4V4I image
Deposition Date 2007-02-15
Release Date 2014-07-09
Last Version Date 2024-10-30
Entry Detail
PDB ID:
4V4I
Keywords:
RIBOSOME
Title:
Crystal Structure of a 70S Ribosome-tRNA Complex Reveals Functional Interactions and Rearrangements.
Biological Source:
Source Organism:
Thermus thermophilus (Taxon ID: 262724)
Escherichia coli (Taxon ID: 562)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.71 Å
R-Value Free:
0.35
R-Value Work:
0.34
R-Value Observed:
0.34
Space Group:
I 4 2 2
4V4I validation report
Macromolecular Entities
Polymer Type:polyribonucleotide
Molecule:E-TRNA
Chain IDs:GA (auth: 0)
Chain Length:76
Number of Molecules:1
Biological Source:Thermus thermophilus
Polymer Type:polyribonucleotide
Molecule:MRNA
Chain IDs:HA (auth: 1)
Chain Length:10
Number of Molecules:1
Biological Source:
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1
Chain IDs:C (auth: A)
Chain Length:65
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SLP7 Pfam ID:PF00687
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Chain IDs:D (auth: B)
Chain Length:37
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P60405 Pfam ID:PF00181, PF03947
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Chain IDs:E (auth: C)
Chain Length:206
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN8 Pfam ID:PF00297
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Chain IDs:F (auth: D)
Chain Length:239
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN9 Pfam ID:PF00573
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Chain IDs:G (auth: E)
Chain Length:209
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:H (auth: F)
Chain Length:162
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P0DOY8 Pfam ID:PF00347
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Chain IDs:I (auth: G)
Chain Length:148
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SLQ1 Pfam ID:PF01281, PF03948
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Chain IDs:J (auth: H)
Chain Length:156
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P60488 Pfam ID:PF00572
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Chain IDs:K (auth: I)
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP8 Pfam ID:PF00238
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Chain IDs:L (auth: J)
Chain Length:128
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ7 Pfam ID:PF00828
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Chain IDs:M (auth: K)
Chain Length:105
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P60489 Pfam ID:PF00252
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Chain IDs:N (auth: L)
Chain Length:129
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q9Z9H5 Pfam ID:PF01196
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Chain IDs:O (auth: M)
Chain Length:132
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ4 Pfam ID:PF00861
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Chain IDs:P (auth: N)
Chain Length:146
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P60490 Pfam ID:PF01245
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Chain IDs:Q (auth: O)
Chain Length:61
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P60491 Pfam ID:PF00453
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Chain IDs:R (auth: P)
Chain Length:89
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P60492 Pfam ID:PF00829
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Chain IDs:S (auth: Q)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP3 Pfam ID:PF00237
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Chain IDs:T (auth: R)
Chain Length:105
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP0 Pfam ID:PF00276
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Chain IDs:U (auth: S)
Chain Length:110
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP9 Pfam ID:PF00467, PF17136
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Chain IDs:V (auth: T)
Chain Length:93
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Chain IDs:W (auth: U)
Chain Length:85
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P60493 Pfam ID:PF01016
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Chain IDs:X (auth: V)
Chain Length:27
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P60494 Pfam ID:PF00830
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Chain IDs:Y (auth: W)
Chain Length:72
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP6 Pfam ID:PF00831
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Chain IDs:Z (auth: X)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ6 Pfam ID:PF00327
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Chain IDs:AA (auth: Y)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80339 Pfam ID:PF01783
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:BA (auth: Z)
Chain Length:76
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80340 Pfam ID:PF00468
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Chain IDs:CA (auth: a)
Chain Length:65
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SKU1 Pfam ID:PF01632
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Chain IDs:DA (auth: b)
Chain Length:37
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHR2 Pfam ID:PF00444
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Chain IDs:IA (auth: c)
Chain Length:206
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80371 Pfam ID:PF00318
