auth DO],
VA [auth BO]		122Thermus thermophilus HB8Mutation(s): 0 
UniProt
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L15DD [auth DP],
WA [auth BP]		150Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHQ7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ5SHQ7
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L16ED [auth DQ],
XA [auth BQ]		141Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P60489 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L17FD [auth DR],
YA [auth BR]		118Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for Q9Z9H5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L18GD [auth DS],
ZA [auth BS]		112Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHQ4 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 52
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L19AB [auth BT],
HD [auth DT]		146Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P60490 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 53
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L20BB [auth BU],
ID [auth DU]		118Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P60491 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 54
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L21CB [auth BV],
JD [auth DV]		101Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for P60492 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 55
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L22DB [auth BW],
KD [auth DW]		113Thermus thermophilus HB8Mutation(s): 0 
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Find proteins for Q5SHP3 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 56
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L23EB [auth BX],
LD [auth DX]		96Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHP0 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 57
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L24FB [auth BY],
MD [auth DY]		110Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHP9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 58
MoleculeChains Sequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L25GB [auth BZ],
ND [auth DZ]		206Thermus thermophilus HB8Mutation(s): 0 
UniProt
Find proteins for Q5SHZ1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 1
MoleculeChains LengthOrganismImage
16S RIBOSOMAL RNAA [auth AA],
HB [auth CA]		1,522Thermus thermophilus HB8
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Entity ID: 22
MoleculeChains LengthOrganismImage
E-SITE TRNA PHE OR P-SITE TRNA PHECC [auth CV],
DC [auth CW],
V [auth AV],
W [auth AW]		76Escherichia coli K-12
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Entity ID: 23
MoleculeChains LengthOrganismImage
MRNAEC [auth CX],
X [auth AX]		27synthetic construct
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Entity ID: 24
MoleculeChains LengthOrganismImage
A-SITE TRNA THRFC [auth CY],
Y [auth AY]		77Thermus thermophilus HB8
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Entity ID: 36
MoleculeChains LengthOrganismImage
23S RIBOSOMAL RNAKA [auth BA],
RC [auth DA]		2,915Thermus thermophilus HB8
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Entity ID: 37
MoleculeChains LengthOrganismImage
5S RIBOSOMAL RNALA [auth BB],
SC [auth DB]		122Thermus thermophilus HB8
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Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
KIR
Query on KIR
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BE [auth CZ],
TD [auth AZ]		KIRROMYCIN
C43 H60 N2 O12
HMSYAPGFKGSXAJ-PAHGNTJYSA-N
PAR
Query on PAR
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OD [auth AA],
WD [auth CA]		PAROMOMYCIN
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
GDP
Query on GDP
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AE [auth CZ],
SD [auth AZ]		GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
ZN
Query on ZN
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CE [auth D4]
DE [auth D9]
PD [auth AD]
QD [auth AN]
UD [auth B4]
CE [auth D4],
DE [auth D9],
PD [auth AD],
QD [auth AN],
UD [auth B4],
VD [auth B9],
XD [auth CD],
YD [auth CN]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG
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RD [auth AY],
ZD [auth CY]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.281 
  • R-Value Observed: 0.281 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 289.566α = 90
b = 268.363β = 91.01
c = 403.884γ = 90
Software Package:
Software NamePurpose
CNSmodel building
CNSrefinement
XDSdata reduction
XDSdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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: 2018-04-18
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 1.4: 2024-10-23
    Changes: Structure summary