ISDA

Deposition Date 2003-05-06

Release Date 2014-07-09

Last Version Date 2024-02-28

Entry Detail

PDB ID:

4V48

Keywords:

RIBOSOME

Title:

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

Biological Source:

Source Organism:

Escherichia coli (Taxon ID: 562)

Method Details:

Experimental Method:

ELECTRON MICROSCOPY

Resolution:

11.50 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:AA (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:BA (auth: A4)
Chain Length:38
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P0A7Q6 Pfam ID:PF00444

Polymer Type:polyribonucleotide
Molecule:tRNA-PHE
Chain IDs:C (auth: A6)
Chain Length:76
Number of Molecules:1
Biological Source:Escherichia coli

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:D (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:E (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:F (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:G (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:H (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:I (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:J (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:K (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:L (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:M (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:N (auth: AK)
Chain Length:136
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Chain IDs:O (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:P (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:Q (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:R (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:S (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:T (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:U (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:V (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:W (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:X (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:Y (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:Z (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:CA (auth: BA)
Chain Length:1543
Number of Molecules:1
Biological Source:Escherichia coli

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S2
Chain IDs:DA (auth: BB)
Chain Length:240
Number of Molecules:1
Biological Source:Escherichia coli

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

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

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

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S RIBOSOMAL PROTEIN S6
Gene (Uniprot):rpsF
Chain IDs:HA (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:IA (auth: BG)
Chain Length:178
Number of Molecules:1
Biological Source:Escherichia coli

UniProt ID:P02359 Pfam ID:PF00177

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

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

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

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

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

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

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

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

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

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

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

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

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

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.

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Primary Citation of related structures