1Y64 - JenaLib

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Title :   BNI1P FORMIN HOMOLOGY 2 DOMAIN COMPLEXED WITH ATP-ACTIN

Authors :   T. Otomo, D. R. Tomchick, C. Otomo, S. C. Panchal, M. Machius, M. K. Rosen

Date :   03 Dec 04 (Deposition) - 18 Jan 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.05

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

Keywords :   Fh2 Actin Cytoskeleton, Coiled Coil, Actin, Tetramethylrhodamine-5-Maleimide, Atp-State, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Otomo, D. R. Tomchick, C. Otomo, S. C. Panchal, M. Machius, M. K. Rosen
Structural Basis Of Actin Filament Nucleation And Processive Capping By A Formin Homology 2 Domain
Nature V. 433 488 2005
PubMed-ID: 15635372 | Reference-DOI: 10.1038/NATURE03251
(for further references see the PDB file header)

Molecule 1 - ACTIN, ALPHA SKELETAL MUSCLE
	Chains	:	A
	Organism Common	:	RABBIT
	Organism Scientific	:	ORYCTOLAGUS CUNICULUS
	Organism Taxid	:	9986
	Synonym	:	ALPHA-ACTIN 1
	Tissue	:	MUSCLE

Molecule 2 - BNI1 PROTEIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	FH2 DOMAIN, RESIDUES 1327-1769
	Gene	:	BNI1, PPF3, SHE5
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	SYNTHETIC LETHAL 39

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	CA	1	Ligand/Ion	CALCIUM ION
3	HIC	1	Mod. Amino Acid	4-METHYL-HISTIDINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:137 , ATP A:2000	BINDING SITE FOR RESIDUE CA A 382
2	AC2	SOFTWARE	GLY A:13 , SER A:14 , GLY A:15 , LEU A:16 , LYS A:18 , GLY A:156 , ASP A:157 , GLY A:158 , VAL A:159 , GLY A:182 , LYS A:213 , GLU A:214 , GLY A:302 , THR A:303 , MET A:305 , TYR A:306 , CA A:382	BINDING SITE FOR RESIDUE ATP A 2000

(no "SS Bond" information available for 1Y64)

(no "Cis Peptide Bond" information available for 1Y64)

(no "SAP(SNP)/Variant" information available for 1Y64)

Asymmetric/Biological Unit (3, 3)

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

Asymmetric/Biological Unit (1, 1)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YNL271C	1	YNL271C.1	XIV:135384-129523	5862	BNI1_YEAST	1-1953	1953	1	B:1350-1760	411

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
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Chain A from PDB  Type:PROTEIN  Length:357
 aligned with ACTS_RABIT | P68135 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:369
                                    15        25        35        45        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         
          ACTS_RABIT      6 ETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHR  374
               SCOP domains d1y64a1 A:4-146 automated matches                                                                                                              d1y64a2 A:147-372 automated matches                                                                                                                                                                                                SCOP domains
               CATH domains 1y64A01 A:4-137,A:339-372  [code=3.3            0.420.40, no name defined]                                                            1y64A02 A:138-179,A:272-338               1y64A03 A:180-271 Actin; Chain A, domain 4                                                  1y64A02 A:138-179,A:272-338  [code=3.30.420.40, no name defined]   1y64A01 A:4-137,A:339-372          CATH domains
               Pfam domains Actin-1y64A01 A:4-372                                                                                                                                                                                                                                                                                                                                                             Pfam domains
         Sec.struct. author ....eee.....eeeeee........eee..eeee.------------.ee..........eeee..ee..ee.hhhhhhhhhhhhh............eeeee....hhhhhhhhhhhhhhhh....eeeeehhhhhhhh.......eee.....eeee.......hhhhheee..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh......................eeee.....eeee.......hhhhhhhhhhh....hhhhhhhhhhh..hhhhhhhhhhh.eeehhhhh...hhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------ACTINS_1   ----------------------------------------ACTINS_ACT_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTINS_2 -------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1y64 A    4 ETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPR------------SYVGDEAQSKRGILTLKYPIEhGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHR  372
                                    13        23        33     |   -        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         
                                                              39           52                   73-HIC

Chain B from PDB  Type:PROTEIN  Length:411
 aligned with BNI1_YEAST | P41832 from UniProtKB/Swiss-Prot  Length:1953

