1YXQ - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF ACTIN IN COMPLEX WITH SWINHOLIDE A

Authors :   V. A. Klenchin, R. King, J. Tanaka, G. Marriott, I. Rayment

Date :   22 Feb 05 (Deposition) - 17 May 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.01

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

Keywords :   Actin; Swinholide A; Macrolide Toxin, Contractile Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   V. A. Klenchin, R. King, J. Tanaka, G. Marriott, I. Rayment
Structural Basis Of Swinholide A Binding To Actin
Chem. Biol. V. 12 287 2005
PubMed-ID: 15797212 | Reference-DOI: 10.1016/J.CHEMBIOL.2005.02.011

Molecule 1 - ACTIN, ALPHA SKELETAL MUSCLE
	Chains	:	A, B
	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 (5, 10)

No.	Name	Count	Type	Full Name
1	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	HIC	2	Mod. Amino Acid	4-METHYL-HISTIDINE
4	MG	3	Ligand/Ion	MAGNESIUM ION
5	SWI	1	Ligand/Ion	SWINHOLIDE A

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ATP A:1380 , HOH A:9002 , HOH A:9003 , HOH A:9004 , HOH A:9005	BINDING SITE FOR RESIDUE MG A 1390
2	AC2	SOFTWARE	ATP B:2380 , HOH B:9003 , HOH B:9004 , HOH B:9005 , HOH B:9006	BINDING SITE FOR RESIDUE MG B 2390
3	AC3	SOFTWARE	GLU A:205 , HOH A:9006 , HOH A:9007 , HOH A:9008 , HOH A:9009 , HOH A:9010	BINDING SITE FOR RESIDUE MG A 5001
4	AC4	SOFTWARE	GLY A:13 , SER A:14 , GLY A:15 , LEU A:16 , LYS A:18 , GLY A:156 , ASP A:157 , GLY A:182 , ARG A:183 , ARG A:210 , LYS A:213 , GLU A:214 , GLY A:301 , GLY A:302 , THR A:303 , MET A:305 , TYR A:306 , LYS A:336 , MG A:1390 , HOH A:9003 , HOH A:9004 , HOH A:9005 , HOH A:9064 , HOH A:9083 , HOH A:9089 , HOH A:9098 , HOH A:9169 , HOH A:9175 , HOH A:9190	BINDING SITE FOR RESIDUE ATP A 1380
5	AC5	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 , THR B:303 , MET B:305 , TYR B:306 , MG B:2390 , HOH B:9003 , HOH B:9004 , HOH B:9005 , HOH B:9006	BINDING SITE FOR RESIDUE ATP B 2380
6	AC6	SOFTWARE	ASP A:24 , ASP A:25 , TYR A:143 , ALA A:144 , SER A:145 , GLY A:146 , TYR A:169 , SER A:344 , ILE A:345 , SER A:348 , LEU A:349 , THR A:351 , MET A:355 , HOH A:9224 , GLY B:23 , ASP B:24 , TYR B:133 , TYR B:143 , ALA B:144 , SER B:145 , GLY B:146 , ARG B:147 , ILE B:341 , SER B:344 , SER B:348 , LEU B:349 , THR B:351 , MET B:355 , HOH B:9011 , HOH B:9013 , HOH B:9027 , HOH B:9033 , HOH B:9036	BINDING SITE FOR RESIDUE SWI B 600
7	AC7	SOFTWARE	ALA A:144 , SER A:145 , PRO A:332 , GLU A:334 , ILE A:341 , HOH A:9176 , HOH A:9222	BINDING SITE FOR RESIDUE EDO A 9001
8	AC8	SOFTWARE	ALA B:144 , PRO B:332	BINDING SITE FOR RESIDUE EDO B 9002

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

(no "Cis Peptide Bond" information available for 1YXQ)

(no "SAP(SNP)/Variant" information available for 1YXQ)

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACTINS_1	PS00406	Actins signature 1.	ACTS_RABIT	55-65	2	A:53-63 B:53-63
2	ACTINS_ACT_LIKE	PS01132	Actins and actin-related proteins signature.	ACTS_RABIT	106-118	2	A:104-116 B:104-116
3	ACTINS_2	PS00432	Actins signature 2.	ACTS_RABIT	358-366	2	A:356-364 B:356-364

(no "Exon" information available for 1YXQ)

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:356
 aligned with ACTS_RABIT | P68135 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:367
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       
           ACTS_RABIT     7 TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVH 373
               SCOP domains d1yxqa1 A:5-146 Actin                                                                                                                         d1yxqa2 A:147-371 Actin                                                                                                                                                                                                           SCOP domains
               CATH domains 1yxqA01 A:5-137,A:339-371  [code=3.           30.420.40, no name defined]                                                            1yxqA02 A:138-179,A:272-338               1yxqA03 A:180-271 Actin; Chain A, domain 4                                                  1yxqA02 A:138-179,A:272-338  [code=3.30.420.40, no name defined]   1yxqA01 A:5-137,A:339-371         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...eeeeee.......eeee..eeee.-----------..eehhhhhhh...eeee..ee..ee.hhhhhhhhhhhhhhh....hhhhh.eeeee....hhhhhhhhhhhhhhh....eeeeeehhhhhhhhh....eeeeee....eeeeeee..ee.hhhheee..hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh....hhhhhhhhhhhh....eeee.....eeee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.eeeehhhhh..hhhhhhhhhhhhhh.......ee...hhhhhhhhhhhhhhhhhhhhhhheehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------ACTINS_1   ----------------------------------------ACTINS_ACT_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTINS_2 ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yxq A   5 TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPR-----------DSYVGDEAQSKRGILTLKYPIEhGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVH 371
                                    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       
                                                             39          51                    73-HIC

