ISDA

Entry Detail

PDB ID:

4V5E

Keywords:

RIBOSOME

Title:

Insights into translational termination from the structure of RF2 bound to the ribosome

Biological Source:

Source Organism:

Escherichia coli K-12, synthetic construct, THERMUS THERMOPHILUS

Host Organism:

Escherichia coli

PDB Version:

Deposition Date:

2009-04-30

Release Date:

2014-07-09

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

3.45 Å

R-Value Free:

0.25

R-Value Work:

0.21

R-Value Observed:

0.21

Space Group:

P 21 21 21

Download Validation Report

Macromolecular Entities

Polymer Type:polyribonucleotide
Description:16S ribosomal RNA
Chain IDs:A (auth: AA), HB (auth: CA)
Chain Length:1522
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S2
Chain IDs:B (auth: AB), IB (auth: CB)
Chain Length:256
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80371 Pfam ID:PF00318

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S3
Chain IDs:C (auth: AC), JB (auth: CC)
Chain Length:239
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80372 Pfam ID:PF07650, PF00189

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S4
Chain IDs:D (auth: AD), KB (auth: CD)
Chain Length:209
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80373 Pfam ID:PF00163, PF01479

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S5
Chain IDs:E (auth: AE), LB (auth: CE)
Chain Length:162
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHQ5 Pfam ID:PF00333, PF03719

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S6
Chain IDs:F (auth: AF), MB (auth: CF)
Chain Length:101
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SLP8 Pfam ID:PF01250

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S7
Chain IDs:G (auth: AG), NB (auth: CG)
Chain Length:156
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P17291 Pfam ID:PF00177

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S8
Chain IDs:H (auth: AH), OB (auth: CH)
Chain Length:138
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P0DOY9 Pfam ID:PF00410

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S9
Chain IDs:I (auth: AI), PB (auth: CI)
Chain Length:128
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80374 Pfam ID:PF00380

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S10
Chain IDs:J (auth: AJ), QB (auth: CJ)
Chain Length:105
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHN7 Pfam ID:PF00338

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S11
Chain IDs:K (auth: AK), RB (auth: CK)
Chain Length:129
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80376 Pfam ID:PF00411

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S12
Chain IDs:L (auth: AL), SB (auth: CL)
Chain Length:132
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHN3 Pfam ID:PF00164

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S13
Chain IDs:M (auth: AM), TB (auth: CM)
Chain Length:126
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80377 Pfam ID:PF00416

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S14 TYPE Z
Chain IDs:N (auth: AN), UB (auth: CN)
Chain Length:61
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P0DOY6 Pfam ID:PF00253

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S15
Chain IDs:O (auth: AO), VB (auth: CO)
Chain Length:89
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SJ76 Pfam ID:PF00312

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S16
Chain IDs:P (auth: AP), WB (auth: CP)
Chain Length:88
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SJH3 Pfam ID:PF00886

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S17
Chain IDs:Q (auth: AQ), XB (auth: CQ)
Chain Length:105
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P0DOY7 Pfam ID:PF00366

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S18
Chain IDs:R (auth: AR), YB (auth: CR)
Chain Length:88
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SLQ0 Pfam ID:PF01084

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S19
Chain IDs:S (auth: AS), ZB (auth: CS)
Chain Length:93
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP2 Pfam ID:PF00203

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN S20
Chain IDs:T (auth: AT), AC (auth: CT)
Chain Length:106
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80380 Pfam ID:PF01649

Protein Blast

Polymer Type:polypeptide(L)
Description:30S RIBOSOMAL PROTEIN THX
Chain IDs:U (auth: AU), BC (auth: CU)
Chain Length:27
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SIH3 Pfam ID:PF17070

Polymer Type:polyribonucleotide
Description:E-SITE TRNA PHE OR P-SITE TRNA PHE (UNMODIFIED BASES)
Chain IDs:V (auth: AV), W (auth: AW), CC (auth: CV), DC (auth: CW)
Chain Length:76
Number of Molecules:4
Biological Source:Escherichia coli K-12

Polymer Type:polyribonucleotide
Description:MRNA
Chain IDs:X (auth: AX), EC (auth: CX)
Chain Length:8
Number of Molecules:2
Biological Source:synthetic construct

Protein Blast

Polymer Type:polypeptide(L)
Description:PEPTIDE CHAIN RELEASE FACTOR 2
Chain IDs:Y (auth: AY), FC (auth: CY)
Chain Length:351
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SM01 Pfam ID:PF03462, PF00472

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L27
Chain IDs:Z (auth: B0), GC (auth: D0)
Chain Length:85
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60493 Pfam ID:PF01016

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L28
Chain IDs:AA (auth: B1), HC (auth: D1)
Chain Length:98
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60494 Pfam ID:PF00830

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L29
Chain IDs:BA (auth: B2), IC (auth: D2)
Chain Length:72
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP6 Pfam ID:PF00831

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L30
Chain IDs:CA (auth: B3), JC (auth: D3)
Chain Length:60
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHQ6 Pfam ID:PF00327

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L31
Chain IDs:DA (auth: B4), KC (auth: D4)
Chain Length:71
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SJE1 Pfam ID:PF01197

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L32
Chain IDs:EA (auth: B5), LC (auth: D5)
Chain Length:60
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80339 Pfam ID:PF01783

