3AA7 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF ACTIN CAPPING PROTEIN

Authors :   S. Takeda, S. Minakata, A. Narita, M. Kitazawa, T. Yamakuni, Y. Maeda, Y

Date :   11 Nov 09 (Deposition) - 04 Aug 10 (Release) - 04 Aug 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Actin Capping Protein, Barbed End Regulation, Carmil Family Protein, Conformational Change, Cell Motility, Actin Capping, Actin-Binding, Cytoskeleton, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Takeda, S. Minakata, R. Koike, I. Kawahata, A. Narita, M. Kitazawa, M. Ota, T. Yamakuni, Y. Maeda, Y. Nitanai
Two Distinct Mechanisms For Actin Capping Protein Regulation--Steric And Allosteric Inhibition
Plos Biol. V. 8 E1000 2010
PubMed-ID: 20625546 | Reference-DOI: 10.1371/JOURNAL.PBIO.1000416

Molecule 1 - F-ACTIN-CAPPING PROTEIN SUBUNIT ALPHA-1
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETDUET1
	Expression System Strain	:	ROSETTA2 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CAPZA1
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031
	Synonym	:	CAPZ 36/32, BETA-ACTININ SUBUNIT I

Molecule 2 - F-ACTIN-CAPPING PROTEIN SUBUNIT BETA ISOFORMS 1 AND 2
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PETDUET1
	Expression System Strain	:	ROSETTA2 (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CAPZB
	Mutation	:	YES
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031
	Other Details	:	BETA TENTACLE DELETION
	Synonym	:	CAPZ B1 AND B2, CAPZ 36/32, BETA-ACTININ SUBUNIT II

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	BA	1	Ligand/Ion	BARIUM ION
2	MES	1	Ligand/Ion	2-(N-MORPHOLINO)-ETHANESULFONIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER B:41 , TYR B:64 , HOH B:392 , HOH B:439 , HOH B:441	BINDING SITE FOR RESIDUE BA B 245
2	AC2	SOFTWARE	ASN A:42 , ASP A:81 , GLY A:83 , ARG B:51 , LYS B:53 , VAL B:54 , GLY B:56	BINDING SITE FOR RESIDUE MES B 246

(no "SS Bond" information available for 3AA7)

Asymmetric/Biological Unit

No.	Residues
1	Pro A:183	-	Pro A:184
2	Asp B:80	-	Pro B:81
3	Ser B:160	-	Ser B:161
4	Ser B:161	-	Gly B:162

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_CAZA1_CHICK_001 *	F	163	I	CAZA1_CHICK	---	---	A	F	163	I
	* ID not provided by source

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

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	F_ACTIN_CAPPING_BETA	PS00231	F-actin capping protein beta subunit signature.	CAPZB_CHICK	62-67	1	B:62-67
2	F_ACTIN_CAPPING_A_1	PS00748	F-actin capping protein alpha subunit signature 1.	CAZA1_CHICK	196-204	1	A:196-204
3	F_ACTIN_CAPPING_A_2	PS00749	F-actin capping protein alpha subunit signature 2.	CAZA1_CHICK	256-266	1	A:256-266

Asymmetric/Biological Unit (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENSGALT00000006425	2a	ENSGALE00000042043	chr21:4747591-4747501	91	CAPZB_CHICK	1-30	30	1	B:2-30	29
1.3	ENSGALT00000006425	3	ENSGALE00000042051	chr21:4734482-4734361	122	CAPZB_CHICK	31-71	41	1	B:31-71	41
1.4	ENSGALT00000006425	4	ENSGALE00000042045	chr21:4723866-4723753	114	CAPZB_CHICK	71-109	39	1	B:71-109	39
1.5	ENSGALT00000006425	5	ENSGALE00000042044	chr21:4709816-4709675	142	CAPZB_CHICK	109-156	48	1	B:109-156	48
1.6	ENSGALT00000006425	6	ENSGALE00000042049	chr21:4709146-4709030	117	CAPZB_CHICK	157-195	39	1	B:157-195	39
1.7	ENSGALT00000006425	7	ENSGALE00000042042	chr21:4702101-4702036	66	CAPZB_CHICK	196-217	22	1	B:196-217	22
1.8	ENSGALT00000006425	8	ENSGALE00000042048	chr21:4701227-4701151	77	CAPZB_CHICK	218-243	26	1	B:218-243	26
1.9	ENSGALT00000006425	9	ENSGALE00000042047	chr21:4699862-4699750	113	CAPZB_CHICK	243-276	34	1	B:243-244	2
1.10a	ENSGALT00000006425	10a	ENSGALE00000042050	chr21:4697971-4697725	247	CAPZB_CHICK	-	0	0	-	-

