4GY2 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF APO-IA-ACTIN COMPLEX

Authors :   T. Tsurumura, M. Oda, M. Nagahama, H. Tsuge

Date :   05 Sep 12 (Deposition) - 20 Feb 13 (Release) - 10 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.71

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

Keywords :   Adp-Ribosyltransferase, Toxin-Structural Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Tsurumura, Y. Tsumori, H. Qiu, M. Oda, J. Sakurai, M. Nagahama, H. Tsuge
Arginine Adp-Ribosylation Mechanism Based On Structural Snapshots Of Iota-Toxin And Actin Complex
Proc. Natl. Acad. Sci. Usa V. 110 4267 2013
PubMed-ID: 23382240 | Reference-DOI: 10.1073/PNAS.1217227110

Molecule 1 - IOTA TOXIN COMPONENT IA
	Chains	:	A
	EC Number	:	2.4.2.31
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	CLOSTRIDIUM PERFRINGENS
	Organism Taxid	:	1502

Molecule 2 - ACTIN, ALPHA SKELETAL MUSCLE
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	ACTA1
	Organism Common	:	RABBIT
	Organism Scientific	:	ORYCTOLAGUS CUNICULUS
	Organism Taxid	:	9986
	Synonym	:	ALPHA-ACTIN-1

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 4)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	CA	1	Ligand/Ion	CALCIUM ION
3	LAR	1	Ligand/Ion	LATRUNCULIN A
4	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:5 , TRP A:19 , GLU A:23 , ILE A:85 , ASP A:86	BINDING SITE FOR RESIDUE PO4 A 600
2	AC2	SOFTWARE	ATP B:402 , HOH B:502 , HOH B:503 , HOH B:505 , HOH B:535 , HOH B:536	BINDING SITE FOR RESIDUE CA B 401
3	AC3	SOFTWARE	GLY B:13 , SER B:14 , GLY B:15 , LEU B:16 , LYS B:18 , GLY B:156 , ASP B:157 , GLY B:158 , VAL B:159 , GLY B:182 , ARG B:210 , LYS B:213 , GLU B:214 , GLY B:301 , GLY B:302 , MET B:305 , TYR B:306 , LYS B:336 , CA B:401 , HOH B:502 , HOH B:503 , HOH B:504 , HOH B:506 , HOH B:536 , HOH B:539	BINDING SITE FOR RESIDUE ATP B 402
4	AC4	SOFTWARE	GLY B:15 , LEU B:16 , PRO B:32 , LEU B:67 , TYR B:69 , ASP B:157 , GLY B:182 , ARG B:183 , THR B:186 , GLU B:207 , ARG B:210 , LYS B:213	BINDING SITE FOR RESIDUE LAR B 403

(no "SS Bond" information available for 4GY2)

Asymmetric/Biological Unit

No.	Residues
1	Gly B:63	-	Ile B:64

(no "SAP(SNP)/Variant" information available for 4GY2)

(no "PROSITE Motif" information available for 4GY2)

(no "Exon" information available for 4GY2)

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:411
                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4gy2a1 A:3-209 automated matches                                                                                                                                                                              d4gy2a2 A:210-413 automated matches                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh......eeeeee.hhhhhh.............hhhhhhhhhhhhh..eeeeeeeeee..............eeeeeee......eeeee..eeeeeeeeeeeeeeeeeeeeee..eeeeeeeeeee.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh........eeeeeeehhhhhh....hhhhh..hhhhhhhhhhhhh..eee....eeee.....hhhhh...eeeeeee.......hhhhh.......eeee....eeeeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gy2 A   3 IERPEDFLKDKENAIQWEKKEAERVEKNLDTLEKEALELYKKDSEQISNYSQTRQYFYDYQIESNPREKEYKNLRNAISKNKIDKPINVYYFESPEKFAFNKEIRTENQNEISLEKFNELKETIQDKLFKQDGFKDVSLYEPGNGDEKPTPLLIHLKLPKNTGMLPYINSNDVKTLIEQDYSIKIDKIVRIVIEGKQYIKAEASIVNSLDFKDDVSKGDLWGKENYSDWSNKLTPNELADVNDYMRGGYTAINNYLISNGPLNNPNPELDSKVNNIENALKLTPIPSNLIVYRRSGPQEFGLTLTSPEYDFNKIENIDAFKEKWEGKVITYPNFISTSIGSVNMSAFAKRKIILRINIPKDSPGAYLSAIPGYAGEYEVLLNHGSKFKINKVDSYKDGTVTKLILDATLIN 413
                                    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

Chain B from PDB  Type:PROTEIN  Length:360
                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4gy2b1 B:5-146 Actin                                                                                                               d4gy2b2 B:147-374 Actin                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee...eeeeee.......eeee...........hhhhhh...........ee..ee.hhhhhhhhhhhhhh.....hhhhh.eeeee....hhhhhhhhhhhhhhh....eeeeeehhhhhhhhh....eeeeee....eeeeeee..ee.hhhheee..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhh....eeee.....eeee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhh.eeeehhhhh..hhhhhhhhhhhhhh.......ee......hhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4gy2 B   5 TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKC 374
                                    14        24        34    ||  54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374
                                                             39|                                                                                                                                                                                                                                                                                                                                    
                                                              50

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: ADP-ribosylation (157)

Superfamily: ADP-ribosylation (157)

Family: ADP-ribosylating toxins (85)

Protein domain: automated matches (21)

Clostridium perfringens [TaxId: 1502] (6)

1a	d4gy2a1	A:3-209
1b	d4gy2a2	A:210-413

Class: Alpha and beta proteins (a/b) (23833)

Fold: Ribonuclease H-like motif (1424)

Superfamily: Actin-like ATPase domain (426)

Family: Actin/HSP70 (199)

Protein domain: Actin (69)

Rabbit (Oryctolagus cuniculus) [TaxId: 9986] (55)

2a	d4gy2b1	B:5-146
2b	d4gy2b2	B:147-374

(no "CATH Domain" information available for 4GY2)

(no "Pfam Domain" information available for 4GY2)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		ATP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly B:63 - Ile B:64	[ RasMol ]

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	4gy2
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	2.4.2.31
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1giq	CRYSTAL STRUCTURE OF THE ENZYMATIC COMPONET OF IOTA-TOXIN FROM CLOSTRIDIUM PERFRINGENS WITH NADH
1gir	CRYSTAL STRUCTURE OF THE ENZYMATIC COMPONET OF IOTA-TOXIN FROM CLOSTRIDIUM PERFRINGENS WITH NADPH
3buz	CRYSTAL STRUCTURE OF IA-BTAD-ACTIN COMPLEX
4h03	STRUCTURAL SNAPSHOTS OF ARGININE SPECIFIC ADP-RIBOSYLATION, NAD+-IA-ACTIN
4h0t	STRUCTURAL SNAPSHOTS OF ARGININE SPECIFIC ADP-RIBOSYLATION, IA-ADPR-ACTIN
4h0v	STRUCTURAL SNAPSHOTS OF ARGININE SPECIFIC ADP-RIBOSYLATION, NAD+-IA(E378S)-ACTIN
4h0x	STRUCTURAL SNAPSHOTS OF ARGININE SPECIFIC ADP-RIBOSYLATION, NAD+-IA(E380A)-ACTIN
4h0y	STRUCTURAL SNAPSHOTS OF ARGININE SPECIFIC ADP-RIBOSYLATION, NAD+-IA(E380S)-ACTIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (19, 20)

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