3MN9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURES OF ACTIN-BOUND WH2 DOMAINS OF SPIRE AND THE IMPLICATION FOR FILAMENT NUCLEATION

Authors :   A. M. Ducka, T. Sitar, G. M. Popowicz, R. Huber, T. A. Holak

Date :   21 Apr 10 (Deposition) - 26 May 10 (Release) - 01 Sep 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Wh2 Domain, Spire, Actin Complex, Contractile Protein-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. M. Ducka, P. Joel, G. M. Popowicz, K. M. Trybus, M. Schleicher, A. A. Noegel, R. Huber, T. A. Holak, T. Sitar
Structures Of Actin-Bound Wiskott-Aldrich Syndrome Protein Homology 2 (Wh2) Domains Of Spire And The Implication For Filament Nucleation.
Proc. Natl. Acad. Sci. Usa V. 107 11757 2010
PubMed-ID: 20538977 | Reference-DOI: 10.1073/PNAS.1005347107

Molecule 1 - ACTIN-5C
	Chains	:	A
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Taxid	:	7108
	Gene	:	ACT5C, CG4027
	Mutation	:	YES
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227

Molecule 2 - PROTEIN SPIRE
	Chains	:	X
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 371-485
	Gene	:	SPIR, P150-SPIR, CG10076
	Organism Common	:	FRUIT FLY
	Organism Scientific	:	DROSOPHILA MELANOGASTER
	Organism Taxid	:	7227

		1	2
Asymmetric/Biological Unit	:	A	X

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 21)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	CA	1	Ligand/Ion	CALCIUM ION
3	UNK	19	Mod. Amino Acid

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:1 , GLY A:13 , SER A:14 , GLY A:15 , MET 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:301 , GLY A:302 , THR A:303 , MET A:305 , TYR A:306 , LYS A:336 , HOH A:380 , HOH A:394 , HOH A:396 , HOH A:409 , HOH A:496 , CA A:901	BINDING SITE FOR RESIDUE ATP A 800
2	AC2	SOFTWARE	HOH A:396 , HOH A:409 , HOH A:479 , HOH A:496 , ATP A:800	BINDING SITE FOR RESIDUE CA A 901

(no "SS Bond" information available for 3MN9)

Asymmetric/Biological Unit

No.	Residues
1	Unk X:1	-	Unk X:2
2	Unk X:13	-	Unk X:14

(no "SAP(SNP)/Variant" information available for 3MN9)

Asymmetric/Biological Unit (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACTINS_1	PS00406	Actins signature 1.	ACT1_DROME	54-64	1	A:53-63
2	ACTINS_ACT_LIKE	PS01132	Actins and actin-related proteins signature.	ACT1_DROME	105-117	1	A:104-116
3	ACTINS_2	PS00432	Actins signature 2.	ACT1_DROME	357-365	1	A:356-364

(no "Exon" information available for 3MN9)

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:360
 aligned with ACT1_DROME | P10987 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:371
                                    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       375 
          ACT1_DROME      6 VAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMEACGIHETTYNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF  376
               SCOP domains d3mn9a1 A:5-146 automated matches                                                                                                             d3mn9a2 A:147-375 automated matches                                                                                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Actin-3mn9A01 A:5-375                                                                                                                                                                                                                                                                                                                                                               Pfam domains
         Sec.struct. author ...eeeee...eeeeee.......eeee..eeee.-----------..eehhhhhhh...eeee..ee..ee.hhhhhhhhhhhhhhh....hhhhh.eeeee....hhhhhhhhhhhhhhhh...eeeeeehhhhhhhhh....eeeeee....eeeeeee..ee.hhhheee..hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh....hhhhhhhhhhhh....eeee.....eeee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhh.....hhhhhhh.eeeehhhhh..hhhhhhhhhhhhhh.......ee......hhhhhhhhhhhhhhhhhhh.eehhhhhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------ACTINS_1   ----------------------------------------ACTINS_ACT_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTINS_2 ----------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3mn9 A    5 VAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPR-----------DSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVLDSGDGVSHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTEEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELKDGQVITIGNERFRCPEALFQPSFLGMEACGIHETTYNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF  375
                                    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          51

Chain X from PDB  Type:PROTEIN  Length:19
 aligned with SPIR_DROME | Q9U1K1 from UniProtKB/Swiss-Prot  Length:1020

    Alignment length:19
                                  1011         
          SPIR_DROME   1002 SARNRTIQNLTLDLTPVWK 1020
               SCOP domains ------------------- SCOP domains
               CATH domains ------------------- CATH domains
               Pfam domains ------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------- SAPs(SNPs)
                    PROSITE ------------------- PROSITE
                 Transcript ------------------- Transcript
                3mn9 X    1 xxxxxxxxxxxxxxxxxxx   19
                            ||||||||10|||||||||
                            1-UNK|||10-UNK|||19-UNK
                             2-UNK|||11-UNK||| 
                              3-UNK|| 12-UNK|| 
                               4-UNK|  13-UNK| 
                                5-UNK   14-UNK 
                                 6-UNK   15-UNK
                                  7-UNK   16-UNK
                                   8-UNK   17-UNK
                                    9-UNK   18-UNK

