1JNY - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SULFOLOBUS SOLFATARICUS ELONGATION FACTOR 1 ALPHA IN COMPLEX WITH GDP

Authors :   L. Vitagliano, M. Masullo, F. Sica, A. Zagari, V. Bocchini

Date :   26 Jul 01 (Deposition) - 23 Jan 02 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Gtpase, Alpha/Beta Structure, Protein Biosynthesis, Translation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Vitagliano, M. Masullo, F. Sica, A. Zagari, V. Bocchini
The Crystal Structure Of Sulfolobus Solfataricus Elongation Factor 1Alpha In Complex With Gdp Reveals Novel Features In Nucleotide Binding And Exchange.
Embo J. V. 20 5305 2001
PubMed-ID: 11574461 | Reference-DOI: 10.1093/EMBOJ/20.19.5305
(for further references see the PDB file header)

Molecule 1 - ELONGATION FACTOR 1-ALPHA
	Chains	:	A, B
	Organism Scientific	:	SULFOLOBUS SOLFATARICUS
	Organism Taxid	:	2287
	Synonym	:	EF-1-ALPHA; ELONGATION FACTOR TU; EF-TU; TUF-1

		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:16 , HIS A:17 , GLY A:18 , LYS A:19 , SER A:20 , THR A:21 , ASN A:152 , LYS A:153 , ASP A:155 , LEU A:156 , VAL A:193 , ALA A:194 , PRO A:195 , HOH A:567 , HOH A:580 , HOH A:626 , HOH A:674 , HOH A:735 , HOH A:798	BINDING SITE FOR RESIDUE GDP A 500
2	AC2	SOFTWARE	ASP B:16 , HIS B:17 , GLY B:18 , LYS B:19 , SER B:20 , THR B:21 , ASN B:152 , LYS B:153 , ASP B:155 , LEU B:156 , VAL B:193 , ALA B:194 , PRO B:195 , HOH B:669	BINDING SITE FOR RESIDUE GDP B 600

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

Asymmetric Unit

No.	Residues
1	Glu A:158	-	Pro A:159
2	Met A:268	-	Pro A:269
3	Glu B:158	-	Pro B:159
4	Met B:268	-	Pro B:269

Asymmetric Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_EF1A_SULSO_001 *	A	196	S	EF1A_SULSO	---	---	A/B	S	196	S
2	UniProt	VAR_EF1A_SULSO_002 *	R	203	K	EF1A_SULSO	---	---	A/B	K	203	K
3	UniProt	VAR_EF1A_SULSO_003 *	I	347	L	EF1A_SULSO	---	---	A/B	L	347	L
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_EF1A_SULSO_001 *	A	196	S	EF1A_SULSO	---	---	A	S	196	S
2	UniProt	VAR_EF1A_SULSO_002 *	R	203	K	EF1A_SULSO	---	---	A	K	203	K
3	UniProt	VAR_EF1A_SULSO_003 *	I	347	L	EF1A_SULSO	---	---	A	L	347	L
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (3, 3)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_EF1A_SULSO_001 *	A	196	S	EF1A_SULSO	---	---	B	S	196	S
2	UniProt	VAR_EF1A_SULSO_002 *	R	203	K	EF1A_SULSO	---	---	B	K	203	K
3	UniProt	VAR_EF1A_SULSO_003 *	I	347	L	EF1A_SULSO	---	---	B	L	347	L
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

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.	EF1A_SULSO	60-75	2	A:60-65 B:60-61

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.	EF1A_SULSO	60-75	1	A:60-65 -

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.	EF1A_SULSO	60-75	1	- B:60-61

(no "Exon" information available for 1JNY)

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:415
 aligned with EF1A_SULSO | P35021 from UniProtKB/Swiss-Prot  Length:435

