4M4S - JenaLib

Title :   GAMMA SUBUNIT OF THE TRANSLATION INITIATION FACTOR 2 FROM SULFOLOBUS SOLFATARICUS IN COMPLEX WITH GDP AND FORMATE ION MIMIC AIF2GAMMA*GDP*PI COMPLEX (A FORMATE ION SUBSTITUTES FOR PI)

Authors :   O. S. Nikonov, E. A. Stolboushkina, V. I. Arkhipova, A. G. Gabdulkhakov A. D. Nikulin, M. B. Garber, S. V. Nikonov

Date :   07 Aug 13 (Deposition) - 12 Mar 14 (Release) - 12 Mar 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.25

Chains :   Asym./Biol. Unit : A

Keywords :   Aif2, Aif2 Gamma Subunit, G-Protein, Translation, Translation Initiation, Protein Biosynthesis, Rna-Binding, Gtp-Binding, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Nikonov, E. Stolboushkina, V. Arkhipova, O. Kravchenko, S. Nikonov, M. Garber
Conformational Transitions In The Gamma Subunit Of The Archaeal Translation Initiation Factor 2
Acta Crystallogr. , Sect. D V. 70 658 2014
PubMed: search | Reference-DOI: 10.1107/S1399004713032240

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 36)

Sites (36, 36)

