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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF THE TRANSLATION FACTOR RF3
 
Authors :  K. Kihira, Y. Shomura, N. Shibata, M. Kitamura, Y. Higuchi
Date :  30 Mar 12  (Deposition) - 05 Sep 12  (Release) - 31 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  A,B  (1x)
Biol. Unit 6:  C,D  (1x)
Keywords :  Translation, Release Factor, Gtpase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Kihira, Y. Shimizu, Y. Shomura, N. Shibata, M. Kitamura, A. Nakagawa, T. Ueda, K. Ochi, Y. Higuchi
Crystal Structure Analysis Of The Translation Factor Rf3 (Release Factor 3)
Febs Lett. V. 586 3705 2012
PubMed-ID: 22975312  |  Reference-DOI: 10.1016/J.FEBSLET.2012.08.029

(-) Compounds

Molecule 1 - PEPTIDE CHAIN RELEASE FACTOR 3
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUT7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DVMF_2372, PRFC
    Organism Scientific: DESULFOVIBRIO VULGARIS
    Organism Taxid: 883
    Strain: MIYAZAKI F
    Synonym: RF-3

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (1x): AB  
Biological Unit 6 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1GDP4Ligand/IonGUANOSINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
Biological Unit 5 (1, 2)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
Biological Unit 6 (1, 2)
No.NameCountTypeFull Name
1GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:22 , ALA A:23 , GLY A:24 , LYS A:25 , THR A:26 , THR A:27 , HIS A:91 , ASN A:141 , LYS A:142 , ASP A:144 , ARG A:145 , SER A:256 , ALA A:257 , ILE A:258 , HOH A:706 , HOH A:817 , HOH A:908BINDING SITE FOR RESIDUE GDP A 601
2AC2SOFTWAREASP B:22 , ALA B:23 , GLY B:24 , LYS B:25 , THR B:26 , THR B:27 , HIS B:91 , ASN B:141 , LYS B:142 , ASP B:144 , ARG B:145 , SER B:256 , ALA B:257 , ILE B:258 , HOH B:708BINDING SITE FOR RESIDUE GDP B 601
3AC3SOFTWAREASP C:22 , ALA C:23 , GLY C:24 , LYS C:25 , THR C:26 , THR C:27 , HIS C:91 , ASN C:141 , LYS C:142 , ASP C:144 , ARG C:145 , SER C:256 , ALA C:257 , ILE C:258 , HOH C:710 , HOH C:854BINDING SITE FOR RESIDUE GDP C 601
4AC4SOFTWAREASP D:22 , ALA D:23 , GLY D:24 , LYS D:25 , THR D:26 , THR D:27 , HIS D:91 , ASN D:141 , LYS D:142 , ASP D:144 , ARG D:145 , SER D:256 , ALA D:257 , ILE D:258 , HOH D:1006 , HOH D:1091BINDING SITE FOR RESIDUE GDP D 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3VQT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3VQT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3VQT)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TR_1PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature.RF3_DESVM57-72
 
 
 		  4A:69-72
B:70-72
C:69-72
D:70-72
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TR_1PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature.RF3_DESVM57-72
 
 
 		  1A:69-72
-
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TR_1PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature.RF3_DESVM57-72
 
 
 		  1-
B:70-72
-
-
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TR_1PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature.RF3_DESVM57-72
 
 
 		  1-
-
C:69-72
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TR_1PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature.RF3_DESVM57-72
 
 
 		  1-
-
-
D:70-72
Biological Unit 5 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TR_1PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature.RF3_DESVM57-72
 
 
 		  2A:69-72
B:70-72
-
-
Biological Unit 6 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_TR_1PS00301 Translational (tr)-type guanine nucleotide-binding (G) domain signature.RF3_DESVM57-72
 
 
 		  2-
-
C:69-72
D:70-72

(-) Exons   (0, 0)

(no "Exon" information available for 3VQT)

