2H5E - JenaLib

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Title :   CRYSTAL STRUCTURE OF E.COLI POLYPEPTIDE RELEASE FACTOR RF3

Authors :   H. W. Song, Z. H. Zhou

Date :   26 May 06 (Deposition) - 15 May 07 (Release) - 24 Nov 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Beta Barrel, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Gao, Z. Zhou, U. Rawat, C. Huang, L. Bouakaz, C. Wang, Z. Cheng, Y. Liu A. Zavialov, R. Gursky, S. Sanyal, M. Ehrenberg, J. Frank, H. Song
Rf3 Induces Ribosomal Conformational Changes Responsible Fo Dissociation Of Class I Release Factors
Cell(Cambridge, Mass. ) V. 129 929 2007
PubMed-ID: 17540173 | Reference-DOI: 10.1016/J.CELL.2007.03.050

Molecule 1 - PEPTIDE CHAIN RELEASE FACTOR RF-3
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-6P-1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	DH5A

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	GDP	2	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:23 , ALA A:24 , GLY A:25 , LYS A:26 , THR A:27 , THR A:28 , HIS A:92 , ASN A:142 , LYS A:143 , ASP A:145 , ARG A:146 , THR A:258 , ALA A:259 , LEU A:260	BINDING SITE FOR RESIDUE GDP A 2567
2	AC2	SOFTWARE	GLY A:220 , GLU A:221 , ASP B:23 , ALA B:24 , GLY B:25 , LYS B:26 , THR B:27 , THR B:28 , HIS B:92 , ASN B:142 , LYS B:143 , ASP B:145 , THR B:258 , ALA B:259 , LEU B:260	BINDING SITE FOR RESIDUE GDP B 3567

(no "SS Bond" information available for 2H5E)

Asymmetric Unit

No.	Residues
1	Asp A:405	-	Pro A:406

(no "SAP(SNP)/Variant" information available for 2H5E)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_TR_1	PS00301	Translational (tr)-type guanine nucleotide-binding (G) domain signature.	RF3_ECOLI	58-73	2	A:70-73 B:71-73

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_TR_1	PS00301	Translational (tr)-type guanine nucleotide-binding (G) domain signature.	RF3_ECOLI	58-73	1	A:70-73 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_TR_1	PS00301	Translational (tr)-type guanine nucleotide-binding (G) domain signature.	RF3_ECOLI	58-73	1	- B:71-73

(no "Exon" information available for 2H5E)

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:488
 aligned with RF3_ECOLI | P0A7I4 from UniProtKB/Swiss-Prot  Length:529

    Alignment length:527
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       
            RF3_ECOLI     3 LSPYLQEVAKRRTFAIISHPDAGKTTITEKVLLFGQAIQTAGTVKGRGSNQHAKSDWMEMEKQRGISITTSVMQFPYHDCLVNLLDTPGHEDFSEDTYRTLTAVDCCLMVIDAAKGVEDRTRKLMEVTRLRDTPILTFMNKLDRDIRDPMELLDEVENELKIGCAPITWPIGCGKLFKGVYHLYKDETYLYQSGKGHTIQEVRIVKGLNNPDLDAAVGEDLAQQLRDELELVKGASNEFDKELFLAGEITPVFFGTALGNFGVDHMLDGLVEWAPAPMPRQTDTRTVEASEDKFTGFVFKIQANMDPKHRDRVAFMRVVSGKYEKGMKLRQVRTAKDVVISDALTFMAGDRSHVEEAYPGDILGLHNHGTIQIGDTFTQGEMMKFTGIPNFAPELFRRIRLKDPLKQKQLLKGLVQLSEEGAVQVFRPISNNDLIVGAVGVLQFDVVVARLKSEYNVEAVYESVNVATARWVECADAKKFEEFKRKNESQLALDGGDNLAYIATSMVNLRLAQERYPDVQFHQTREH 529
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhheeeeeeee....hhhhhhhhhhhh..-------------------------------....eeeeee..eeeeee........hhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhh.eeee.eeee.hhhhh.eeee....eeee.............ee....hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh..eeeeee.......hhhhhhhhhhhhh.....ee....ee.......eeeeeee............eeeeeee..ee...eeee.....eee...ee....-----..ee....eeee..........eee..........eee...eeeeeee...---.hhhhhhhhhhhh...eeeee.....eeeee..hhhhhhhhhhhhhhh...eeee.....eeeeee..hhhhhhhhhhhh...eee.....eeeee.hhhhhhhhhhhh...eee.eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------G_TR_1          ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h5e A   3 LSPYLQEVAKRRTFAIISHPDAGKTTITEKVLLFGQ-------------------------------ITTSVMQFPYHDCLVNLLDTPGHEDFSEDTYRTLTAVDCCLMVIDAAKGVEDRTRKLMEVTRLRDTPILTFMNKLDRDIRDPMELLDEVENELKIGCAPITWPIGCGKLFKGVYHLYKDETYLYQSGKGHTIQEVRIVKGLNNPDLDAAVGEDLAQQLRDELELVKGASNEFDKELFLAGEITPVFFGTALGNFGVDHMLDGLVEWAPAPMPRQTDTRTVEASEDKFTGFVFKIQANMDPKHRDRVAFMRVVSGKYEKGMKLRQVRTAKDVVISDALTFMA-----VEEAYPGDILGLHNHGTIQIGDTFTQGEMMKFTGIPNFAPELFRRIRLKDP---KQLLKGLVQLSEEGAVQVFRPISNNDLIVGAVGVLQFDVVVARLKSEYNVEAVYESVNVATARWVECADAKKFEEFKRKNESQLALDGGDNLAYIATSMVNLRLAQERYPDVQFHQTREH 529
                                    12        22        32     |   -         -         -       |72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       | -   |   362       372       382       392       402   |   412       422       432       442       452       462       472       482       492       502       512       522       
                                                              38                              70                                                                                                                                                                                                                                                                                     350   356                                               406 410

