ISDA: 4V83

Deposition Date 2010-12-13

Release Date 2014-07-09

Last Version Date 2024-11-20

Entry Detail

PDB ID:

4V83

Keywords:

RIBOSOME

Title:

Crystal structure of a complex containing domain 3 from the PSIV IGR IRES RNA bound to the 70S ribosome.

Biological Source:

Source Organism(s):

Thermus thermophilus (Taxon ID: 262724)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.50 Å

R-Value Free:

0.26

R-Value Work:

0.23

R-Value Observed:

0.23

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Molecule:ribosomal RNA 16S
Chain IDs:A (auth: AA), BB (auth: CA)
Chain Length:1506
Number of Molecules:2
Biological Source:Thermus thermophilus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S2
Gene (Uniprot):rpsB
Chain IDs:B (auth: AB), CB
Chain Length:234
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62662 Pfam ID:PF00318

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S3
Gene (Uniprot):rpsC
Chain IDs:C (auth: AC), DB (auth: CC)
Chain Length:206
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62663 Pfam ID:PF07650, PF00189

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S4
Gene (Uniprot):rpsD
Chain IDs:D (auth: AD), EB (auth: CD)
Chain Length:208
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62664 Pfam ID:PF01479, PF00163

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S5
Gene (Uniprot):rpsE
Chain IDs:E (auth: AE), FB (auth: CE)
Chain Length:151
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62665 Pfam ID:PF03719, PF00333

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S6
Gene (Uniprot):rpsF
Chain IDs:F (auth: AF), GB (auth: CF)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62666 Pfam ID:PF01250

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S7
Gene (Uniprot):rpsG
Chain IDs:G (auth: AG), HB (auth: CG)
Chain Length:155
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62667 Pfam ID:PF00177

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S8
Gene (Uniprot):rpsH
Chain IDs:H (auth: AH), IB (auth: CH)
Chain Length:138
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62668 Pfam ID:PF00410

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S9
Gene (Uniprot):rpsI
Chain IDs:I (auth: AI), JB (auth: CI)
Chain Length:127
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62669 Pfam ID:PF00380

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S10
Gene (Uniprot):rpsJ
Chain IDs:J (auth: AJ), KB (auth: CJ)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62653 Pfam ID:PF00338

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S11
Gene (Uniprot):rpsK
Chain IDs:K (auth: AK), LB (auth: CK)
Chain Length:119
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62654 Pfam ID:PF00411

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S12
Gene (Uniprot):rpsL
Chain IDs:L (auth: AL), MB (auth: CL)
Chain Length:124
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P61941 Pfam ID:PF00164

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S13
Gene (Uniprot):rpsM
Chain IDs:M (auth: AM), NB (auth: CM)
Chain Length:116
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62655 Pfam ID:PF00416

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S14 type Z
Gene (Uniprot):rpsZ
Chain IDs:N (auth: AN), OB (auth: CN)
Chain Length:60
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62656 Pfam ID:PF00253

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S15
Gene (Uniprot):rpsO
Chain IDs:O (auth: AO), PB (auth: CO)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62657 Pfam ID:PF00312

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S16
Gene (Uniprot):rpsP
Chain IDs:P (auth: AP), QB (auth: CP)
Chain Length:83
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62238 Pfam ID:PF00886

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S17
Gene (Uniprot):rpsQ
Chain IDs:Q (auth: AQ), RB (auth: CQ)
Chain Length:99
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62658 Pfam ID:PF00366

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S18
Gene (Uniprot):rpsR
Chain IDs:R (auth: AR), SB (auth: CR)
Chain Length:70
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62659 Pfam ID:PF01084

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S19
Gene (Uniprot):rpsS
Chain IDs:S (auth: AS), TB (auth: CS)
Chain Length:78
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62660 Pfam ID:PF00203

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein S20
Gene (Uniprot):rpsT
Chain IDs:T (auth: AT), UB (auth: CT)
Chain Length:99
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62661 Pfam ID:PF01649

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:30S ribosomal protein Thx
Gene (Uniprot):rpsU
Chain IDs:U (auth: AU), VB (auth: CU)
Chain Length:24
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62613 Pfam ID:PF17070

Polymer Type:polyribonucleotide
Molecule:domain 3 of PSIC IGR IRES RNA
Chain IDs:V (auth: AV), WB (auth: CV)
Chain Length:35
Number of Molecules:2
Biological Source:Thermus thermophilus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L31
Gene (Uniprot):rpmE
Chain IDs:WA (auth: B1), XC (auth: D1)
Chain Length:30
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72JR0 Pfam ID:PF01197

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L32
Gene (Uniprot):rpmF
Chain IDs:XA (auth: B2), YC (auth: D2)
Chain Length:52
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:P62652 Pfam ID:PF01783

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L33
Gene (Uniprot):rpmG
Chain IDs:YA (auth: B3), ZC (auth: D3)
Chain Length:44
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72GW3 Pfam ID:PF00471

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L34
Gene (Uniprot):rpmH
Chain IDs:ZA (auth: B4), AD (auth: D4)
Chain Length:48
Number of Molecules:2
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
Gene (Uniprot):rpmI
Chain IDs:AB (auth: B5), BD (auth: D5)
Chain Length:63
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72L77 Pfam ID:PF01632

Polymer Type:polyribonucleotide
Molecule:23S ribosomal RNA
Chain IDs:W (auth: BA), XB (auth: DA)
Chain Length:2879
Number of Molecules:2
Biological Source:Thermus thermophilus

Polymer Type:polyribonucleotide
Molecule:5S ribosomal RNA
Chain IDs:X (auth: BB), YB (auth: DB)
Chain Length:119
Number of Molecules:2
Biological Source:Thermus thermophilus

