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(-) Description

Title :  CRYSTAL STRUCTURE OF PEPTIDE RELEASING FACTOR 1
 
Authors :  D. H. Shin, J. Brandsen, J. Jancarik, H. Yokota, R. Kim, S. -H. Kim, Berkeley Structural Genomics Center (Bsgc)
Date :  03 Dec 03  (Deposition) - 17 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  X-Ray, Crystal, Peptide Release Factor 1, Ribosome, Structural Genomics, Bsgc Structure Funded By Nih, Protein Structure Initiative, Psi, Berkeley Structural Genomics Center (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. H. Shin, J. Brandsen, J. Jancarik, H. Yokota, R. Kim, S. H. Kim
Structural Analyses Of Peptide Release Factor 1 From Thermotoga Maritima Reveal Domain Flexibility Required For Its Interaction With The Ribosome.
J. Mol. Biol. V. 341 227 2004
PubMed-ID: 15312775  |  Reference-DOI: 10.1016/J.JMB.2004.05.055
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDE CHAIN RELEASE FACTOR 1
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PRFA, TM1363
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: RF-1

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1RQ0)

(-) Sites  (0, 0)

(no "Site" information available for 1RQ0)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RQ0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1RQ0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RQ0)

(-) PROSITE Motifs  (1, 3)

Asymmetric/Biological Unit (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RF_PROK_IPS00745 Prokaryotic-type class I peptide chain release factors signature.RF1_THEMA204-220
 
 		  3A:204-220
B:604-620
C:1004-1020

(-) Exons   (0, 0)

(no "Exon" information available for 1RQ0)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:319
 aligned with RF1_THEMA | Q9X183 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:333
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330   
           RF1_THEMA      1 MKEKKKEIEKLLARPDLTPEQMKNYGMEYAKIEEIENITNRIKETQEFIELLREEGENELEIEKYEKELDQLYQELLFLLSPEASDKAIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVAEIHETDLGGIREVVFFVKGKNAYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRARLYQLQKEQKEREISQKRKSQIGTGERSEKIRTYNFPQNRVTDHRINYTSYRLQEILDGDLDEIISKLIEHDIENNLEEVL  333
               SCOP domains d1rq0a_ A: Peptide chain release factor 1, RF1                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhh.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeee.....eeeeeeeee..hhhhhhhhhheeeeeee..........eeeeeeeeeee..hhhhh..hhh.eeeeee....----......eeeeeee.....eeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh....----------...eeeeee....eeee....eee.hhhhhhh..hhhhhhhhhhhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RF_PROK_I        ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1rq0 A    1 MKEKKKEIEKLLARPDLTPEQMKNYGMEYAKIEEIENITNRIKETQEFIELLREEGENELEIEKYEKELDQLYQELLFLLSPEASDKAIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVAEIHETDLGGIREVVFFVKGKNAYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASG----YVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRARLYQLQKEQKEREISQ----------RSEKIRTYNFPQNRVTDHRINYTSYRLQEILDGDLDEIISKLIEHDIENNLEEVL  333
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      |  - |     220       230       240       250       260       | -       280       290       300       310       320       330   
                                                                                                                                                                                                                                        207  212                                                     268        279                                                      


Chain B from PDB  Type:PROTEIN  Length:314
 aligned with RF1_THEMA | Q9X183 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:333
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330   
           RF1_THEMA      1 MKEKKKEIEKLLARPDLTPEQMKNYGMEYAKIEEIENITNRIKETQEFIELLREEGENELEIEKYEKELDQLYQELLFLLSPEASDKAIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVAEIHETDLGGIREVVFFVKGKNAYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRARLYQLQKEQKEREISQKRKSQIGTGERSEKIRTYNFPQNRVTDHRINYTSYRLQEILDGDLDEIISKLIEHDIENNLEEVL  333
               SCOP domains d1rq0b_ B: Peptide chain release factor 1, RF1                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee.....eeeeeeeee..hhhhhhhhhheeeeeee..........eeeeeeeeee..........hhh.eeeeee....---------.eeeeeee....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.......----------...eeeeee....eeee....eee.hhhhhhh..hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RF_PROK_I        ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1rq0 B  401 MKEKKKEIEKLLARPDLTPEQMKNYGMEYAKIEEIENITNRIKETQEFIELLREEGENELEIEKYEKELDQLYQELLFLLSPEASDKAIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVAEIHETDLGGIREVVFFVKGKNAYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASG---------ESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRARLYQLQKEQKEREISQ----------RSEKIRTYNFPQNRVTDHRINYTSYRLQEILDGDLDEIISKLIEHDIENNLEEVL  733
                                   410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600      |  -      |620       630       640       650       660       | -       680       690       700       710       720       730   
                                                                                                                                                                                                                                        607       617                                                668        679                                                      