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: automated matches (47)

Fruit fly (Drosophila melanogaster) [TaxId: 7227] (11)

1a	d3mn9a1	A:5-146
1b	d3mn9a2	A:147-375

(no "CATH Domain" information available for 3MN9)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Actin_ATPase (173)

Family: Actin (70)

Drosophila melanogaster (Fruit fly) (4)

Actin-3mn9A01

A:5-375

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ACT1_DROME | P10987)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	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:0005200	structural constituent of cytoskeleton	The action of a molecule that contributes to the structural integrity of a cytoskeletal structure.
biological process
	GO:0006338	chromatin remodeling	Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
	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:0002121	inter-male aggressive behavior	Aggressive behavior based on competition between males of the same species over access to resources such as females, dominance, status, etc. and characterized by noise, threats, and is often less injurious.
	GO:0032507	maintenance of protein location in cell	Any process in which a protein is maintained in a specific location within, or in the membrane of, a cell, and is prevented from moving elsewhere.
	GO:0000281	mitotic cytokinesis	A cell cycle process that results in the division of the cytoplasm of a cell after mitosis, resulting in the separation of the original cell into two daughter cells.
	GO:0016319	mushroom body development	The process whose specific outcome is the progression of the mushroom body over time, from its formation to the mature structure. The mushroom body is composed of the prominent neuropil structures of the insect central brain, thought to be crucial for olfactory associated learning. These consist mainly of a bulbous calyx and tightly packaged arrays of thin parallel fibers of the Kenyon cells.
	GO:0006909	phagocytosis	An endocytosis process that results in the engulfment of external particulate material by phagocytes. The particles are initially contained within phagocytic vacuoles (phagosomes), which then fuse with primary lysosomes to effect digestion of the particles.
	GO:0007291	sperm individualization	The resolution of the male germline syncytium or cyst into individual gametes by packaging each spermatid into its own plasma membrane.
	GO:0035148	tube formation	Creation of the central hole of a tube in an anatomical structure through which gases and/or liquids flow.
cellular component
	GO:0031011	Ino80 complex	A multisubunit protein complex that contains the Ino80p ATPase; exhibits chromatin remodeling activity and 3' to 5' DNA helicase activity.
	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:0035060	brahma complex	A SWI/SNF-type complex that contains the ATPase product of the Drosophila brahma gene, or an ortholog thereof.
	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:0005811	lipid droplet	An intracellular non-membrane-bounded organelle comprising a matrix of coalesced lipids surrounded by a phospholipid monolayer. May include associated proteins.
	GO:0005875	microtubule associated complex	Any multimeric complex connected to a microtubule.

Chain X (SPIR_DROME | Q9U1K1)

molecular function
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	GO:0008017	microtubule binding	Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
	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:0051639	actin filament network formation	The assembly of a network of actin filaments; actin filaments on different axes and with differing orientations are crosslinked together to form a mesh of filaments.
	GO:0007015	actin filament 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. Includes processes that control the spatial distribution of actin filaments, such as organizing filaments into meshworks, bundles, or other structures, as by cross-linking.
	GO:0030029	actin filament-based process	Any cellular process that depends upon or alters the actin cytoskeleton, that part of the cytoskeleton comprising actin filaments and their associated proteins.
	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:0007304	chorion-containing eggshell formation	The construction of a chorion-containing eggshell. An example of this is found in Drosophila melanogaster.
	GO:0030717	karyosome formation	The chromosome organization process in which meiotic chromosomes in the oocyte nucleus cluster together to form a compact spherical structure called the karyosome.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0048477	oogenesis	The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
	GO:0007316	pole plasm RNA localization	Any process in which RNA is transported to, or maintained in, the oocyte pole plasm. An example of this is found in Drosophila melanogaster.
	GO:0007315	pole plasm assembly	Establishment of the specialized cytoplasm found at the poles of the egg. An example of this is found in Drosophila melanogaster.
	GO:0045451	pole plasm oskar mRNA localization	Any process in which oskar mRNA is transported to, or maintained in, the oocyte pole plasm.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0051493	regulation of cytoskeleton organization	Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
	GO:0016192	vesicle-mediated transport	A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
	GO:0005938	cell cortex	The region of a cell that lies just beneath the plasma membrane and often, but not always, contains a network of actin filaments and associated proteins.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0031410	cytoplasmic vesicle	A vesicle found in the cytoplasm of a cell.
	GO:0030659	cytoplasmic vesicle membrane	The lipid bilayer surrounding a cytoplasmic vesicle.
	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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	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.

Asymmetric/Biological Unit
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2hf4	CRYSTAL STRUCTURE OF MONOMERIC ACTIN IN ITS ATP-BOUND STATE
3mmv
3mn5
3mn6
3mn7

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (3, 21)

Sites (2, 2)

SS Bonds (0, 0)

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