2DCU - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF TRANSLATION INITIATION FACTOR AIF2BETAGAMMA HETERODIMER WITH GDP

Authors :   M. Sokabe, M. Yao, N. Sakai, S. Toya, I. Tanaka

Date :   16 Jan 06 (Deposition) - 25 Jul 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.40

Chains :   Asym./Biol. Unit : A,B

Keywords :   Protein Complex, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Sokabe, M. Yao, N. Sakai, S. Toya, I. Tanaka
Structure Of Archaeal Translational Initiation Factor 2 Betagamma-Gdp Reveals Significant Conformational Change Of The Beta-Subunit And Switch 1 Region.
Proc. Natl. Acad. Sci. Usa V. 103 13016 2006
PubMed-ID: 16924118 | Reference-DOI: 10.1073/PNAS.0604165103

Molecule 1 - TRANSLATION INITIATION FACTOR 2 GAMMA SUBUNIT
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-26B
	Expression System Strain	:	BL21(DE3)-CODONPLUS-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PF1717
	Mutation	:	YES
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	186497
	Strain	:	DSM 3638
	Synonym	:	EIF-2-GAMMA, AIF2-GAMMA

Molecule 2 - TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-26B
	Expression System Strain	:	BL21(DE3)-CODONPLUS-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PF0481
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	186497
	Strain	:	DSM 3638
	Synonym	:	EIF-2-BETA, AIF2-BETA

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	GDP	1	Ligand/Ion	GUANOSINE-5'-DIPHOSPHATE
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:25 , PRO A:92 , GDP A:2001 , HOH A:3057	BINDING SITE FOR RESIDUE MG A 1001
2	AC2	SOFTWARE	CYS A:61 , CYS A:64 , CYS A:73 , CYS A:76	BINDING SITE FOR RESIDUE ZN A 3001
3	AC3	SOFTWARE	CYS B:107 , CYS B:110 , CYS B:128 , CYS B:131	BINDING SITE FOR RESIDUE ZN B 3002
4	AC4	SOFTWARE	HIS A:19 , VAL A:20 , ASP A:21 , GLY A:23 , LYS A:24 , THR A:25 , THR A:26 , ASN A:146 , LYS A:147 , GLU A:149 , LEU A:150 , SER A:181 , ALA A:182 , LEU A:183 , MG A:1001 , HOH A:3060 , HOH A:3083	BINDING SITE FOR RESIDUE GDP A 2001

Asymmetric/Biological Unit

No.	Residues
1	B:110	-	B:131

(no "Cis Peptide Bond" information available for 2DCU)

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

(no "PROSITE Motif" information available for 2DCU)

(no "Exon" information available for 2DCU)