(-) Sequences/Alignments

Asymmetric 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:495
 aligned with RF3_DESVM | B8DIL5 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:529
                                    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       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520         
            RF3_DESVM     1 MSSRLEREAARRRTFAIISHPDAGKTTLTEKLLLFGGAIQMAGSVKARKAARHATSDWMAMERERGISVTTSVMQFPYRDRVVNLLDTPGHQDFSEDTYRVLTAVDSALVVIDAAKGVEAQTRKLMDVCRMRATPVMTFVNKMDREALHPLDVMADIEQHLQIECAPMTWPIGMGSSFKGTYDLLHKQLHLFSATHGGRIQSGIVIHGADDPQLDEYLGDQAEQLRMDLALLEEAGTPFDEERYLKGELTPVFFGSAINNFGVREMLDMFVEFAPGPQPRPAATRVVEPGEEAFTGVVFKIQANMDKAHRDRMAFLRICSGTFTRGMRLKHHRTGKDVTVANATIFMAQDRTGVEEAFPGDIIGIPNHGTIKIGDTFTESKEVLKFVGIPNFAPEHFRRVRLKNPLKAKQLQKGLEQLAEEGAVQLFRPLVNNDYILGAVGVLQFDVIVARLADEYGVDAVYEGVSTHTARWVYCEDKKIFADFQDYHRGELAVDAEGALAYLAPNPWRLESAMERYPKVEFRTTREIS 529
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhheeeeeee.....hhhhhhhhhhhhh.hhhhhhhhhhh--------------------....eeeeee..eeeeee...hhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhh.eeee.eeee.hhhhh.eeee....eeee..-------...ee......hhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhh..eeeeee.hhhhh.hhhhhhhhhhhhh.....ee....ee.......eeeeeeee..-------.eeeeeeee..ee...eeee....eeee....ee..........ee....eeeee.........eee...........eee...eeeeeee.hhhhhhhhhhhhhhhhhh...eeeee......eeee..hhhhhhhhhhhhhhhh..eeeee....eeeeee..hhhhhhhhhhhh...eeee....eeeee.hhhhhhhhhhhh...eee.eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------G_TR_1          ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vqt A   1 MSSRLEREAARRRTFAIISHPDAGKTTLTEKLLLFGGAIQMAGSVKAR--------------------VTTSVMQFPYRDRVVNLLDTPGHQDFSEDTYRVLTAVDSALVVIDAAKGVEAQTRKLMDVCRMRATPVMTFVNKMDREALHPLDVMADIEQHLQIECAPMTWPIGMGSSFKGTYDLLHKQLHLFS-------QSGIVIHGADDPQLDEYLGDQAEQLRMDLALLEEAGTPFDEERYLKGELTPVFFGSAINNFGVREMLDMFVEFAPGPQPRPAATRVVEPGEEAFTGVVFKIQAN-------RMAFLRICSGTFTRGMRLKHHRTGKDVTVANATIFMAQDRTGVEEAFPGDIIGIPNHGTIKIGDTFTESKEVLKFVGIPNFAPEHFRRVRLKNPLKAKQLQKGLEQLAEEGAVQLFRPLVNNDYILGAVGVLQFDVIVARLADEYGVDAVYEGVSTHTARWVYCEDKKIFADFQDYHRGELAVDAEGALAYLAPNPWRLESAMERYPKVEFRTTREIS 529
                                    10        20        30        40       | -         -        70        80        90       100       110       120       130       140       150       160       170       180       190  |      -|      210       220       230       240       250       260       270       280       290       300   |     - |     320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520         
                                                                          48                   69                                                                                                                         193     201                                                                                                    304     312                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:490
 aligned with RF3_DESVM | B8DIL5 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:527
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       
            RF3_DESVM     2 SSRLEREAARRRTFAIISHPDAGKTTLTEKLLLFGGAIQMAGSVKARKAARHATSDWMAMERERGISVTTSVMQFPYRDRVVNLLDTPGHQDFSEDTYRVLTAVDSALVVIDAAKGVEAQTRKLMDVCRMRATPVMTFVNKMDREALHPLDVMADIEQHLQIECAPMTWPIGMGSSFKGTYDLLHKQLHLFSATHGGRIQSGIVIHGADDPQLDEYLGDQAEQLRMDLALLEEAGTPFDEERYLKGELTPVFFGSAINNFGVREMLDMFVEFAPGPQPRPAATRVVEPGEEAFTGVVFKIQANMDKAHRDRMAFLRICSGTFTRGMRLKHHRTGKDVTVANATIFMAQDRTGVEEAFPGDIIGIPNHGTIKIGDTFTESKEVLKFVGIPNFAPEHFRRVRLKNPLKAKQLQKGLEQLAEEGAVQLFRPLVNNDYILGAVGVLQFDVIVARLADEYGVDAVYEGVSTHTARWVYCEDKKIFADFQDYHRGELAVDAEGALAYLAPNPWRLESAMERYPKVEFRTTREI 528