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:269
 aligned with CAZA1_CHICK | P13127 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:269
                                    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         
          CAZA1_CHICK     8 VSDEEKVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMDQFTPVKIEGYDDQVLITEHGDLGNGRFLDPRNKISFKFDHLRKEASDPQPEDTESALKQWRDACDSALRAYVKDHYPNGFCTVYGKSIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFTITPPTAQVAAVLKIQVHYYEDGNVQLVSHKDIQDSVQVSSDVQTAKEFIKIIENAENEYQTAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILS 276
               SCOP domains d3aa7a_ A: Capz alpha-1 subunit                                                                                                                                                                                                                                               SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee........ee.hhh.eee..eeee....eeeeee....eeeeeee......hhhhhhhhhhhhhhhhhhhh...eeeeeeeee..eeeeeeeeeeeeeehhh.eeeeeeeeeeeeee..eeeeeeeeeeeeee.....eeeeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhh. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------I----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------F_ACTIN_C---------------------------------------------------F_ACTIN_CAP---------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3aa7 A   8 VSDEEKVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMDQFTPVKIEGYDDQVLITEHGDLGNGRFLDPRNKISFKFDHLRKEASDPQPEDTESALKQWRDACDSALRAYVKDHYPNGFCTVYGKSIDGQQTIIACIESHQFQPKNFWNGRWRSEWKFTITPPTAQVAAVLKIQVHYYEDGNVQLVSHKDIQDSVQVSSDVQTAKEFIKIIENAENEYQTAISENYQTMSDTTFKALRRQLPVTRTKIDWNKILS 276
                                    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

Chain B from PDB  Type:PROTEIN  Length:243
 aligned with CAPZB_CHICK | P14315 from UniProtKB/Swiss-Prot  Length:277

    Alignment length:243
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241   
          CAPZB_CHICK     2 SDQQLDCALDLMRRLPPQQIEKNLSDLIDLVPSLCEDLLSSVDQPLKIARDKVVGKDYLLCDYNRDGDSYRSPWSNKYDPPLEDGAMPSARLRKLEVEANNAFDQYRDLYFEGGVSSVYLWDLDHGFAGVILIKKAGDGSKKIKGCWDSIHVVEVQEKSSGRTAHYKLTSTVMLWLQTNKTGSGTMNLGGSLTRQMEKDETVSDSSPHIANIGRLVEDMENKIRSTLNEIYFGKTKDIVNGLR 244
               SCOP domains d3aa7b_ B: Capz beta-1 subunit                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhh....eeeee....eeeeehhh.ee..eee......ee.........hhhhhhhhhhhhhhhhhhhhhhhh..eeeeeeeee..eeeeeeeeeee......eeeeeeeeeeeeeee.....eeeeeeeeeeeeeeeeee...eeeeeeeeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------F_ACTI--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: B:2-30       Exon 1.3  PDB: B:31-71 UniProt: 31-71    -------------------------------------Exon 1.5  PDB: B:109-156 UniProt: 109-156       Exon 1.6  PDB: B:157-195               Exon 1.7              Exon 1.8  PDB: B:218-243  - Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------Exon 1.4  PDB: B:71-109 UniProt: 71-109-------------------------------------------------------------------------------------------------------------------------------------1. Transcript 1 (2)
                 3aa7 B   2 SDQQLDCALDLMRRLPPQQIEKNLSDLIDLVPSLCEDLLSSVDQPLKIARDKVVGKDYLLCDYNRDGDSYRSPWSNKYDPPLEDGAMPSARLRKLEVEANNAFDQYRDLYFEGGVSSVYLWDLDHGFAGVILIKKAGDGSKKIKGCWDSIHVVEVQEKSSGRTAHYKLTSTVMLWLQTNKTGSGTMNLGGSLTRQMEKDETVSDSSPHIANIGRLVEDMENKIRSTLNEIYFGKTKDIVNGLR 244
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241

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 "CATH Domain" information available for 3AA7)

(no "Pfam Domain" information available for 3AA7)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CAZA1_CHICK | P13127)

molecular function
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
biological process
	GO:0051693	actin filament capping	The binding of a protein or protein complex to the end of an actin filament, thus preventing the addition, exchange or removal of further actin subunits.
	GO:0051016	barbed-end actin filament capping	The binding of a protein or protein complex to the barbed (or plus) end of an actin filament, thus preventing the addition, exchange or removal of further actin subunits.
cellular component
	GO:0008290	F-actin capping protein complex	A heterodimer consisting of alpha and beta subunits that binds to and caps the barbed ends of actin filaments, thereby regulating the polymerization of actin monomers but not severing actin filaments.
	GO:0071203	WASH complex	A protein complex that localizes at the surface of endosomes, where it recruits and activates the Arp2/3 complex to induce actin polymerization. In human, the WASH complex is composed of F-actin-capping protein subunits alpha and beta, WASH1, FAM21, KIAA1033, KIAA0196 and CCDC53.
	GO:0030018	Z disc	Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