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:407
 aligned with IF2G_PYRFU | Q8U082 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:407
                                                                                                                                                                                                                                                                                                                                                                                                                                               411 
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405     | 
           IF2G_PYRFU     6 KTRQAEVNIGMVGHVDHGKTTLTKALTGVWTDTHSEELRRGITIKIGFADAEIRRCSNCGRYSTSPICPYCGHETEFIRRVSFIDSPGHEALMTTMLAGASLMDGAILVIAANEPCPRPQTREHLMALQIIGQKNIIIAQNKIELVDKEKALENYRQIKEFIKGTVAENAPIIPISALHGANIDVLVKAIEEFIPTPKRDSNKPPKMLVLRSFDVNKPGTPPEKLVGGVLGGSIVQGKLKVGDEIEIRPGVPYEEHGRIKYEPITTEIVSLQAGGQFVEEAYPGGLVGIGTKLDPYLTKGDLMAGNVVGKPGKLPPVWTDLRLEVHLLERVVGTEQELNVEPIKRKEVLLLNVGTARTMGLVTALGKDEIELKLQIPVCAEPGERVAISRQIGSRWRLIGYGIIKE-   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2dcuA01 A:6-204 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                   2dcuA02 A:205-319 Translation factors                                                                              2dcuA03 A:320-412 Translation factors                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....hhhhhhhhhhhhhh...............eeeeeeeeee.....ee...........eeeeeeeeeee..hhhhhhhhhhhh.....eeeeeee......hhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhhhhhhhh........eee.......hhhhhhhhhhhh............eeeeeeee...............eeeeeeee..ee...eeee...ee........ee..eeeeeeee.......ee.....eeeee..hhhhhhhhh....eee.......eeeeeee..ee......hhhhhh........eeeeee..eeeeeeeeee....eeeeeeeeee.....eeeeee......eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dcu A   6 KTRQAEVNIGMVGHVDHGKTTLTKALTGVWTDTHSEELRRGITIKIGFADAEIRRCSNCGRYSTSPICPYCGHETEFIRRVSFIDSPGHEALMTTMLAGASLMDGAILVIAANEPCPRPQTREHLMALQIIGQKNIIIAQNKIELVDKEKALENYRQIKEFIKGTVAENAPIIPISALHGANIDVLVKAIEEFIPTPKRDSNKPPKMLVLRSFDVNKPGTPPEKLVGGVLDGSIVQGKLKVGDEIEIRPGVPYEEHGRIKYEPITTEIVSLQAGGQFVEEAYPGGLVGIGTKLDPYLTKGDLMAGNVVGKPGKLPPVWTDLRLEVHLLERVVGTEQELNVEPIKRKEVLLLNVGTARTMGLVTALGKDEIELKLQIPVCAEPGERVAISRQIGSRWRLIGYGIIKEL 412
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405

Chain B from PDB  Type:PROTEIN  Length:137
 aligned with IF2B_PYRFU | Q8U3I5 from UniProtKB/Swiss-Prot  Length:140

    Alignment length:137
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       
           IF2B_PYRFU     3 IDYYDYEKLLEKAYQELPENVKHHKSRFEVPGALVTIEGNKTIIENFKDIADALNRDPQHLLKFLLREIATAGTLEGRRVVLQGRFTPYLIANKLKKYIKEYVICPVCGSPDTKIIKRDRFHFLKCEACGAETPIQH 139
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh.hhhhhh...........eeee..eeee.hhhhhhhhhh..hhhhhhhhhhhh...eeee..eeee....hhhhhhhhhhhhhhhhh.................................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dcu B   3 IDYYDYEKLLEKAYQELPENVKHHKSRFEVPGALVTIEGNKTIIENFKDIADALNRDPQHLLKFLLREIATAGTLEGRRVVLQGRFTPYLIANKLKKYIKEYVICPVCGSPDTKIIKRDRFHFLKCEACGAETPIQH 139
                                    12        22        32        42        52        62        72        82        92       102       112       122       132

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 2DCU)

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (IF2G_PYRFU | Q8U082)

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:0003746	translation elongation factor activity	Functions in chain elongation during polypeptide synthesis at the ribosome.
	GO:0003743	translation initiation factor activity	Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
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:0006414	translational elongation	The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
	GO:0006413	translational initiation	The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.

Chain B (IF2B_PYRFU | Q8U3I5)

molecular function
	GO:0003743	translation initiation factor activity	Functions in the initiation of ribosome-mediated translation of mRNA into a polypeptide.
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:0006413	translational initiation	The process preceding formation of the peptide bond between the first two amino acids of a protein. This includes the formation of a complex of the ribosome, mRNA or circRNA, and an initiation complex that contains the first aminoacyl-tRNA.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		GDP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2dcu)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2dcu
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	IF2B_PYRFU \| Q8U3I5
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	IF2G_PYRFU \| Q8U082
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	IF2B_PYRFU \| Q8U3I5
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	IF2G_PYRFU \| Q8U082
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	IF2B_PYRFU \| Q8U3I5	:	2d74
	IF2G_PYRFU \| Q8U082	:	2d74

2d74	THE SAME PROTEIN IN APO FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (2, 3)

Pfam Domains (0, 0)

Gene Ontology (8, 11)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File