Chain B from PDB  Type:PROTEIN  Length:359
 aligned with ACTS_RABIT | P68135 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:369
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367         
           ACTS_RABIT     8 TALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKC 376
               SCOP domains d1yxqb1 B:6-146 Actin                                                                                                                        d1yxqb2 B:147-374 Actin                                                                                                                                                                                                              SCOP domains
               CATH domains 1yxqB01 B:6-137,B:339-374  [code=3.          30.420.40, no name defined]                                                            1yxqB02 B:138-179,B:272-338               1yxqB03 B:180-271 Actin; Chain A, domain 4                                                  1yxqB02 B:138-179,B:272-338  [code=3.30.420.40, no name defined]   1yxqB01 B:6-137,B:339-374            CATH domains
           Pfam domains (1) Actin-1yxqB01 B:6-374                                                                                                                                                                                                                                                                                                                                                             Pfam domains (1)
           Pfam domains (2) Actin-1yxqB02 B:6-374                                                                                                                                                                                                                                                                                                                                                             Pfam domains (2)
         Sec.struct. author ..eeeee...eeeeee.......eeee..eeee..----------..eehhhhhhh...eeee..ee..ee.hhhhhhhhhhhhhhh....hhhhh.eeeee....hhhhhhhhhhhhhhh....eeeeeehhhhhhhhh....eeeeee....eeeeeee..ee.hhhheee..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh....hhhhhhhhhh......eeee.....eeee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhh.eeeehhhhh..hhhhhhhhhhhhhh.......ee...hhhhhhhhhhhhhhhhhhhhhhheehhhhhhhh.hhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------ACTINS_1   ----------------------------------------ACTINS_ACT_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTINS_2 ---------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yxq B   6 TALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRH----------DSYVGDEAQSKRGILTLKYPIEhGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKC 374
                                    15        25        35    |    -     |  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         
                                                             40         51                    73-HIC

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) (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)

1a	d1yxqa1	A:5-146
1b	d1yxqa2	A:147-371
1c	d1yxqb1	B:6-146
1d	d1yxqb2	B:147-374

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Nucleotidyltransferase; domain 5 (788)

Homologous Superfamily: [code=3.30.420.40, no name defined] (217)

Rabbit (Oryctolagus cuniculus) (44)

1a	1yxqA01	A:5-137,A:339-371
1b	1yxqB01	B:6-137,B:339-374
1c	1yxqA02	A:138-179,A:272-338
1d	1yxqB02	B:138-179,B:272-338

Architecture: Alpha-Beta Complex (3881)

Topology: Actin; Chain A, domain 4 (156)

Homologous Superfamily: Actin; Chain A, domain 4 (155)

Rabbit (Oryctolagus cuniculus) (44)

2a	1yxqA03	A:180-271
2b	1yxqB03	B:180-271

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Actin_ATPase (173)

Family: Actin (70)

Oryctolagus cuniculus (Rabbit) (47)

1a	Actin-1yxqB01	B:6-374
1b	Actin-1yxqB02	B:6-374

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ACTS_RABIT | P68135)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0048306	calcium-dependent protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules), in the presence of calcium.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0090131	mesenchyme migration	The process in which the population of cells that make up a mesenchyme undergo directed movement.
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0048741	skeletal muscle fiber development	The process whose specific outcome is the progression of the skeletal muscle fiber over time, from its formation to the mature structure. Muscle fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast.
	GO:0030240	skeletal muscle thin filament assembly	The aggregation, arrangement and bonding together of proteins to form the actin-based thin filaments of myofibrils in skeletal muscle.
cellular component
	GO:0005884	actin filament	A filamentous structure formed of a two-stranded helical polymer of the protein actin and associated proteins. Actin filaments are a major component of the contractile apparatus of skeletal muscle and the microfilaments of the cytoskeleton of eukaryotic cells. The filaments, comprising polymerized globular actin molecules, appear as flexible structures with a diameter of 5-9 nm. They are organized into a variety of linear bundles, two-dimensional networks, and three dimensional gels. In the cytoskeleton they are most highly concentrated in the cortex of the cell just beneath the plasma membrane.
	GO:0044297	cell body	The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005856	cytoskeleton	Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
	GO:0030175	filopodium	Thin, stiff, actin-based protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal or dendritic growth cone, or a dendritic shaft.
	GO:0030027	lamellipodium	A thin sheetlike process extended by the leading edge of a migrating cell or extending cell process; contains a dense meshwork of actin filaments.
	GO:0001725	stress fiber	A contractile actin filament bundle that consists of short actin filaments with alternating polarity, cross-linked by alpha-actinin and possibly other actin bundling proteins, and with myosin present in a periodic distribution along the fiber.
	GO:0005865	striated muscle thin filament	Filaments formed of actin and associated proteins; attached to Z discs at either end of sarcomeres in myofibrils.

Asymmetric/Biological Unit
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	1yxq
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(no "Related Entries Specified in the PDB File" available for 1YXQ)

Description

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Ligands, Modified Residues, Ions (5, 10)

Sites (8, 8)

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