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L2
Gene (Uniprot):rplB
Chain IDs:Y (auth: BC), ZB (auth: DC)
Chain Length:271
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I07 Pfam ID:PF00181, PF03947

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L3
Gene (Uniprot):rplC
Chain IDs:Z (auth: BD), AC (auth: DD)
Chain Length:204
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I04 Pfam ID:PF00297

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L4
Gene (Uniprot):rplD
Chain IDs:AA (auth: BE), BC (auth: DE)
Chain Length:202
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I05 Pfam ID:PF00573

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L5
Gene (Uniprot):rplE
Chain IDs:BA (auth: BF), CC (auth: DF)
Chain Length:181
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I16 Pfam ID:PF00281, PF00673

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L6
Gene (Uniprot):rplF
Chain IDs:CA (auth: BG), DC (auth: DG)
Chain Length:159
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I19 Pfam ID:PF00347

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L9
Gene (Uniprot):rplI
Chain IDs:DA (auth: BH), EC (auth: DH)
Chain Length:145
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72GV5 Pfam ID:PF03948, PF01281

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L10
Gene (Uniprot):rplJ
Chain IDs:EA (auth: BI), FC (auth: DI)
Chain Length:65
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72GS1 Pfam ID:PF00466

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L13
Gene (Uniprot):rplM
Chain IDs:FA (auth: BJ), GC (auth: DJ)
Chain Length:137
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72IN1 Pfam ID:PF00572

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L14
Gene (Uniprot):rplN
Chain IDs:GA (auth: BK), HC (auth: DK)
Chain Length:122
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I14 Pfam ID:PF00238

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L15
Gene (Uniprot):rplO
Chain IDs:HA (auth: BL), IC (auth: DL)
Chain Length:146
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I23 Pfam ID:PF00828

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L16
Gene (Uniprot):rplP
Chain IDs:IA (auth: BM), JC (auth: DM)
Chain Length:136
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I11 Pfam ID:PF00252

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L17
Gene (Uniprot):rplQ
Chain IDs:JA (auth: BN), KC (auth: DN)
Chain Length:117
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I33 Pfam ID:PF01196

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L18
Gene (Uniprot):rplR
Chain IDs:KA (auth: BO), LC (auth: DO)
Chain Length:98
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I20 Pfam ID:PF00861

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L19
Gene (Uniprot):rplS
Chain IDs:LA (auth: BP), MC (auth: DP)
Chain Length:137
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72JU9 Pfam ID:PF01245

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L20
Gene (Uniprot):rplT
Chain IDs:MA (auth: BQ), NC (auth: DQ)
Chain Length:116
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72L76 Pfam ID:PF00453

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L21
Gene (Uniprot):rplU
Chain IDs:NA (auth: BR), OC (auth: DR)
Chain Length:101
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72HR2 Pfam ID:PF00829

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L22
Gene (Uniprot):rplV
Chain IDs:OA (auth: BS), PC (auth: DS)
Chain Length:112
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I09 Pfam ID:PF00237

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L23
Gene (Uniprot):rplW
Chain IDs:PA (auth: BT), QC (auth: DT)
Chain Length:92
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I06 Pfam ID:PF00276

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L24
Gene (Uniprot):rplX
Chain IDs:QA (auth: BU), RC (auth: DU)
Chain Length:100
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I15 Pfam ID:PF00467, PF17136

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L25
Gene (Uniprot):rplY
Chain IDs:RA (auth: BV), SC (auth: DV)
Chain Length:188
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72IA7 Pfam ID:PF01386, PF14693

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L27
Gene (Uniprot):rpmA
Chain IDs:SA (auth: BW), TC (auth: DW)
Chain Length:76
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72HR3 Pfam ID:PF01016

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L28
Gene (Uniprot):rpmB
Chain IDs:TA (auth: BX), UC (auth: DX)
Chain Length:88
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72G84 Pfam ID:PF00830

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L29
Gene (Uniprot):rpmC
Chain IDs:UA (auth: BY), VC (auth: DY)
Chain Length:62
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I12 Pfam ID:PF00831

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:50S ribosomal protein L30
Gene (Uniprot):rpmD
Chain IDs:VA (auth: BZ), WC (auth: DZ)
Chain Length:59
Number of Molecules:2
Biological Source:Thermus thermophilus

UniProt ID:Q72I22 Pfam ID:PF00327

Ligand Molecules

Primary Citation

Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome.

Zhu, J, Korostelev, A, Costantino, D.A, Donohue, J.P, Noller, H.F, Kieft, J.S.Show

Proc.Natl.Acad.Sci.USA 108 1839 1844 (2011)

PMID: 21245352 DOI: 10.1073/pnas.1018582108

Abstact

Internal ribosome entry site (IRES) RNAs are elements of viral or cellular mRNAs that bypass steps of canonical eukaryotic cap-dependent translation initiation. Understanding of the structural basis of IRES mechanisms is limited, partially due to a lack of high-resolution structures of IRES RNAs bound to their cellular targets. Prompted by the universal phylogenetic conservation of the ribosomal P site, we solved the crystal structures of proposed P site binding domains from two intergenic region IRES RNAs bound to bacterial 70S ribosomes. The structures show that these IRES domains nearly perfectly mimic a tRNA • mRNA interaction. However, there are clear differences in the global shape and position of this IRES domain in the intersubunit space compared to those of tRNA, supporting a mechanism for IRES action that invokes hybrid state mimicry to drive a noncanonical mode of translocation. These structures suggest how relatively small structured RNAs can manipulate complex biological machines.

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Primary Citation of related structures

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