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L33
Chain IDs:FA (auth: B6), MC (auth: D6)
Chain Length:54
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P35871 Pfam ID:PF00471

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L34
Chain IDs:GA (auth: B7), NC (auth: D7)
Chain Length:49
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P80340 Pfam ID:PF00468

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L35
Chain IDs:HA (auth: B8), OC (auth: D8)
Chain Length:65
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SKU1 Pfam ID:PF01632

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L36
Chain IDs:IA (auth: B9), PC (auth: D9)
Chain Length:37
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHR2 Pfam ID:PF00444

Polymer Type:polyribonucleotide
Description:23S RIBOSOMAL RNA
Chain IDs:JA (auth: BA), QC (auth: DA)
Chain Length:2901
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

Polymer Type:polyribonucleotide
Description:5S RIBOSOMAL RNA
Chain IDs:KA (auth: BB), RC (auth: DB)
Chain Length:122
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L1
Chain IDs:LA (auth: BC), SC (auth: DC)
Chain Length:229
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SLP7 Pfam ID:PF00687

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L2
Chain IDs:MA (auth: BD), TC (auth: DD)
Chain Length:276
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60405 Pfam ID:PF00181, PF03947

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L3
Chain IDs:NA (auth: BE), UC (auth: DE)
Chain Length:206
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHN8 Pfam ID:PF00297

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L4
Chain IDs:OA (auth: BF), VC (auth: DF)
Chain Length:210
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHN9 Pfam ID:PF00573

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L5
Chain IDs:PA (auth: BG), WC (auth: DG)
Chain Length:182
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHQ0 Pfam ID:PF00281, PF00673

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L6
Chain IDs:QA (auth: BH), XC (auth: DH)
Chain Length:180
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P0DOY8 Pfam ID:PF00347

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L9
Chain IDs:RA (auth: BI)
Chain Length:148
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SLQ1 Pfam ID:PF01281, PF03948

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L10
Chain IDs:SA (auth: BJ), ZC (auth: DJ)
Chain Length:130
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L11
Chain IDs:TA (auth: BK), AD (auth: DK)
Chain Length:147
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SLP6 Pfam ID:PF03946, PF00298

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L13
Chain IDs:UA (auth: BN), BD (auth: DN)
Chain Length:140
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60488 Pfam ID:PF00572

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L14
Chain IDs:VA (auth: BO), CD (auth: DO)
Chain Length:122
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP8 Pfam ID:PF00238

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L15
Chain IDs:WA (auth: BP), DD (auth: DP)
Chain Length:150
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHQ7 Pfam ID:PF00828

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L16
Chain IDs:XA (auth: BQ), ED (auth: DQ)
Chain Length:141
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60489 Pfam ID:PF00252

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L17
Chain IDs:YA (auth: BR), FD (auth: DR)
Chain Length:118
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q9Z9H5 Pfam ID:PF01196

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L18
Chain IDs:ZA (auth: BS), GD (auth: DS)
Chain Length:112
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHQ4 Pfam ID:PF00861

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L19
Chain IDs:AB (auth: BT), HD (auth: DT)
Chain Length:146
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60490 Pfam ID:PF01245

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L20
Chain IDs:BB (auth: BU), ID (auth: DU)
Chain Length:118
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60491 Pfam ID:PF00453

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L21
Chain IDs:CB (auth: BV), JD (auth: DV)
Chain Length:101
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:P60492 Pfam ID:PF00829

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L22
Chain IDs:DB (auth: BW), KD (auth: DW)
Chain Length:113
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP3 Pfam ID:PF00237

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L23
Chain IDs:EB (auth: BX), LD (auth: DX)
Chain Length:96
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP0 Pfam ID:PF00276

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L24
Chain IDs:FB (auth: BY), MD (auth: DY)
Chain Length:110
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHP9 Pfam ID:PF00467, PF17136

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L25
Chain IDs:GB (auth: BZ), ND (auth: DZ)
Chain Length:206
Number of Molecules:2
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SHZ1 Pfam ID:PF01386, PF14693

Protein Blast

Polymer Type:polypeptide(L)
Description:50S RIBOSOMAL PROTEIN L9
Chain IDs:YC (auth: DI)
Chain Length:148
Number of Molecules:1
Biological Source:THERMUS THERMOPHILUS

UniProt ID:Q5SLQ1 Pfam ID:PF01281, PF03948

Ligand Molecules

Primary Citation

Insights Into Translational Termination from the Structure of Rf2 Bound to the Ribosome.

Weixlbaumer, A, Jin, H, Neubauer, C, Voorhees, R.M, Petry, S, Kelley, A.C, Ramakrishnan, V.Show

Science 322 953 956 (2008)

PMID: 18988853 DOI: 10.1126/science.1164840

Abstact

The termination of protein synthesis occurs through the specific recognition of a stop codon in the A site of the ribosome by a release factor (RF), which then catalyzes the hydrolysis of the nascent protein chain from the P-site transfer RNA. Here we present, at a resolution of 3.5 angstroms, the crystal structure of RF2 in complex with its cognate UGA stop codon in the 70S ribosome. The structure provides insight into how RF2 specifically recognizes the stop codon; it also suggests a model for the role of a universally conserved GGQ motif in the catalysis of peptide release.

Legend

Protein

Chemical

Disease

Primary Citation of related structures