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhheeeeeeee....hhhhhhhhhhhhh.hhhhhhhhh.----------------------...eeeeee..eeeeee...hhhhhhhhhhhhhhh..eeeeeee.....hhhhhhhhhhhhhhh..eeeeee.......hhhhhhhhhhhhhh.eeee.eeee.hhhhh.eeee....eeee.-------....ee.....hhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhh..eeeeee.hhhhh.hhhhhhhhhhhhh.....ee....ee.......eeeeeeee.--------.eeeeeeee..ee...eeee....eeee....ee..........ee....eeeee.........eee...........eee...eeeeeee.hhhhhhhhhhhhhhhhhh...eeeee......eeee...hhhhhhhhhhhhhhh..eeeee....eeeeee..hhhhhhhhhhhh...eeee....eeeee.hhhhhhhhhhhh...eee.eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------G_TR_1          ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vqt B   2 SSRLEREAARRRTFAIISHPDAGKTTLTEKLLLFGGAIQMAGSVKA----------------------TTSVMQFPYRDRVVNLLDTPGHQDFSEDTYRVLTAVDSALVVIDAAKGVEAQTRKLMDVCRMRATPVMTFVNKMDREALHPLDVMADIEQHLQIECAPMTWPIGMGSSFKGTYDLLHKQLHLF-------IQSGIVIHGADDPQLDEYLGDQAEQLRMDLALLEEAGTPFDEERYLKGELTPVFFGSAINNFGVREMLDMFVEFAPGPQPRPAATRVVEPGEEAFTGVVFKIQA--------RMAFLRICSGTFTRGMRLKHHRTGKDVTVANATIFMAQDRTGVEEAFPGDIIGIPNHGTIKIGDTFTESKEVLKFVGIPNFAPEHFRRVRLKNPLKAKQLQKGLEQLAEEGAVQLFRPLVNNDYILGAVGVLQFDVIVARLADEYGVDAVYEGVSTHTARWVYCEDKKIFADFQDYHRGELAVDAEGALAYLAPNPWRLESAMERYPKVEFRTTREI 528
                                    11        21        31        41     |   -         -        71        81        91       101       111       121       131       141       151       161       171       181       191|      201       211       221       231       241       251       261       271       281       291       301 |       -|      321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       
                                                                        47                     70                                                                                                                       192     200                                                                                                    303      312                                                                                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:491
 aligned with RF3_DESVM | B8DIL5 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:528
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521        
            RF3_DESVM     2 SSRLEREAARRRTFAIISHPDAGKTTLTEKLLLFGGAIQMAGSVKARKAARHATSDWMAMERERGISVTTSVMQFPYRDRVVNLLDTPGHQDFSEDTYRVLTAVDSALVVIDAAKGVEAQTRKLMDVCRMRATPVMTFVNKMDREALHPLDVMADIEQHLQIECAPMTWPIGMGSSFKGTYDLLHKQLHLFSATHGGRIQSGIVIHGADDPQLDEYLGDQAEQLRMDLALLEEAGTPFDEERYLKGELTPVFFGSAINNFGVREMLDMFVEFAPGPQPRPAATRVVEPGEEAFTGVVFKIQANMDKAHRDRMAFLRICSGTFTRGMRLKHHRTGKDVTVANATIFMAQDRTGVEEAFPGDIIGIPNHGTIKIGDTFTESKEVLKFVGIPNFAPEHFRRVRLKNPLKAKQLQKGLEQLAEEGAVQLFRPLVNNDYILGAVGVLQFDVIVARLADEYGVDAVYEGVSTHTARWVYCEDKKIFADFQDYHRGELAVDAEGALAYLAPNPWRLESAMERYPKVEFRTTREIS 529
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhheeeeeee.....hhhhhhhhhhhhh.hhhhhhhhhh---------------------....eeeeee..eeeeee...hhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhh.eeee.eeee.hhhhh.eeee....eeee.-------....ee.....hhhhhhhhh.hhhhhhhhhhhhhhhh...hhhhhhh..eeeeee.hhhhh.hhhhhhhhhhhhh.....ee....ee.......eeeeeee.---------.eeeeeeee..ee...eeee.....eee....ee..........ee....eeeee.........eee...........eee...eeeeeee.hhhhhhhhhhhhhhhhhh...eeeee......eeee..hhhhhhhhhhhhhhhh..eeeee....eeeeee..hhhhhhhhhhhh...eeee....eeeee.hhhhhhhhhhhh...eee.eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------G_TR_1          ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3vqt C   2 SSRLEREAARRRTFAIISHPDAGKTTLTEKLLLFGGAIQMAGSVKA---------------------VTTSVMQFPYRDRVVNLLDTPGHQDFSEDTYRVLTAVDSALVVIDAAKGVEAQTRKLMDVCRMRATPVMTFVNKMDREALHPLDVMADIEQHLQIECAPMTWPIGMGSSFKGTYDLLHKQLHLF-------IQSGIVIHGADDPQLDEYLGDQAEQLRMDLALLEEAGTPFDEERYLKGELTPVFFGSAINNFGVREMLDMFVEFAPGPQPRPAATRVVEPGEEAFTGVVFKIQ---------RMAFLRICSGTFTRGMRLKHHRTGKDVTVANATIFMAQDRTGVEEAFPGDIIGIPNHGTIKIGDTFTESKEVLKFVGIPNFAPEHFRRVRLKNPLKAKQLQKGLEQLAEEGAVQLFRPLVNNDYILGAVGVLQFDVIVARLADEYGVDAVYEGVSTHTARWVYCEDKKIFADFQDYHRGELAVDAEGALAYLAPNPWRLESAMERYPKVEFRTTREIS 529
                                    11        21        31        41     |   -         -       |71        81        91       101       111       121       131       141       151       161       171       181       191|      201       211       221       231       241       251       261       271       281       291       301|        -|      321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521        