    Alignment length:426
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423      
           EF1A_SULSO     4 KPHLNLIVIGHIDHGKSTLVGRLLMDRGFIDEKTVKEAEEAAKKLGKESEKFAFLLDRLKEERERGVTINLTFMRFETKKYFFTIIDAPGHRDFVKNMITGASQADAAILVVSAKKGEYEAGMSVEGQTREHIILAKTMGLDQLIVAVNKMDLTEPPYDEKRYKEIVDQVSKFMRSYGFNTNKVRFVPVVAPAGDNITHRSENMKWYNGPTLEEYLDQLELPPKPVDKPLRIPIQDVYSISGVGTVPVGRVESGVLKVGDKIVFMPAGKVGEVRSIETHHTKMDKAEPGDNIGFNVRGVEKKDIKRGDVVGHPNNPPTVADEFTARIIVVWHPTALANGYTPVIHVHTASVACRVSELVSKLDPRTGQEAEKNPQFLKQGDVAIVKFKPIKPLCVEKYNEFPPLGRFAMRDMGKTVGVGIIVDVKP 429
               SCOP domains d1jnya3 A:4-227 Elongation factor eEF-1alpha, N-terminal (G) d           omain                                                                                                                                                  d1jnya1 A:228-322 Elongation factor eEF-1alpha, domain 2                                       d1jnya2 A:323-429 Elongation factor eEF-1alpha, C-terminal domain                                           SCOP domains
               CATH domains 1jnyA01 A:4-225 P-loop containing nucleotide triphosphate hydr           olases                                                                                                                                               --1jnyA02 A:228-316 Translation factors                                                    ----1jnyA03 A:321-428 Translation factors                                                                       - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh-----------.eee....eeee.......hhhhhhhh......eeeeeee...hhhhhhhh..hhhhhhhhhhhhh.....eeeeehhhhh....hhhhhhhhhhhhhhhhhhh.......eeee......................hhhhhhh......hhhhh...eeeeeeeee...eeeeeee..........eeeee...eeeeeeeeee..eee.......eeeeeee..hhhhh....eee..........eeeeeeee.............eeee..eeeeeeeeeeeeee......eeee.........eeeeeeee...........hhhh.eeeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------K-----------------------------------------------------------------------------------------------------------------------------------------------L---------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------G_TR_1          ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jny A   4 KPHLNLIVIGHVDHGKSTLVGRLLMDRGFIDEKTVKEAEEAAKKLGKESEKFAFLLDRLKEE-----------MRFETKKYFFTIIDAPGHRDFVKNMITGASQADAAILVVSAKKGEYEAGMSVEGQTREHIILAKTMGLDQLIVAVNKMDLTEPPYDEKRYKEIVDQVSKFMRSYGFNTNKVRFVPVVAPSGDNITHKSENMKWYNGPTLEEYLDQLELPPKPVDKPLRIPIQDVYSISGVGTVPVGRVESGVLKVGDKIVFMPAGKVGEVRSIETHHTKMDKAEPGDNIGFNVRGVEKKDIKRGDVVGHPNNPPTVADEFTARIIVVWHPTALANGYTPVLHVHTASVACRVSELVSKLDPRTGQEAEKNPQFLKQGDVAIVKFKPIKPLCVEKYNEFPPLGRFAMRDMGKTVGVGIIVDVKP 429
                                    13        23        33        43        53        63 |       -   |    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423      
                                                                                        65          77

Chain B from PDB  Type:PROTEIN  Length:412
 aligned with EF1A_SULSO | P35021 from UniProtKB/Swiss-Prot  Length:435