Chain B from PDB  Type:PROTEIN  Length:479
 aligned with RF3_ECOLI | P0A7I4 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_ECOLI     2 TLSPYLQEVAKRRTFAIISHPDAGKTTITEKVLLFGQAIQTAGTVKGRGSNQHAKSDWMEMEKQRGISITTSVMQFPYHDCLVNLLDTPGHEDFSEDTYRTLTAVDCCLMVIDAAKGVEDRTRKLMEVTRLRDTPILTFMNKLDRDIRDPMELLDEVENELKIGCAPITWPIGCGKLFKGVYHLYKDETYLYQSGKGHTIQEVRIVKGLNNPDLDAAVGEDLAQQLRDELELVKGASNEFDKELFLAGEITPVFFGTALGNFGVDHMLDGLVEWAPAPMPRQTDTRTVEASEDKFTGFVFKIQANMDPKHRDRVAFMRVVSGKYEKGMKLRQVRTAKDVVISDALTFMAGDRSHVEEAYPGDILGLHNHGTIQIGDTFTQGEMMKFTGIPNFAPELFRRIRLKDPLKQKQLLKGLVQLSEEGAVQVFRPISNNDLIVGAVGVLQFDVVVARLKSEYNVEAVYESVNVATARWVECADAKKFEEFKRKNESQLALDGGDNLAYIATSMVNLRLAQERYPDVQFHQTREH 529
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhheeeeeee.....hhhhhhhhhhhhh.--------------------------------...eeeeee..eeeeee........hhhhhhhhhhh.eeeeeee.....hhhhhhhhhhhh.....eeeeee.......hhhhhhhhhhhhhh.eeee.eeee.hhhhh.eeee....eeee............eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.eeeeee.......hhhhhhhhhhhhh.....ee....ee.......eeeeeee..--------..eeeeeee.......eeee....eeee...ee....-----........eeee..........eee..........eee...eeeeeee..----.hhhhhhhhhhhh...eeeee.....eeeee..hhhhhhhhhhhhhh....eeee.....eeeeee..hhhhhhhhhhhh...eee.....eeeee.hhhhhhhhhhhh...eee.eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------G_TR_1          ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2h5e B   2 TLSPYLQEVAKRRTFAIISHPDAGKTTITEKVLLFGQ--------------------------------TTSVMQFPYHDCLVNLLDTPGHEDFSEDTYRTLTAVDCCLMVIDAAKGVEDRTRKLMEVTRLRDTPILTFMNKLDRDIRDPMELLDEVENELKIGCAPITWPIGCGKLFKGVYHLYKDETYLYQSGKGHTIQEVRIVKGLNNPDLDAAVGEDLAQQLRDELELVKGASNEFDKELFLAGEITPVFFGTALGNFGVDHMLDGLVEWAPAPMPRQTDTRTVEASEDKFTGFVFKIQA--------RVAFMRVVSGKYEKGMKLRQVRTAKDVVISDALTFMA-----VEEAYPGDILGLHNHGTIQIGDTFTQGEMMKFTGIPNFAPELFRRIRLKD----KQLLKGLVQLSEEGAVQVFRPISNNDLIVGAVGVLQFDVVVARLKSEYNVEAVYESVNVATARWVECADAKKFEEFKRKNESQLALDGGDNLAYIATSMVNLRLAQERYPDVQFHQTREH 529
                                    11        21        31      |  -         -         -        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        |-    |  361       371       381       391       401   |   411       421       431       441       451       461       471       481       491       501       511       521        
                                                               38                               71                                                                                                                                                                                                                                       305      314                                 350   356                                              405  410

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 '\|'

(no "SCOP Domain" information available for 2H5E)

(no "CATH Domain" information available for 2H5E)

(no "Pfam Domain" information available for 2H5E)

Asymmetric Unit(hide GO term definitions)

Chain A,B (RF3_ECOLI | P0A7I4)

molecular function
	GO:0019003	GDP binding	Interacting selectively and non-covalently with GDP, guanosine 5'-diphosphate.
	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:0016150	translation release factor activity, codon nonspecific	A translation release factor that is not specific to particular codons; binds to guanine nucleotides.
	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.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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Biological Units
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(no "Related Entries Specified in the PDB File" available for 2H5E)

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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