3U4L - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYOCOOLED BOVINE PROFILIN:ACTIN CRYSTAL STRUCTURE TO 2.4 A

Authors :   J. C. Porta, G. E. Borgstahl

Date :   09 Oct 11 (Deposition) - 25 Apr 12 (Release) - 25 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Atpase, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. C. Porta, G. E. Borgstahl
Structural Basis For Profilin-Mediated Actin Nucleotide Exchange.
J. Mol. Biol. V. 418 103 2012
PubMed-ID: 22366544 | Reference-DOI: 10.1016/J.JMB.2012.02.012

Molecule 1 - ACTIN, CYTOPLASMIC 1
	Chains	:	A
	Organ	:	THYMUS
	Organism Common	:	BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	BETA-ACTIN, ACTIN, CYTOPLASMIC 1, N-TERMINALLY PROCESSED

Molecule 2 - PROFILIN-1
	Chains	:	P
	Organ	:	THYMUS
	Organism Common	:	BOVINE,COW,DOMESTIC CATTLE,DOMESTIC COW
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	PROFILIN I

		1	2
Asymmetric/Biological Unit	:	A	P

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

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

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:13 , SER A:14 , GLY A:15 , MET A:16 , LYS A:18 , SER A:155 , GLY A:156 , ASP A:157 , GLY A:158 , 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 , CA A:402 , HOH A:502 , HOH A:511	BINDING SITE FOR RESIDUE ATP A 401
2	AC2	SOFTWARE	ATP A:401 , HOH A:510 , HOH A:511	BINDING SITE FOR RESIDUE CA A 402
3	AC3	SOFTWARE	ASP A:288 , ASN P:61 , HOH P:210	BINDING SITE FOR RESIDUE CA A 403

(no "SS Bond" information available for 3U4L)

(no "Cis Peptide Bond" information available for 3U4L)

(no "SAP(SNP)/Variant" information available for 3U4L)

Asymmetric/Biological Unit (4, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROFILIN	PS00414	Profilin signature.	PROF1_BOVIN	1-9	1	P:1-8
2	ACTINS_1	PS00406	Actins signature 1.	ACTB_BOVIN	53-63	1	A:53-63
3	ACTINS_ACT_LIKE	PS01132	Actins and actin-related proteins signature.	ACTB_BOVIN	104-116	1	A:104-116
4	ACTINS_2	PS00432	Actins signature 2.	ACTB_BOVIN	356-364	1	A:356-364

Asymmetric/Biological Unit (3, 3)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSBTAT00000006465	1	ENSBTAE00000051693	chr19:26821468-26821753	286	PROF1_BOVIN	1-44	44	1	P:0-43	44
1.2	ENSBTAT00000006465	2	ENSBTAE00000051699	chr19:26823296-26823488	193	PROF1_BOVIN	45-109	65	1	P:44-108	65
1.3	ENSBTAT00000006465	3	ENSBTAE00000051703	chr19:26824096-26824443	348	PROF1_BOVIN	109-140	32	1	P:108-139	32

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:353
 aligned with ACTB_BOVIN | P60712 from UniProtKB/Swiss-Prot  Length:375

    Alignment length:370
                                    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
           ACTB_BOVIN     6 AALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF 375
               SCOP domains d3u4la1 A:6-146 automated match              es                                                                                              d3u4la2 A:147-375 automated matches                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...eeeeee.......eeee....--------------..............---...ee..ee.hhhhhhhhhhhhhhh....hhhhh.eeeee....hhhhhhhhhhhhhhh....eeeeeehhhhhhhhh...eeeeeee....eeeeeee..ee.hhhheee..hhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhh....hhhhhhhh........eeee.....eeee.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.eeeehhhhh..hhhhhhhhhhhhhh.......ee......hhhhhhhhhhhhhhhhhhh.eehhhhhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------ACTINS_1   ----------------------------------------ACTINS_ACT_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTINS_2 ----------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3u4l A   6 AALVVDNGSGMCKAGFAGDDAPRAVFPSIVG--------------DSYVGDEAQSKRGI---KYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF 375
                                    15        25        35|        -     |  55        |-  |     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
                                                         36             51           64  68

Chain P from PDB  Type:PROTEIN  Length:140
 aligned with PROF1_BOVIN | P02584 from UniProtKB/Swiss-Prot  Length:140

    Alignment length:140
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
          PROF1_BOVIN     1 MAGWNAYIDNLMADGTCQDAAIVGYKDSPSVWAAVPGKTFVNITPAEVGILVGKDRSSFFVNGLTLGGQKCSVIRDSLLQDGEFTMDLRTKSTGGAPTFNITVTMTAKTLVLLMGKEGVHGGMINKKCYEMASHLRRSQY 140
               SCOP domains d3u4lp_ P: Profilin (actin-binding protein)                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh.eeeeeeee.....eeeee....hhhhhhhhhhhhhhh...hhhhhhheee..eeeeeeee........eeeeee.........eeeeee...eeeeeee....hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE PROFILIN ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: P:0-43 UniProt: 1-44         Exon 1.2  PDB: P:44-108 UniProt: 45-109                          ------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------Exon 1.3  PDB: P:108-139         Transcript 1 (2)
                 3u4l P   0 xAGWNAYIDNLMADGTCQDAAIVGYKDSPSVWAAVPGKTFVNITPAEVGILVGKDRSSFFVNGLTLGGQKCSVIRDSLLQDGEFTMDLRTKSTGGAPTFNITVTMTAKTLVLLMGKEGVHGGMINKKCYEMASHLRRSQY 139
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139
                            0-ACE

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 3U4L)

(no "Pfam Domain" information available for 3U4L)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ACTB_BOVIN | P60712)

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: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:0051086	chaperone mediated protein folding independent of cofactor	The process of assisting in the correct noncovalent assembly of posttranslational proteins and does not depend on additional protein cofactors. This function occurs over one or more cycles of nucleotide-dependent binding and release.
	GO:0006457	protein folding	The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
cellular component
	GO:0035267	NuA4 histone acetyltransferase complex	A complex having histone acetylase activity on chromatin, as well as ATPase, DNA helicase and structural DNA binding activities. The complex is thought to be involved in double-strand DNA break repair. Subunits of the human complex include HTATIP/TIP60, TRRAP, RUVBL1, BUVBL2, beta-actin and BAF53/ACTL6A. In yeast, the complex has 13 subunits, including the catalytic subunit Esa1 (homologous to human Tip60).
	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:0097433	dense body	An electron dense body which may contain granules.
	GO:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	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.

Chain P (PROF1_BOVIN | P02584)

molecular function
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
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:0032233	positive regulation of actin filament bundle assembly	Any process that activates or increases the frequency, rate or extent of the assembly of actin filament bundles.
	GO:0030833	regulation of actin filament polymerization	Any process that modulates the frequency, rate or extent of the assembly of actin filaments by the addition of actin monomers to a filament.
cellular component
	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.

Asymmetric/Biological 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
		ACE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ATP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3u4l)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - 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
	3u4l
		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
	ACTB_BOVIN \| P60712
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	PROF1_BOVIN \| P02584
		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
	ACTB_BOVIN \| P60712
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	PROF1_BOVIN \| P02584
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ACTB_BOVIN \| P60712	:	1hlu 2btf 2oan 3ub5
	PROF1_BOVIN \| P02584	:	1hlu 1pne 2btf 3ub5

(no "Related Entries Specified in the PDB File" available for 3U4L)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (4, 4)

Exons (3, 3)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (16, 18)

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