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Asym./Biol. Unit (Jmol Viewer)

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Title :   ACTIN CRYSTAL DYNAMICS: STRUCTURAL IMPLICATIONS FOR F-ACTIN NUCLEATION, POLYMERIZATION AND BRANCHING MEDIATED BY THE ANTI-PARALLEL DIMER

Authors :   R. Reutzel, C. Yoshioka, L. Govindasamy, E. G. Yarmola, M. Agbandje- Mckenna, M. R. Bubb, R. Mckenna

Date :   10 Nov 03 (Deposition) - 16 Dec 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.00

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

Keywords :   Anti-Parallel Dimer, Polymerization, Nucleation, Filament, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Reutzel, C. Yoshioka, L. Govindasamy, E. G. Yarmola, M. Agbandje-Mckenna, M. R. Bubb, R. Mckenna
Actin Crystal Dynamics: Structural Implications For F-Actin Nucleation, Polymerization, And Branching Mediated By The Anti-Parallel Dimer.
J. Struct. Biol. V. 146 291 2004
PubMed-ID: 15099571 | Reference-DOI: 10.1016/J.JSB.2003.12.006
(for further references see the PDB file header)

Molecule 1 - ACTIN, ALPHA SKELETAL MUSCLE
	Chains	:	A, B
	Engineered	:	YES
	Fragment	:	ACTIN
	Gene	:	ACTA1, ACTA
	Organism Common	:	RABBIT
	Organism Scientific	:	ORYCTOLAGUS CUNICULUS
	Organism Taxid	:	9986
	Synonym	:	ALPHA-ACTIN 1
	Tissue	:	MUSCLE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

No.	Name	Count	Type	Full Name
1	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	LAR	2	Ligand/Ion	LATRUNCULIN A
3	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:137 , ASP A:154 , ATP A:376	BINDING SITE FOR RESIDUE MG A 378
2	AC2	SOFTWARE	ASP B:11 , GLY B:13 , SER B:14 , GLN B:137 , ATP B:386	BINDING SITE FOR RESIDUE MG B 388
3	AC3	SOFTWARE	GLY A:13 , SER A:14 , GLY A:15 , LEU A:16 , LYS A:18 , GLY A:74 , GLY A:156 , ASP A:157 , GLY A:158 , VAL A:159 , GLY A:182 , 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 , LAR A:377 , MG A:378	BINDING SITE FOR RESIDUE ATP A 376
4	AC4	SOFTWARE	GLY A:15 , LEU A:16 , TYR A:69 , ASP A:157 , GLY A:182 , ARG A:183 , THR A:186 , ARG A:206 , GLU A:207 , ARG A:210 , ATP A:376	BINDING SITE FOR RESIDUE LAR A 377
5	AC5	SOFTWARE	GLY B:13 , SER B:14 , GLY B:15 , LEU B:16 , LYS B:18 , GLN B:137 , ASP B:154 , GLY B:156 , ASP B:157 , 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 , LYS B:336 , LAR B:387 , MG B:388 , HOH B:410	BINDING SITE FOR RESIDUE ATP B 386
6	AC6	SOFTWARE	LEU B:16 , ASP B:56 , GLN B:59 , ARG B:183 , THR B:186 , ARG B:206 , GLU B:207 , ARG B:210 , LYS B:213 , ATP B:386	BINDING SITE FOR RESIDUE LAR B 387

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

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

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

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 1RFQ)