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Chain IDs:JA (auth: d)
Chain Length:239
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80372 Pfam ID:PF07650, PF00189
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Chain IDs:KA (auth: e)
Chain Length:209
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80373 Pfam ID:PF00163, PF01479
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Chain IDs:LA (auth: f)
Chain Length:162
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Chain IDs:MA (auth: g)
Chain Length:148
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SLP8 Pfam ID:PF01250
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Chain IDs:NA (auth: h)
Chain Length:156
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P17291 Pfam ID:PF00177
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:OA (auth: i)
Chain Length:138
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P0DOY9 Pfam ID:PF00410
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Chain IDs:PA (auth: j)
Chain Length:128
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80374 Pfam ID:PF00380
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:QA (auth: k)
Chain Length:105
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN7 Pfam ID:PF00338
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Chain IDs:RA (auth: l)
Chain Length:129
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80376 Pfam ID:PF00411
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:SA (auth: m)
Chain Length:132
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHN3 Pfam ID:PF00164
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Chain IDs:TA (auth: n)
Chain Length:146
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80377 Pfam ID:PF00416
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Chain IDs:UA (auth: o)
Chain Length:61
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P0DOY6 Pfam ID:PF00253
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Chain IDs:VA (auth: p)
Chain Length:89
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SJ76 Pfam ID:PF00312
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Chain IDs:WA (auth: q)
Chain Length:88
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SJH3 Pfam ID:PF00886
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:XA (auth: r)
Chain Length:105
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P0DOY7 Pfam ID:PF00366
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Chain IDs:YA (auth: s)
Chain Length:110
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SLQ0 Pfam ID:PF01084
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:ZA (auth: t)
Chain Length:93
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SHP2 Pfam ID:PF00203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Chain IDs:AB (auth: u)
Chain Length:85
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:P80380 Pfam ID:PF01649
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Chain IDs:BB (auth: v)
Chain Length:27
Number of Molecules:1
Biological Source:Thermus thermophilus
UniProt ID:Q5SIH3 Pfam ID:PF17070
Polymer Type:polyribonucleotide
Molecule:23S LARGE SUBUNIT RIBOSOMAL RNA
Chain IDs:A (auth: w)
Chain Length:72
Number of Molecules:1
Biological Source:Thermus thermophilus
Polymer Type:polyribonucleotide
Molecule:5S LARGE SUBUNIT RIBOSOMAL RNA
Chain IDs:B (auth: x)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus
Polymer Type:polyribonucleotide
Molecule:16S SMALL SUBUNIT RIBOSOMAL RNA
Chain IDs:EA (auth: y)
Chain Length:60
Number of Molecules:1
Biological Source:Thermus thermophilus
Polymer Type:polyribonucleotide
Molecule:P-site PHE-tRNA
Chain IDs:FA (auth: z)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
2MG EA G 2N-METHYLGUANOSINE-5'-MONOPHOSPHATE
4OC EA C 4N,O2'-METHYLCYTIDINE-5'-MONOPHOSPHATE
4SU FA U 4-THIOURIDINE-5'-MONOPHOSPHATE
5MC EA C 5-METHYLCYTIDINE-5'-MONOPHOSPHATE
5MU FA U 5-METHYLURIDINE 5'-MONOPHOSPHATE
7MG EA G ?
H2U FA U 5,6-DIHYDROURIDINE-5'-MONOPHOSPHATE
M2G EA G N2-DIMETHYLGUANOSINE-5'-MONOPHOSPHATE
MA6 EA A 6N-DIMETHYLADENOSINE-5'-MONOPHOSHATE
MIA FA A ?
PSU EA U PSEUDOURIDINE-5'-MONOPHOSPHATE
UR3 EA U 3-METHYLURIDINE-5'-MONOPHOSHATE
Ligand Molecules
NA
Primary Citation
Crystal Structure of a 70S Ribosome-tRNA Complex Reveals Functional Interactions and Rearrangements
Cell(Cambridge,Mass.) 126 1065 1077 (2006)
PMID: 16962654 DOI: 10.1016/j.cell.2006.08.032

Abstact

Our understanding of the mechanism of protein synthesis has undergone rapid progress in recent years as a result of low-resolution X-ray and cryo-EM structures of ribosome functional complexes and high-resolution structures of ribosomal subunits and vacant ribosomes. Here, we present the crystal structure of the Thermus thermophilus 70S ribosome containing a model mRNA and two tRNAs at 3.7 A resolution. Many structural details of the interactions between the ribosome, tRNA, and mRNA in the P and E sites and the ways in which tRNA structure is distorted by its interactions with the ribosome are seen. Differences between the conformations of vacant and tRNA-bound 70S ribosomes suggest an induced fit of the ribosome structure in response to tRNA binding, including significant changes in the peptidyl-transferase catalytic site.

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Protein

Chemical

Disease

Primary Citation of related structures
4V4I
1VSA
2OW8
1GIX
1GIY
2OW8