Asymmetric Unit (36, 36)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	MET A:45 , THR A:46 , PRO A:95 , GLY A:96 , HIS A:97 , HOH A:901 , HOH A:908	BINDING SITE FOR RESIDUE FMT A 501
02	AC2	SOFTWARE	SER A:268 , TYR A:269 , TRP A:327 , HOH A:1013	BINDING SITE FOR RESIDUE FMT A 502
03	AC3	SOFTWARE	ARG A:219 , SER A:220 , THR A:306 , HOH A:621 , HOH A:669	BINDING SITE FOR RESIDUE FMT A 503
04	AC4	SOFTWARE	SER A:314 , VAL A:361 , SER A:364 , VAL A:386 , ALA A:387 , HOH A:643 , HOH A:667	BINDING SITE FOR RESIDUE FMT A 504
05	AC5	SOFTWARE	HIS A:37 , SER A:38 , ASN A:190 , SER A:193 , HOH A:607 , HOH A:821	BINDING SITE FOR RESIDUE FMT A 505
06	AC6	SOFTWARE	ALA A:342 , LYS A:343 , GLU A:344 , HOH A:711	BINDING SITE FOR RESIDUE FMT A 506
07	AC7	SOFTWARE	ASN A:121 , LYS A:150 , ASP A:152 , GDP A:530 , HOH A:697	BINDING SITE FOR RESIDUE FMT A 507
08	AC8	SOFTWARE	LEU A:367 , ARG A:384 , HOH A:872	BINDING SITE FOR RESIDUE FMT A 508
09	AC9	SOFTWARE	LYS A:254 , ALA A:319 , HOH A:729 , HOH A:825	BINDING SITE FOR RESIDUE FMT A 509
10	BC1	SOFTWARE	SER A:35 , LYS A:36 , GLU A:39 , THR A:46 , ASN A:224 , HOH A:824	BINDING SITE FOR RESIDUE FMT A 510
11	BC2	SOFTWARE	HIS A:37 , LEU A:41 , HOH A:716 , HOH A:973 , HOH A:974 , HOH A:975	BINDING SITE FOR RESIDUE FMT A 511
12	BC3	SOFTWARE	ARG A:88 , FMT A:513 , HOH A:630 , HOH A:915 , HOH A:1025	BINDING SITE FOR RESIDUE FMT A 512
13	BC4	SOFTWARE	ASN A:55 , ARG A:88 , FMT A:512 , HOH A:724 , HOH A:785	BINDING SITE FOR RESIDUE FMT A 513
14	BC5	SOFTWARE	LYS A:64 , TYR A:68 , HOH A:847 , HOH A:917 , HOH A:1010	BINDING SITE FOR RESIDUE FMT A 514
15	BC6	SOFTWARE	LYS A:64 , TYR A:68 , HOH A:730	BINDING SITE FOR RESIDUE FMT A 515
16	BC7	SOFTWARE	LYS A:5 , GLU A:285 , PHE A:286	BINDING SITE FOR RESIDUE FMT A 516
17	BC8	SOFTWARE	LYS A:234 , HOH A:800 , HOH A:812	BINDING SITE FOR RESIDUE FMT A 517
18	BC9	SOFTWARE	GLN A:400 , FMT A:519 , HOH A:969	BINDING SITE FOR RESIDUE FMT A 518
19	CC1	SOFTWARE	FMT A:518 , HOH A:762 , HOH A:962	BINDING SITE FOR RESIDUE FMT A 519
20	CC2	SOFTWARE	ARG A:130 , SER A:161 , ARG A:164 , LYS A:343 , HOH A:664 , HOH A:714	BINDING SITE FOR RESIDUE FMT A 520
21	CC3	SOFTWARE	LYS A:42 , TYR A:163 , PRO A:179 , ILE A:180 , HOH A:801	BINDING SITE FOR RESIDUE FMT A 521
22	CC4	SOFTWARE	TRP A:3 , ASN A:55 , PRO A:72 , HOH A:630	BINDING SITE FOR RESIDUE FMT A 522
23	CC5	SOFTWARE	LYS A:48 , SER A:220 , VAL A:223 , ASN A:224 , HOH A:846 , HOH A:869	BINDING SITE FOR RESIDUE FMT A 523
24	CC6	SOFTWARE	ALA A:2 , GLU A:82	BINDING SITE FOR RESIDUE FMT A 524
25	CC7	SOFTWARE	GLN A:27 , ALA A:28 , ALA A:185 , LEU A:186 , LYS A:188	BINDING SITE FOR RESIDUE FMT A 525
26	CC8	SOFTWARE	VAL A:217 , GLY A:313 , SER A:363 , HOH A:620 , HOH A:946 , HOH A:950	BINDING SITE FOR RESIDUE FMT A 526
27	CC9	SOFTWARE	PHE A:286 , LYS A:287 , GLU A:288 , HOH A:753	BINDING SITE FOR RESIDUE FMT A 527
28	DC1	SOFTWARE	LEU A:105 , ILE A:139 , SER A:360 , VAL A:361 , GLY A:362	BINDING SITE FOR RESIDUE FMT A 528
29	DC2	SOFTWARE	VAL A:325 , LEU A:326 , TRP A:327 , ASN A:328	BINDING SITE FOR RESIDUE FMT A 529
30	DC3	SOFTWARE	ASP A:19 , HIS A:20 , GLY A:21 , LYS A:22 , THR A:23 , THR A:24 , ASN A:149 , LYS A:150 , VAL A:151 , ASP A:152 , VAL A:153 , LYS A:156 , SER A:184 , ALA A:185 , LEU A:186 , FMT A:507 , MG A:531 , NA A:534 , HOH A:618 , HOH A:632 , HOH A:901 , HOH A:906 , HOH A:907 , HOH A:908 , HOH A:909 , HOH A:973 , HOH A:991	BINDING SITE FOR RESIDUE GDP A 530
31	DC4	SOFTWARE	THR A:23 , GDP A:530 , HOH A:901 , HOH A:902 , HOH A:906 , HOH A:907	BINDING SITE FOR RESIDUE MG A 531
32	DC5	SOFTWARE	HIS A:187 , HOH A:1037	BINDING SITE FOR RESIDUE MG A 532
33	DC6	SOFTWARE	GLU A:66 , TYR A:68 , SER A:76 , HOH A:921 , HOH A:922	BINDING SITE FOR RESIDUE NA A 533
34	DC7	SOFTWARE	VAL A:151 , VAL A:154 , GDP A:530 , HOH A:614 , HOH A:657 , HOH A:973	BINDING SITE FOR RESIDUE NA A 534
35	DC8	SOFTWARE	MET A:111 , HOH A:613 , HOH A:675 , HOH A:720 , HOH A:779 , HOH A:1004 , HOH A:1017	BINDING SITE FOR RESIDUE NA A 535
36	DC9	SOFTWARE	THR A:54 , THR A:70 , HOH A:630 , HOH A:638 , HOH A:653 , HOH A:683	BINDING SITE FOR RESIDUE NA A 536