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:361
 aligned with ACTS_RABIT | P68135 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:371
                                    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       376 
           ACTS_RABIT     7 TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF 377
               SCOP domains d1rfqa1 A:5-146 Actin                                                                                                                         d1rfqa2 A:147-375 Actin                                                                                                                                                                                                               SCOP domains
               CATH domains -1rfqA01                      1rfqA0          2 A:35-68         --1rfqA01 A:6-34,A:71-134,A:337-369                               -1rfqA03 A:136-181,A:271-332                   1rfqA04 A:182-267 Actin; Chain A, domain 4                                            ---1rfqA03 A:136-181,A:271-332                                   ----1rfqA01 A:6-34,A:71-134,A:337-369------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....eeeeee.......eeee..eeee..----------..eehhhhhh....eeee.........hhhhhhhhhhhhhh.....hhhhh.eeeee....hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhh.....eee........eeeeee..ee.hhhhee....hhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh....hhhhhhhhhhhh..................hhhhhh...............hhhhhhhhhhh..hhhhhhhhh.............hhhhhhhhhhhhhh...............hhhhhhhhhhhh...hhhhheehhhhhhh.hhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------ACTINS_1   ----------------------------------------ACTINS_ACT_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTINS_2 ----------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rfq A   5 TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRH----------DSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF 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 
                                                              40         51

Chain B from PDB  Type:PROTEIN  Length:361
 aligned with ACTS_RABIT | P68135 from UniProtKB/Swiss-Prot  Length:377

    Alignment length:371
                                    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       376 
           ACTS_RABIT     7 TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF 377
               SCOP domains d1rfqb1 B:5-146 Actin                                                                                                                         d1rfqb2 B:147-375 Actin                                                                                                                                                                                                               SCOP domains
               CATH domains -1rfqB01                      1rfqB0          2 B:35-68         --1rfqB01 B:6-34,B:71-134,B:337-369                               -1rfqB03 B:136-181,B:271-332                   1rfqB04 B:182-267 Actin; Chain A, domain 4                                            ---1rfqB03 B:136-181,B:271-332                                   ----1rfqB01 B:6-34,B:71-134,B:337-369------ CATH domains
           Pfam domains (1) Actin-1rfqB01 B:5-375                                                                                                                                                                                                                                                                                                                                                               Pfam domains (1)
           Pfam domains (2) Actin-1rfqB02 B:5-375                                                                                                                                                                                                                                                                                                                                                               Pfam domains (2)
         Sec.struct. author ...eeee.....eeeee.......eee...ee....----------..eehhhhhh.................hhhhhhhhhhhhhh...........eeeee....hhhhhhhhhhhhhhh.....eeeeehhhhhhhh......eee......eeee.ee..ee.....eee...hhhhhhhhhhhh........hhhhhhhhhhhhhhh...................................hhhhhhhhhhhhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhhee...hhhhh.hhhhhhhhhhhh.................hhhhhhhhhhh.hhhhhhh..........hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------ACTINS_1   ----------------------------------------ACTINS_ACT_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTINS_2 ----------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rfq B   5 TTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRH----------DSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHRKCF 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 
                                                              40         51

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	d1rfqa1	A:5-146
1b	d1rfqa2	A:147-375
1c	d1rfqb1	B:5-146
1d	d1rfqb2	B:147-375

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	1rfqA01	A:6-34,A:71-134,A:337-369
1b	1rfqA03	A:136-181,A:271-332
1c	1rfqB03	B:136-181,B:271-332
1d	1rfqB01	B:6-34,B:71-134,B:337-369

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	1rfqA04	A:182-267
2b	1rfqB04	B:182-267

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: Actin; Chain A, domain 2 (36)

Homologous Superfamily: Actin; Chain A, domain 2 (36)

Rabbit (Oryctolagus cuniculus) (17)

3a	1rfqA02	A:35-68
3b	1rfqB02	B:35-68

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Actin_ATPase (173)

Family: Actin (70)

Oryctolagus cuniculus (Rabbit) (47)

1a	Actin-1rfqB01	B:5-375
1b	Actin-1rfqB02	B:5-375

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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1rdw	ACTIN CRYSTAL DYNAMICS: STRUCTURAL IMPLICATIONS FOR F-ACTIN NUCLEATION, POLYMERIZATION AND BRANCHING MEDIATED BY THE ANTI-PARALLEL DIMER

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SCOP Domains (1, 4)

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