Chain C from PDB  Type:PROTEIN  Length:314
 aligned with RF1_THEMA | Q9X183 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:333
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330   
           RF1_THEMA      1 MKEKKKEIEKLLARPDLTPEQMKNYGMEYAKIEEIENITNRIKETQEFIELLREEGENELEIEKYEKELDQLYQELLFLLSPEASDKAIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVAEIHETDLGGIREVVFFVKGKNAYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRARLYQLQKEQKEREISQKRKSQIGTGERSEKIRTYNFPQNRVTDHRINYTSYRLQEILDGDLDEIISKLIEHDIENNLEEVL  333
               SCOP domains d1rq0c_ C: Peptide chain release factor 1, RF1                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------1rq0C03 C:987-1067  [         code=3.30.160.20, no name defined]                 -          ------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------------------------PCRF-1rq0C01 C:839-955                                                                                               ----------------------------RF-1-1rq0C04 C:984-1097                                                                                           ------------------------------------ Pfam domains (1)
           Pfam domains (2) --------------------------------------PCRF-1rq0C02 C:839-955                                                                                               ----------------------------RF-1-1rq0C05 C:984-1097                                                                                           ------------------------------------ Pfam domains (2)
           Pfam domains (3) --------------------------------------PCRF-1rq0C03 C:839-955                                                                                               ----------------------------RF-1-1rq0C06 C:984-1097                                                                                           ------------------------------------ Pfam domains (3)
         Sec.struct. author ...hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.....eeeeeeee...hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee.....eeeeeeeee..hhhhhhhhhheeeeeee..........eeeeeeeeeee..hhhhh..hhh.eeeeee....---------.eeeeeee....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhh......----------...eeeeee....eeee....eee.hhhhhhh..hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------RF_PROK_I        ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1rq0 C  801 MKEKKKEIEKLLARPDLTPEQMKNYGMEYAKIEEIENITNRIKETQEFIELLREEGENELEIEKYEKELDQLYQELLFLLSPEASDKAIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVAEIHETDLGGIREVVFFVKGKNAYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASG---------ESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRARLYQLQKEQKEREISQ----------RSEKIRTYNFPQNRVTDHRINYTSYRLQEILDGDLDEIISKLIEHDIENNLEEVL 1133
                                   810       820       830       840       850       860       870       880       890       900       910       920       930       940       950       960       970       980       990      1000      |  -      1020      1030      1040      1050      1060       | -      1080      1090      1100      1110      1120      1130   
                                                                                                                                                                                                                                       1007      1017                                               1068       1079
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Clan: 2heme_cytochrom (31)
(-)
Family: PCRF (2)
(-)
Thermotoga maritima (1)
1aPCRF-1rq0C01C:839-955
1bPCRF-1rq0C02C:839-955
1cPCRF-1rq0C03C:839-955
(-)
Clan: RF (4)
(-)
Family: RF-1 (4)
(-)
Thermotoga maritima (1)
2aRF-1-1rq0C04C:984-1097
2bRF-1-1rq0C05C:984-1097
2cRF-1-1rq0C06C:984-1097

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (RF1_THEMA | Q9X183)
molecular function
    GO:0043022    ribosome binding    Interacting selectively and non-covalently with any part of a ribosome.
    GO:0003747    translation release factor activity    Involved in catalyzing the release of a nascent polypeptide chain from a ribosome.
    GO:0016149    translation release factor activity, codon specific    A translation release factor that is specific for one or more particular termination codons; acts at the ribosomal A-site and require polypeptidyl-tRNA at the P-site.
biological process
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
    GO:0006415    translational termination    The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RF1_THEMA | Q9X183: 2fvo

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