    Alignment length:411
                                  1359      1369      1379      1389      1399      1409      1419      1429      1439      1449      1459      1469      1479      1489      1499      1509      1519      1529      1539      1549      1559      1569      1579      1589      1599      1609      1619      1629      1639      1649      1659      1669      1679      1689      1699      1709      1719      1729      1739      1749      1759 
          BNI1_YEAST   1350 KYPRPHKKLKQLHWEKLDCTDNSIWGTGKAEKFADDLYEKGVLADLEKAFAAREIKSLASKRKEDLQKITFLSRDISQQFGINLHMYSSLSVADLVKKILNCDRDFLQTPSVVEFLSKSEIIEVSVNLARNYAPYSTDWEGVRNLEDAKPPEKDPNDLQRADQIYLQLMVNLESYWGSRMRALTVVTSYEREYNELLAKLRKVDKAVSALQESDNLRNVFNVILAVGNFMNDTSKQAQGFKLSTLQRLTFIKDTTNSMTFLNYVEKIVRLNYPSFNDFLSELEPVLDVVKVSIEQLVNDCKDFSQSIVNVERSVEIGNLSDSSKFHPLDKVLIKTLPVLPEARKKGDLLEDEVKLTIMEFESLMHTYGEDSGDKFAKISFFKKFADFINEYKKAQAQNLAAEEEERLYIKH 1760
               SCOP domains d1y64b_ B: Bni1                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains FH2-1y64B01 B:1350-1741                                                                                                                                                                                                                                                                                                                                                                                 ------------------- Pfam domains
         Sec.struct. author ...........................hhhhhhhhhhhhh.hhhhhhhhh......................hhhhhhhhhhhhhhh...hhhhhhhhhhh.......hhhhhhhh.hhhhhh.hhhhhhhhhhhh.................hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh..........hhhhhhhhhhhh......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1350-1760 UniProt: 1-1953 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                     Transcript 1
                1y64 B 1350 KYPRPHKKLKQLHWEKLDCTDNSIWGTGKAEKFADDLYEKGVLADLEKAFAAREIKSLASKRKEDLQKITFLSRDISQQFGINLHMYSSLSVADLVKKILNCDRDFLQTPSVVEFLSKSEIIEVSVNLARNYAPYSTDWEGVRNLEDAKPPEKDPNDLQRADQIYLQLMVNLESYWGSRMRALTVVTSYEREYNELLAKLRKVDKAVSALQESDNLRNVFNVILAVGNFMNDTSKQAQGFKLSTLQRLTFIKDTTNSMTFLNYVEKIVRLNYPSFNDFLSELEPVLDVVKVSIEQLVNDCKDFSQSIVNVERSVEIGNLSDSSKFHPLDKVLIKTLPVLPEARKKGDLLEDEVKLTIMEFESLMHTYGEDSGDKFAKISFFKKFADFINEYKKAQAQNLAAEEEERLYIKH 1760
                                  1359      1369      1379      1389      1399      1409      1419      1429      1439      1449      1459      1469      1479      1489      1499      1509      1519      1529      1539      1549      1559      1569      1579      1589      1599      1609      1619      1629      1639      1649      1659      1669      1679      1689      1699      1709      1719      1729      1739      1749      1759

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(

)

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	1y64A01	A:4-137,A:339-372
1b	1y64A02	A:138-179,A: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)

1y64A03

A:180-271

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Actin_ATPase (173)

Family: Actin (70)

Oryctolagus cuniculus (Rabbit) (47)

Actin-1y64A01

A:4-372

Clan: no clan defined [family: FH2] (7)

Family: FH2 (7)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (3)

FH2-1y64B01

B:1350-1741

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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.

Chain B (BNI1_YEAST | P41832)

molecular function
	GO:0017048	Rho GTPase binding	Interacting selectively and non-covalently with Rho protein, any member of the Rho subfamily of the Ras superfamily of monomeric GTPases. Proteins in the Rho subfamily are involved in relaying signals from cell-surface receptors to the actin cytoskeleton.
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005522	profilin binding	Interacting selectively and non-covalently with profilin, an actin-binding protein that forms a complex with G-actin and prevents it from polymerizing to form F-actin.
	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: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:0051017	actin filament bundle assembly	The assembly of actin filament bundles; actin filaments are on the same axis but may be oriented with the same or opposite polarities and may be packed with different levels of tightness.
	GO:0045010	actin nucleation	The initial step in the formation of an actin filament, in which actin monomers combine to form a new filament. Nucleation is slow relative to the subsequent addition of more monomers to extend the filament.
	GO:0071519	actomyosin contractile ring actin filament bundle assembly	A process of actin filament bundle formation that occurs in the context of assembling an actomyosin contractile ring during cytokinesis.
	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:0007118	budding cell apical bud growth	Growth at the tip of a bud, in a cell that reproduces by budding.
	GO:0016043	cellular component organization	A process that results in the assembly, arrangement of constituent parts, or disassembly of a cellular component.
	GO:0000132	establishment of mitotic spindle orientation	A cell cycle process that sets the alignment of mitotic spindle relative to other cellular structures.
	GO:0070649	formin-nucleated actin cable assembly	The aggregation, arrangement and bonding together of a set of components to form a formin-nucleated actin cable. A formin-nucleated actin cable is an actin filament bundle that consists of short filaments organized into bundles of uniform polarity, and is nucleated by formins.
	GO:2000251	positive regulation of actin cytoskeleton reorganization	Any process that activates or increases the frequency, rate or extent of actin cytoskeleton reorganization.
	GO:0032880	regulation of protein localization	Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.
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:0042995	cell projection	A prolongation or process extending from a cell, e.g. a flagellum or axon.
	GO:0005935	cellular bud neck	The constriction between the mother cell and daughter cell (bud) in an organism that reproduces by budding.
	GO:0005934	cellular bud tip	The end of a cellular bud distal to the site of attachment to the mother cell.
	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:0000131	incipient cellular bud site	The portion of the budding yeast plasma membrane where a daughter cell will emerge. The yeast marks this spot with bud-site selection proteins before bud emergence occurs. Actin is polarized to this spot just prior to and during bud emergence.
	GO:0043332	mating projection tip	The apex of the mating projection in unicellular fungi exposed to mating pheromone; site of polarized growth.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
	GO:0000133	polarisome	Protein complex that plays a role in determining cell polarity by directing the localized assembly of actin filaments at polarization sites; in Saccharomyces the polarisome includes Bni1p, Spa2p, Pea2p, and Bud6p.
	GO:0032587	ruffle membrane	The portion of the plasma membrane surrounding a ruffle.

Asymmetric/Biological Unit
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	1y64
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1ux4	UNCOMPLEXED BNIP FORMIN HOMOLOGY 2 DOMAIN
1ux5	UNCOMPLEXED BNIP FORMIN HOMOLOGY 2 DOMAIN

Description

Compounds

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Ligands, Modified Residues, Ions (3, 3)

Sites (2, 2)

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