2Q36 - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   ACTIN DIMER CROSS-LINKED BETWEEN RESIDUES 191 AND 374 AND COMPLEXED WITH KABIRAMIDE C

Authors :   M. R. Sawaya, I. Pashkov, D. S. Kudryashov, E. Reisler, T. O. Yeates

Date :   29 May 07 (Deposition) - 05 Jun 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Cross-Linked Dimer, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. R. Sawaya, D. S. Kudryashov, I. Pashkov, H. Adisetiyo, E. Reisler, T. O. Yeates
Multiple Crystal Structures Of Actin Dimers And Their Implications For Interactions In The Actin Filament.
Acta Crystallogr. , Sect. D V. 64 454 2008
PubMed-ID: 18391412 | Reference-DOI: 10.1107/S0907444908003351

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

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 5)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	CA	1	Ligand/Ion	CALCIUM ION
3	KAB	1	Ligand/Ion	KABIRAMIDE C
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	KAB	2	Ligand/Ion	KABIRAMIDE C
4	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ATP A:400 , HOH A:410 , HOH A:413 , HOH A:430 , HOH A:455	BINDING SITE FOR RESIDUE CA A 401
2	AC2	SOFTWARE	ARG A:62 , ARG A:95 , THR A:202 , THR A:203 , HOH A:421	BINDING SITE FOR RESIDUE SO4 A 403
3	AC3	SOFTWARE	GLY A:308 , ILE A:309 , ALA A:310 , ASP A:311 , HOH A:426	BINDING SITE FOR RESIDUE SO4 A 404
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: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 , CA A:401 , HOH A:406 , HOH A:411 , HOH A:455 , HOH A:456 , HOH A:458	BINDING SITE FOR RESIDUE ATP A 400
5	AC5	SOFTWARE	GLY A:23 , ASP A:24 , ASP A:25 , LYS A:68 , GLU A:72 , THR A:77 , TYR A:133 , TYR A:143 , ALA A:144 , GLY A:146 , ARG A:147 , GLY A:168 , TYR A:169 , GLU A:334 , ILE A:345 , LEU A:346 , SER A:348 , HOH A:417 , HOH A:434	BINDING SITE FOR RESIDUE KAB A 402

(no "SS Bond" information available for 2Q36)

(no "Cis Peptide Bond" information available for 2Q36)

(no "SAP(SNP)/Variant" information available for 2Q36)

Asymmetric 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

Biological Unit 1 (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
2	ACTINS_ACT_LIKE	PS01132	Actins and actin-related proteins signature.	ACTS_RABIT	106-118	2	A:104-116
3	ACTINS_2	PS00432	Actins signature 2.	ACTS_RABIT	358-366	2	A:356-364

(no "Exon" information available for 2Q36)

Asymmetric 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 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 d2q36a1 A:4-146 Actin                                                                                                                          d2q36a2 A:147-372 Actin                                                                                                                                                                                                            SCOP domains
               CATH domains 2q36A01 A:4-137,A:339-372  [code=3.30         .420.40, no name defined]                                                               2q36A02 A:138-179,A:272-338               2q36A03 A:180-271 Actin; Chain A, domain 4                                                  2q36A02 A:138-179,A:272-338  [code=3.30.420.40, no name defined]   2q36A01 A:4-137,A:339-372          CATH domains
               Pfam domains Actin-2q36A01 A:4-372                                                                                                                                                                                                                                                                                                                                                             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......hhhhhhhhhhhhhhhhhhh.eehhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------ACTINS_1   ----------------------------------------ACTINS_ACT_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTINS_2 -------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q36 A   4 ETTALVCDNGSGLVKAGFAGDDAPRAVFPSIVGRPRH---------KDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHTFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVMSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWITKQEYDEAGPSIVHR 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         
                                                               40        50

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 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	d2q36a1	A:4-146
1b	d2q36a2	A:147-372

Asymmetric 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	2q36A01	A:4-137,A:339-372
1b	2q36A02	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)

2q36A03

A:180-271

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Actin_ATPase (173)

Family: Actin (70)

Oryctolagus cuniculus (Rabbit) (47)

Actin-2q36A01

A:4-372

Asymmetric 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.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ATP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		KAB	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2q36)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	2q36
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	ACTS_RABIT \| P68135
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	ACTS_RABIT \| P68135
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

1qz5	SAME COMPLEX WITHOUT THE CROSS-LINK
2q31

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (2, 3)

Pfam Domains (1, 1)

Gene Ontology (17, 17)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File