ISDA: 4V4A

Deposition Date 2003-06-13

Release Date 2014-07-09

Last Version Date 2024-11-20

Entry Detail

PDB ID:

4V4A

Keywords:

RIBOSOME

Title:

Crystal Structure of the Wild Type Ribosome from E. Coli 70S Ribosome.

Biological Source:

Source Organism:

Escherichia coli (Taxon ID: 562)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

9.50 Å

R-Value Free:

0.40

R-Value Work:

0.38

Space Group:

I 4 2 2

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:16S RIBOSOMAL RNA
Chain IDs:A (auth: AA)
Chain Length:1537
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Chain IDs:B (auth: AB)
Chain Length:234
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Chain IDs:C (auth: AC)
Chain Length:206
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Chain IDs:D (auth: AD)
Chain Length:208
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Chain IDs:E (auth: AE)
Chain Length:150
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Chain IDs:F (auth: AF)
Chain Length:101
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Chain IDs:G (auth: AG)
Chain Length:155
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Chain IDs:H (auth: AH)
Chain Length:138
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Chain IDs:I (auth: AI)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Chain IDs:J (auth: AJ)
Chain Length:98
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Chain IDs:K (auth: AK)
Chain Length:119
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Chain IDs:L (auth: AL)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Chain IDs:M (auth: AM)
Chain Length:125
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14
Chain IDs:N (auth: AN)
Chain Length:60
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Chain IDs:O (auth: AO)
Chain Length:88
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Chain IDs:P (auth: AP)
Chain Length:83
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Chain IDs:Q (auth: AQ)
Chain Length:104
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Chain IDs:R (auth: AR)
Chain Length:73
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Chain IDs:S (auth: AS)
Chain Length:80
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Chain IDs:T (auth: AT)
Chain Length:99
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:23S RIBOSOMAL RNA
Chain IDs:U (auth: B0)
Chain Length:2887
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Chain IDs:WA (auth: B1)
Chain Length:53
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Chain IDs:XA (auth: B2)
Chain Length:46
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L35
Chain IDs:YA (auth: B3)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Chain IDs:ZA (auth: B4)
Chain Length:35
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L1P
Chain IDs:AB (auth: B5)
Chain Length:217
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polyribonucleotide
Molecule:5S RIBOSOMAL RNA
Chain IDs:V (auth: B9)
Chain Length:118
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Chain IDs:W (auth: BA)
Chain Length:270
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Chain IDs:X (auth: BB)
Chain Length:205
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Chain IDs:Y (auth: BC)
Chain Length:197
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Chain IDs:Z (auth: BD)
Chain Length:178
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:AA (auth: BE)
Chain Length:177
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Chain IDs:BA (auth: BF)
Chain Length:52
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Chain IDs:CA (auth: BG)
Chain Length:143
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Chain IDs:DA (auth: BH)
Chain Length:143
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Chain IDs:EA (auth: BI)
Chain Length:132
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Chain IDs:FA (auth: BJ)
Chain Length:141
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Chain IDs:GA (auth: BK)
Chain Length:124
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Chain IDs:HA (auth: BL)
Chain Length:114
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Chain IDs:IA (auth: BM)
Chain Length:111
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Chain IDs:JA (auth: BN)
Chain Length:125
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Chain IDs:KA (auth: BO)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Chain IDs:LA (auth: BP)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Chain IDs:MA (auth: BQ)
Chain Length:130
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Chain IDs:NA (auth: BR)
Chain Length:93
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Chain IDs:OA (auth: BS)
Chain Length:113
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:general stress protein Ctc
Chain IDs:PA (auth: BT)
Chain Length:173
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Chain IDs:QA (auth: BU)
Chain Length:86
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S RIBOSOMAL PROTEIN L28
Chain IDs:RA (auth: BV)
Chain Length:16
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Chain IDs:SA (auth: BW)
Chain Length:65
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Chain IDs:TA (auth: BX)
Chain Length:55
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Chain IDs:UA (auth: BY)
Chain Length:73
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Chain IDs:VA (auth: BZ)
Chain Length:58
Number of Molecules:1
Biological Source:Escherichia coli

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
MSE	AB	MET	SELENOMETHIONINE

Ligand Molecules

Primary Citation

X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli

Vila-Sanjurjo, A, Ridgeway, W.K, Seymaner, V, Zhang, W, Santoso, S, Yu, K, Cate, J.H.D.Show

Proc.Natl.Acad.Sci.USA 100 8682 8687 (2003)

PMID: 12853578 DOI: 10.1073/pnas.1133380100

Abstact

Protein biosynthesis on the ribosome requires accurate reading of the genetic code in mRNA. Two conformational rearrangements in the small ribosomal subunit, a closing of the head and body around the incoming tRNA and an RNA helical switch near the mRNA decoding site, have been proposed to select for complementary base-pairing between mRNA codons and tRNA anticodons. We determined x-ray crystal structures of the WT and a hyper-accurate variant of the Escherichia coli ribosome at resolutions of 10 and 9 A, respectively, revealing that formation of the intact 70S ribosome from its two subunits closes the conformation of the head of the small subunit independent of mRNA decoding. Moreover, no change in the conformation of the switch helix is observed in two steps of tRNA discrimination. These 70S ribosome structures indicate that mRNA decoding is coupled primarily to movement of the small subunit body, consistent with previous proposals, whereas closing of the head and the helical switch may function in other steps of protein synthesis.

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Primary Citation of related structures