ISDA

Deposition Date 2003-05-06

Release Date 2014-07-09

Last Version Date 2024-02-28

Entry Detail

PDB ID:

4V47

Keywords:

RIBOSOME

Title:

Real space refined coordinates of the 30S and 50S subunits fitted into the low resolution cryo-EM map of the EF-G.GTP state of E. coli 70S ribosome

Biological Source:

Source Organism:

Escherichia coli (Taxon ID: 562)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

12.30 Å

Aggregation State:

PARTICLE

Reconstruction Method:

SINGLE PARTICLE

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:A (auth: A0)
Chain Length:2904
Number of Molecules:1
Biological Source:Escherichia coli

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:Z (auth: A1)
Chain Length:54
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7N9 Pfam ID:PF00471

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L36
Gene (Uniprot):rpmJ
Chain IDs:AA (auth: A4)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7Q6 Pfam ID:PF00444

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:B (auth: A9)
Chain Length:120
Number of Molecules:1
Biological Source:Escherichia coli

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:C (auth: AA)
Chain Length:272
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P60422 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:D (auth: AB)
Chain Length:209
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P60438 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:E (auth: AC)
Chain Length:201
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P60723 Pfam ID:PF00573

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:F (auth: AD)
Chain Length:178
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P62399 Pfam ID:PF00281, PF00673

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Chain IDs:G (auth: AE)
Chain Length:176
Number of Molecules:1
Biological Source:Escherichia coli

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:H (auth: AF)
Chain Length:149
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7R1 Pfam ID:PF01281, PF03948

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L11
Gene (Uniprot):rplK
Chain IDs:I (auth: AG)
Chain Length:141
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7J7 Pfam ID:PF03946, PF00298

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:J (auth: AH)
Chain Length:142
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0AA10 Pfam ID:PF00572

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Chain IDs:K (auth: AI)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:L (auth: AJ)
Chain Length:144
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P02413 Pfam ID:PF00828

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Chain IDs:M (auth: AK)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Chain IDs:N (auth: AL)
Chain Length:127
Number of Molecules:1
Biological Source:Escherichia coli

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:O (auth: AM)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0C018 Pfam ID:PF00861

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:P (auth: AN)
Chain Length:114
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7K6 Pfam ID:PF01245

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:Q (auth: AO)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7L3 Pfam ID:PF00453

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:R (auth: AQ)
Chain Length:110
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P61175 Pfam ID:PF00237

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Chain IDs:S (auth: AR)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:T (auth: AS)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P60624 Pfam ID:PF00467, PF17136

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:U (auth: AT)
Chain Length:94
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P68919 Pfam ID:PF01386

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:V (auth: AU)
Chain Length:84
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7L8 Pfam ID:PF01016

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:W (auth: AW)
Chain Length:63
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7M6 Pfam ID:PF00831

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Chain IDs:X (auth: AX)
Chain Length:58
Number of Molecules:1
Biological Source:Escherichia coli

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:Y (auth: AZ)
Chain Length:56
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7N4 Pfam ID:PF01783

Polymer Type:polyribonucleotide
Molecule:16S RIBOSOMAL RNA
Chain IDs:BA
Chain Length:1542
Number of Molecules:1
Biological Source:Escherichia coli

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S3
Gene (Uniprot):rpsC
Chain IDs:CA (auth: BC)
Chain Length:232
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7V3 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S4
Gene (Uniprot):rpsD
Chain IDs:DA (auth: BD)
Chain Length:205
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7V8 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S5
Gene (Uniprot):rpsE
Chain IDs:EA (auth: BE)
Chain Length:166
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7W1 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S6
Gene (Uniprot):rpsF
Chain IDs:FA (auth: BF)
Chain Length:135
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P02358 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S7
Gene (Uniprot):rpsG
Chain IDs:GA (auth: BG)
Chain Length:178
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P02359 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S8
Gene (Uniprot):rpsH
Chain IDs:HA (auth: BH)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7W7 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S9
Gene (Uniprot):rpsI
Chain IDs:IA (auth: BI)
Chain Length:129
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7X3 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S10
Gene (Uniprot):rpsJ
Chain IDs:JA (auth: BJ)
Chain Length:103
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7R5 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S11
Gene (Uniprot):rpsK
Chain IDs:KA (auth: BK)
Chain Length:128
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7R9 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S12
Gene (Uniprot):rpsL
Chain IDs:LA (auth: BL)
Chain Length:123
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7S3 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S13
Gene (Uniprot):rpsM
Chain IDs:MA (auth: BM)
Chain Length:117
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7S9 Pfam ID:PF00416

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S14
Chain IDs:NA (auth: BN)
Chain Length:100
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S15
Chain IDs:OA (auth: BO)
Chain Length:88
Number of Molecules:1
Biological Source:Escherichia coli

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S16
Gene (Uniprot):rpsP
Chain IDs:PA (auth: BP)
Chain Length:82
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7T3 Pfam ID:PF00886

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S17
Chain IDs:QA (auth: BQ)
Chain Length:83
Number of Molecules:1
Biological Source:Escherichia coli

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S18
Gene (Uniprot):rpsR
Chain IDs:RA (auth: BR)
Chain Length:74
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7T7 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S19
Gene (Uniprot):rpsS
Chain IDs:SA (auth: BS)
Chain Length:91
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7U3 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S20
Gene (Uniprot):rpsT
Chain IDs:TA (auth: BT)
Chain Length:86
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7U7 Pfam ID:PF01649

Ligand Molecules

Primary Citation

Study of the structural dynamics of the E. coli 70S ribosome using real space refinement

Gao, H, Sengupta, J, Valle, M, Korostelev, A, Eswar, N, Stagg, S.M, Van Roey, P, Agrawal, R.K, Harvey, S.T, Sali, A, Chapman, M.S, Frank, J, Gabashvili, I.S, Agrawal, R.K, Spahn, C.M.T, Grassucci, R, Svergun, D.I, Frank, J, Penczek, P, Frank, J, Agrawal, R.K.Show

Cell(Cambridge,Mass.) 113 789 801 (2003)

PMID: 12809609 DOI: 10.1016/S0092-8674(03)00427-6

Abstact

Cryo-EM density maps showing the 70S ribosome of E. coli in two different functional states related by a ratchet-like motion were analyzed using real-space refinement. Comparison of the two resulting atomic models shows that the ribosome changes from a compact structure to a looser one, coupled with the rearrangement of many of the proteins. Furthermore, in contrast to the unchanged inter-subunit bridges formed wholly by RNA, the bridges involving proteins undergo large conformational changes following the ratchet-like motion, suggesting an important role of ribosomal proteins in facilitating the dynamics of translation.

Legend

Protein

Chemical

Disease

Primary Citation of related structures