                                                                        47                    69                                                                                                                        192     200                                                                                                   302       312                                                                                                                                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:494
 aligned with RF3_DESVM | B8DIL5 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:527
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       
            RF3_DESVM     2 SSRLEREAARRRTFAIISHPDAGKTTLTEKLLLFGGAIQMAGSVKARKAARHATSDWMAMERERGISVTTSVMQFPYRDRVVNLLDTPGHQDFSEDTYRVLTAVDSALVVIDAAKGVEAQTRKLMDVCRMRATPVMTFVNKMDREALHPLDVMADIEQHLQIECAPMTWPIGMGSSFKGTYDLLHKQLHLFSATHGGRIQSGIVIHGADDPQLDEYLGDQAEQLRMDLALLEEAGTPFDEERYLKGELTPVFFGSAINNFGVREMLDMFVEFAPGPQPRPAATRVVEPGEEAFTGVVFKIQANMDKAHRDRMAFLRICSGTFTRGMRLKHHRTGKDVTVANATIFMAQDRTGVEEAFPGDIIGIPNHGTIKIGDTFTESKEVLKFVGIPNFAPEHFRRVRLKNPLKAKQLQKGLEQLAEEGAVQLFRPLVNNDYILGAVGVLQFDVIVARLADEYGVDAVYEGVSTHTARWVYCEDKKIFADFQDYHRGELAVDAEGALAYLAPNPWRLESAMERYPKVEFRTTREI 528
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhheeeeeeee....hhhhhhhhhhhhh.hhhhhhhh------------------------...eeeeee..eeeeee...hhhhhhhhhhhhhh...eeeeeee.....hhhhhhhhhhhhhh...eeeeee.......hhhhhhhhhhhhhh.eeee.eeee.hhhhh.eeee....eeee..-----.....ee......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..eeeeee.hhhhh.hhhhhhhhhhhhh.....ee....ee.......eeeeeeeee.----...eeeeeeeee..ee...eeee....eeee....ee..........ee....eeeeee........eee...........eee...eeeeeee.hhhhhhhhhhhhhhhhhh...eeeee......eeee..hhhhhhhhhhhhhhhh..eeee.....eeeeee..hhhhhhhhhhhh...eeee....eeeee.hhhhhhhhhhhh...eee.eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------G_TR_1          ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vqt D   2 SSRLEREAARRRTFAIISHPDAGKTTLTEKLLLFGGAIQMAGSV------------------------TTSVMQFPYRDRVVNLLDTPGHQDFSEDTYRVLTAVDSALVVIDAAKGVEAQTRKLMDVCRMRATPVMTFVNKMDREALHPLDVMADIEQHLQIECAPMTWPIGMGSSFKGTYDLLHKQLHLFS-----RIQSGIVIHGADDPQLDEYLGDQAEQLRMDLALLEEAGTPFDEERYLKGELTPVFFGSAINNFGVREMLDMFVEFAPGPQPRPAATRVVEPGEEAFTGVVFKIQAN----HRDRMAFLRICSGTFTRGMRLKHHRTGKDVTVANATIFMAQDRTGVEEAFPGDIIGIPNHGTIKIGDTFTESKEVLKFVGIPNFAPEHFRRVRLKNPLKAKQLQKGLEQLAEEGAVQLFRPLVNNDYILGAVGVLQFDVIVARLADEYGVDAVYEGVSTHTARWVYCEDKKIFADFQDYHRGELAVDAEGALAYLAPNPWRLESAMERYPKVEFRTTREI 528
                                    11        21        31        41   |     -         -        71        81        91       101       111       121       131       141       151       161       171       181       191 |     201       211       221       231       241       251       261       271       281       291       301  |    311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       
                                                                      45                       70                                                                                                                        193   199                                                                                                      304  309
   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  (0, 0)

(no "SCOP Domain" information available for 3VQT)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3VQT)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3VQT)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (RF3_DESVM | B8DIL5)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0003924    GTPase activity    Catalysis of the reaction: GTP + H2O = GDP + phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0006449    regulation of translational termination    Any process that modulates the frequency, rate or extent of translational termination.
    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

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3vr1