Chain B (CAPZB_CHICK | P14315)

molecular function
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	GO:0051015	actin filament binding	Interacting selectively and non-covalently with an actin filament, also known as F-actin, a helical filamentous polymer of globular G-actin subunits.
	GO:0048487	beta-tubulin binding	Interacting selectively and non-covalently with the microtubule constituent protein beta-tubulin.
biological process
	GO:0030036	actin cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
	GO:0051693	actin filament capping	The binding of a protein or protein complex to the end of an actin filament, thus preventing the addition, exchange or removal of further actin subunits.
	GO:0051016	barbed-end actin filament capping	The binding of a protein or protein complex to the barbed (or plus) end of an actin filament, thus preventing the addition, exchange or removal of further actin subunits.
	GO:0000902	cell morphogenesis	The developmental process in which the size or shape of a cell is generated and organized.
	GO:0030030	cell projection organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0007010	cytoskeleton organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures.
	GO:0030032	lamellipodium assembly	Formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
	GO:0048747	muscle fiber development	The process whose specific outcome is the progression of the muscle fiber over time, from its formation to the mature structure. In skeletal muscle, fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast.
	GO:0051490	negative regulation of filopodium assembly	Any process that stops, prevents, or reduces the frequency, rate or extent of the assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone.
	GO:0031115	negative regulation of microtubule polymerization	Any process that stops, prevents, or reduces the frequency, rate or extent of microtubule polymerization.
	GO:0031175	neuron projection development	The process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
	GO:0022604	regulation of cell morphogenesis	Any process that modulates the frequency, rate or extent of cell morphogenesis. Cell morphogenesis is the developmental process in which the shape of a cell is generated and organized.
	GO:0010591	regulation of lamellipodium assembly	Any process that modulates the rate, frequency or extent of the formation of a lamellipodium, a thin sheetlike extension of the surface of a migrating cell.
	GO:0090036	regulation of protein kinase C signaling	Any process that modulates the frequency, rate, or extent of a series of reactions, mediated by the intracellular serine/threonine kinase protein kinase C, which occurs as a result of a single trigger reaction or compound.
cellular component
	GO:0008290	F-actin capping protein complex	A heterodimer consisting of alpha and beta subunits that binds to and caps the barbed ends of actin filaments, thereby regulating the polymerization of actin monomers but not severing actin filaments.
	GO:0031674	I band	A region of a sarcomere that appears as a light band on each side of the Z disc, comprising a region of the sarcomere where thin (actin) filaments are not overlapped by thick (myosin) filaments; contains actin, troponin, and tropomyosin; each sarcomere includes half of an I band at each end.
	GO:0030018	Z disc	Platelike region of a muscle sarcomere to which the plus ends of actin filaments are attached.
	GO:0001669	acrosomal vesicle	A structure in the head of a spermatozoon that contains acid hydrolases, and is concerned with the breakdown of the outer membrane of the ovum during fertilization. It lies just beneath the plasma membrane and is derived from the lysosome.
	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:0005903	brush border	The dense covering of microvilli on the apical surface of a epithelial cells in tissues such as the intestine, kidney, and choroid plexus; the microvilli aid absorption by increasing the surface area of the cell.
	GO:0030863	cortical cytoskeleton	The portion of the cytoskeleton that lies just beneath the plasma membrane.
	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:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	GO:0014704	intercalated disc	A complex cell-cell junction at which myofibrils terminate in cardiomyocytes; mediates mechanical and electrochemical integration between individual cardiomyocytes. The intercalated disc contains regions of tight mechanical attachment (fasciae adherentes and desmosomes) and electrical coupling (gap junctions) between adjacent cells.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric/Biological Unit
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		Ser B:161 - Gly B:162	[ RasMol ]

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	3aa7
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1izn	THE SAME PROTEIN IN APO-FORM
3aa0	THE SAME PROTEIN IN COMPLEXED WITH THE 21 AA LENGTH CARMIL FRAGMENT
3aa1	THE SAME PROTEIN IN COMPLEXED WITH THE 23 AA LENGTH CKIP-1 FRAGMENT
3aa6	THE SAME PROTEIN IN COMPLEXED WITH THE 23 AA LENGTH CD2AP FRAGMENT
3aaa	THE SAME PROTEIN IN COMPLEXED WITH V-1
3aae	THE SAME PROTEIN IN COMPLEXED WITH THE 32 AA LENGTH CARMIL FRAGMENT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (3, 3)

Exons (8, 8)

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SCOP Domains (2, 2)

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Gene Ontology (32, 39)

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