    Alignment length:427
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       
           EF1A_SULSO     4 KPHLNLIVIGHIDHGKSTLVGRLLMDRGFIDEKTVKEAEEAAKKLGKESEKFAFLLDRLKEERERGVTINLTFMRFETKKYFFTIIDAPGHRDFVKNMITGASQADAAILVVSAKKGEYEAGMSVEGQTREHIILAKTMGLDQLIVAVNKMDLTEPPYDEKRYKEIVDQVSKFMRSYGFNTNKVRFVPVVAPAGDNITHRSENMKWYNGPTLEEYLDQLELPPKPVDKPLRIPIQDVYSISGVGTVPVGRVESGVLKVGDKIVFMPAGKVGEVRSIETHHTKMDKAEPGDNIGFNVRGVEKKDIKRGDVVGHPNNPPTVADEFTARIIVVWHPTALANGYTPVIHVHTASVACRVSELVSKLDPRTGQEAEKNPQFLKQGDVAIVKFKPIKPLCVEKYNEFPPLGRFAMRDMGKTVGVGIIVDVKPA 430
               SCOP domains d1jnyb3 B:4-227 Elongation factor eEF-1alpha, N-terminal (               G) domain                                                                                                                                              d1jnyb1 B:228-322 Elongation factor eEF-1alpha, domain 2                                       d1jnyb2 B:323-430 Elongation factor eEF-1alpha, C-terminal domain                                            SCOP domains
               CATH domains 1jnyB01 B:4-225 P-loop containing nucleotide triphosphate                hydrolases                                                                                                                                           --1jnyB02 B:228-316 Translation factors                                                    ----1jnyB03 B:321-428 Translation factors                                                                       -- CATH domains
           Pfam domains (1) GTP_EFTU-1jnyB01 B:4-266                                                                                                                                                                                                                                               ----------------------------------------------------GTP_EFTU_D3-1jnyB05 B:319-428                                                                                 -- Pfam domains (1)
           Pfam domains (2) GTP_EFTU-1jnyB02 B:4-266                                                                                                                                                                                                                                               ----------------------------------------------------GTP_EFTU_D3-1jnyB06 B:319-428                                                                                 -- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTP_EFTU_D2-1jnyB03 B:247-314                                       -------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTP_EFTU_D2-1jnyB04 B:247-314                                       -------------------------------------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhhhh....hhhhhhhhhhhhhh..hhhhhhhhhh---------------.eee....eeeeee.....hhhhhhhhh.....eeeeeee...hhhhhhhh..hhhhhhhhhhhhhh...eeeeeehhhhh....hhhhhhhhhhhhhhhhhh.......eeeee......................hhhhhhh..............eeeeeeeee...eeeeeee..........eeeee...eeeeeeeeee...ee.......eeeeeee..hhhhh....eee........eeeeeeeeee.............eeee..eeeeeeeeeeeeee......eeee.........eeeeeeee...........hhhh.eeeeee..eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------K-----------------------------------------------------------------------------------------------------------------------------------------------L----------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------G_TR_1          ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jny B   4 KPHLNLIVIGHVDHGKSTLVGRLLMDRGFIDEKTVKEAEEAAKKLGKESEKFAFLLDR---------------MRFETKKYFFTIIDAPGHRDFVKNMITGASQADAAILVVSAKKGEYEAGMSVEGQTREHIILAKTMGLDQLIVAVNKMDLTEPPYDEKRYKEIVDQVSKFMRSYGFNTNKVRFVPVVAPSGDNITHKSENMKWYNGPTLEEYLDQLELPPKPVDKPLRIPIQDVYSISGVGTVPVGRVESGVLKVGDKIVFMPAGKVGEVRSIETHHTKMDKAEPGDNIGFNVRGVEKKDIKRGDVVGHPNNPPTVADEFTARIIVVWHPTALANGYTPVLHVHTASVACRVSELVSKLDPRTGQEAEKNPQFLKQGDVAIVKFKPIKPLCVEKYNEFPPLGRFAMRDMGKTVGVGIIVDVKPA 430
                                    13        23        33        43        53       | -         -   |    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       
                                                                                    61              77

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 '\|'

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Sulfolobus solfataricus. Organism_taxid: 2287 (1)

1a	1jnyA01	A:4-225
1b	1jnyB01	B:4-225

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Elongation Factor Tu (Ef-tu); domain 3 (323)

Homologous Superfamily: Translation factors (223)

Sulfolobus solfataricus. Organism_taxid: 2287 (1)

2a	1jnyA03	A:321-428
2b	1jnyB03	B:321-428
2c	1jnyA02	A:228-316
2d	1jnyB02	B:228-316

Asymmetric Unit(hide GO term definitions)

Chain A,B (EF1A_SULSO | P35021)

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.
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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Asymmetric Unit
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		Glu B:158 - Pro B:159	[ RasMol ]
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		Met B:268 - Pro B:269	[ RasMol ]

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