SS Bonds (2, 2)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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:414
                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4m4sa1 A:2-206 Initiation factor eIF2 gamma subunit, N-terminal (G) domain                                                                                                                                  d4m4sa2 A:207-320 Initiation factor eIF2 gamma subunit, domain II                                                 d4m4sa3 A:321-415 Initiation factor eIF2 gamma subunit                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeee.....hhhhhhhhhhh....hhhhhhhhh....eeeeeeeeee.........ee....hhhhh.....eeeeeeeeee...hhhhhhhhhhhhh...eeeeeee......hhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhhhh........eee.......hhhhhhhhhhhhh...........eeee.hhh.ee............eeeeeeee..ee...eeeeeeeee........eeeeeee..eeee..ee..ee.....eeee...hhhhhh...eeeeeeee......eeeeeeeeeee....................eeeeee..eeeeeeeeeee..eeeeeeeeeee.....eeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4m4s A   2 AWPKVQPEVNIGVVGHVDHGKTTLVQAITGIWTSKHSEELKRGMTIKLGYAETNIGVCESCKKPEAYVTEPSCKSCGSDDEPKFLRRISFIDAPGHEVLMATMLSGAALMDGAILVVAANEPFPQPQTREHFVALGIIGVKNLIIVQNKVDVVSKEEALSQYRQIKQFTKGTWAENVPIIPVSALHKINIDSLIEGIEEYIKTPYRDLSQKPVMLVIRSADVNAPGTQFNELKGGVIGGSIIQGLFKVDQEIKVLPGLRVEKQGKVSYEPIFTKISSIAFGDEEFKEAKPGGLVAIGTYLDPSLTKADNLLGSIITLADAEVPVLWNIRIKYNLLERVVGAKEMLKVDPIRAKETLMLSVGSSTTLGIVTSVKKDEIEVELRRPVAVWSNNIRTVISRQIAGRWRMIGWGLVEI 415
                                    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

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 (3, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Visualization

Interactive Views

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
		FMT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GDP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]
		CC1	[ RasMol ]	+environment [ RasMol ]
		CC2	[ RasMol ]	+environment [ RasMol ]
		CC3	[ RasMol ]	+environment [ RasMol ]
		CC4	[ RasMol ]	+environment [ RasMol ]
		CC5	[ RasMol ]	+environment [ RasMol ]
		CC6	[ RasMol ]	+environment [ RasMol ]
		CC7	[ RasMol ]	+environment [ RasMol ]
		CC8	[ RasMol ]	+environment [ RasMol ]
		CC9	[ RasMol ]	+environment [ RasMol ]
		DC1	[ RasMol ]	+environment [ RasMol ]
		DC2	[ RasMol ]	+environment [ RasMol ]
		DC3	[ RasMol ]	+environment [ RasMol ]
		DC4	[ RasMol ]	+environment [ RasMol ]
		DC5	[ RasMol ]	+environment [ RasMol ]
		DC6	[ RasMol ]	+environment [ RasMol ]
		DC7	[ RasMol ]	+environment [ RasMol ]
		DC8	[ RasMol ]	+environment [ RasMol ]
		DC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Leu A:256 - Pro A:257	[ RasMol ]
		Lys A:64 - Pro A:65	[ RasMol ]
		Phe A:124 - Pro A:125	[ RasMol ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	4m4s
		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
	IF2G_SULSO \| Q980A5
		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

Description