4V42

Crystal structure of the ribosome at 5.5 A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.5 Å

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the ribosome at 5.5 A resolution

Yusupov, M.M.Yusupova, G.Z.Baucom, A.Lieberman, K.Earnest, T.N.Cate, J.H.D.Noller, H.F.

(2001) Science 292: 883-896

  • DOI: 10.1126/science.1060089
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We describe the crystal structure of the complete Thermus thermophilus 70S ribosome containing bound messenger RNA and transfer RNAs (tRNAs) at 5.5 angstrom resolution. All of the 16S, 23S, and 5S ribosomal RNA (rRNA) chains, the A-, P-, and E-site t ...

    We describe the crystal structure of the complete Thermus thermophilus 70S ribosome containing bound messenger RNA and transfer RNAs (tRNAs) at 5.5 angstrom resolution. All of the 16S, 23S, and 5S ribosomal RNA (rRNA) chains, the A-, P-, and E-site tRNAs, and most of the ribosomal proteins can be fitted to the electron density map. The core of the interface between the 30S small subunit and the 50S large subunit, where the tRNA substrates are bound, is dominated by RNA, with proteins located mainly at the periphery, consistent with ribosomal function being based on rRNA. In each of the three tRNA binding sites, the ribosome contacts all of the major elements of tRNA, providing an explanation for the conservation of tRNA structure. The tRNAs are closely juxtaposed with the intersubunit bridges, in a way that suggests coupling of the 20 to 50 angstrom movements associated with tRNA translocation with intersubunit movement.


    Organizational Affiliation

    Center for Molecular Biology of RNA, Sinsheimer Laboratories, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S2
AE
256Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsB (rps2)
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80371
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S3
AF
239Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsC (rps3)
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80372
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S4
AG
209Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsD (rps4)
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80373
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S5
AH
162Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsE
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ5
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S6
AI
101Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsF
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP8
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S7
AJ
156Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsG (rps7)
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S8
AK
138Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY9
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S9
AL
128Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsI (rps9)
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S10
AM
105Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsJ
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN7
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S11
AN
129Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsK (rps11)
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80376
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S12
AO
135Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsL
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN3
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S13
AP
126Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsM (rps13)
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80377
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S14
AQ
61Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsZ (rpsN)
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY6
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S15
AR
89Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsO
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ76
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S16
AS
91N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S17
AT
105N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S18
AU
88N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S19
AV
93Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsS
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP2
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN S20
AW
106N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
30S RIBOSOMAL PROTEIN THX
AX
26Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsU
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIH3
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L1
BC
228Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplA
Find proteins for Q5SLP7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP7
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L2
BD
178Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60405 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60405
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L3
BE
338Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplC
Find proteins for Q5SHN8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN8
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L4
BF
246Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplD
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN9
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L5
BG
176Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplE
Find proteins for Q5SHQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ0
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L6
BH
177Thermus aquaticusMutation(s): 0 
Gene Names: rplF
Find proteins for A0A0M9ADP1 (Thermus aquaticus)
Go to UniProtKB:  A0A0M9ADP1
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L7/L12
BI, BJ
128Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplL
Find proteins for Q8VVE2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q8VVE2
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L9
BK
149Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplI
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ1
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L11
BL
141Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplK
Find proteins for Q5SLP6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP6
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L13
BM
145Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplM
Find proteins for P60488 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60488
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L14
BN
122Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplN
Find proteins for Q5SHP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP8
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L15
BO
164Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplO
Find proteins for Q5SHQ7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ7
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L16
BP
138N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L18
BQ
186Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplR
Find proteins for Q5SHQ4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ4
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L19
BR
66Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl24e
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14116
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L22
BS
113Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplV
Find proteins for Q5SHP3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP3
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L23
BT
84Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplW
Find proteins for Q5SHP0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP0
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L24
BU
119Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplX
Find proteins for Q5SHP9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP9
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L25
BV
94Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplY (rpl25, rptL5)
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHZ1
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L29
BW
70Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmC
Find proteins for Q5SHP6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP6
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
50S RIBOSOMAL PROTEIN L30
BX
60Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmD
Find proteins for Q5SHQ6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ6
Entity ID: 1
MoleculeChainsLengthOrganism
30S 16S RIBOSOMAL RNAAA1522Thermus thermophilus
Entity ID: 2
MoleculeChainsLengthOrganism
TRNA(PHE)AB,AC76N/A
Entity ID: 3
MoleculeChainsLengthOrganism
TRNA(PHE)AD74N/A
Entity ID: 4
MoleculeChainsLengthOrganism
A- AND P-SITE MESSENGER RNA CODONSA16N/A
Entity ID: 25
MoleculeChainsLengthOrganism
50S 23S RIBOSOMAL RNABA2916Thermus thermophilus
Entity ID: 26
MoleculeChainsLengthOrganism
50S 5S RIBOSOMAL RNABB123Thermus thermophilus
Small Molecules
Modified Residues  12 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
AB, AC, AD
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
AB, AC, AD
RNA LINKINGC10 H16 N3 O8 PC
M2G
Query on M2G
AB, AC
RNA LINKINGC12 H18 N5 O8 PG
1MA
Query on 1MA
AB, AC
RNA LINKINGC11 H16 N5 O7 PA
OMC
Query on OMC
AB, AC
RNA LINKINGC10 H16 N3 O8 PC
4SU
Query on 4SU
AD
RNA LINKINGC9 H13 N2 O8 P SU
2MG
Query on 2MG
AB, AC
RNA LINKINGC11 H16 N5 O8 PG
OMG
Query on OMG
AB, AC
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
AB, AC
RNA LINKINGC11 H18 N5 O8 PG
YG
Query on YG
AB, AC
RNA LINKINGC21 H29 N6 O12 PG
5MU
Query on 5MU
AB, AC, AD
RNA LINKINGC10 H15 N2 O9 PU
H2U
Query on H2U
AB, AC, AD
RNA LINKINGC9 H15 N2 O9 PU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.5 Å
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 507.200α = 90.00
b = 507.200β = 90.00
c = 803.660γ = 90.00
Software Package:
Software NamePurpose
CCP4phasing
SCALEPACKdata scaling
CCP4model building
DENZOdata reduction
Omodel building

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