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Title :   CRYSTAL STRUCTURE OF SMOOTH MUSCLE G ACTIN DNASE I COMPLEX

Authors :   N. Sakabe, K. Sakabe, K. Sasaki, H. Kondo, M. Shimomur

Date :   20 Dec 12 (Deposition) - 30 Jan 13 (Release) - 30 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Smooth Muscle Actin, Actin, Dnase I, Structural Protein, G-Actin, Atp Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Sasaki, K. Sakabe, N. Sakabe, H. Kondo, M. Shimomur
Refined Structure And Solvent Network Of Chicken Gizzard G-Actin Dnase 1 Complex At 1. 8A Resolution
Acta Crystallogr. , Sect. A V. 49 C111 1993
PubMed: search
(for further references see the PDB file header)

Molecule 1 - ACTIN, GAMMA-ENTERIC SMOOTH MUSCLE
	Chains	:	A
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031
	Other Details	:	GIZZARD
	Synonym	:	ALPHA-ACTIN-3, GAMMA-2-ACTIN, SMOOTH MUSCLE GAMMA-ACTIN

Molecule 2 - DEOXYRIBONUCLEASE-1
	Chains	:	B
	EC Number	:	3.1.21.1
	Organism Common	:	BOVINE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Other Details	:	PANCREAS
	Synonym	:	DEOXYRIBONUCLEASE I, DNASE I

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 11)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	BMA	3	Ligand/Ion	BETA-D-MANNOSE
3	CA	2	Ligand/Ion	CALCIUM ION
4	HIC	1	Mod. Amino Acid	4-METHYL-HISTIDINE
5	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
6	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:12 , SER A:13 , GLY A:14 , LEU A:15 , LYS A:17 , GLY A:155 , ASP A:156 , GLY A:157 , VAL A:158 , GLY A:181 , LYS A:212 , GLU A:213 , GLY A:300 , GLY A:301 , THR A:302 , MET A:304 , TYR A:305 , LYS A:335 , CA A:402 , HOH A:501 , HOH A:506 , HOH A:514 , HOH A:632	BINDING SITE FOR RESIDUE ATP A 401
2	AC2	SOFTWARE	ATP A:401 , HOH A:501 , HOH A:502 , HOH A:503 , HOH A:514 , HOH A:632	BINDING SITE FOR RESIDUE CA A 402
3	AC3	SOFTWARE	ASP B:201 , THR B:203 , THR B:205 , THR B:207 , HOH B:408 , HOH B:409	BINDING SITE FOR RESIDUE CA B 308
4	AC4	SOFTWARE	ASP A:362 , GLU A:363 , ASN B:18 , SER B:242 , ALA B:248 , HOH B:461 , HOH B:473 , HOH B:479 , HOH B:480 , HOH B:491 , HOH B:493 , HOH B:522 , HOH B:537 , HOH B:549 , HOH B:567 , HOH B:570	BINDING SITE FOR LINKED RESIDUES B 301 to 307

Asymmetric/Biological Unit

No.	Residues
1	B:101	-	B:104
2	B:173	-	B:209

(no "Cis Peptide Bond" information available for 3W3D)

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_DNAS1_BOVIN_001 *	H	143	P	DNAS1_BOVIN	---	---	B	H	121	P
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (5, 5)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ACTINS_1	PS00406	Actins signature 1.	ACTH_CHICK	54-64	1	A:52-62
2	ACTINS_ACT_LIKE	PS01132	Actins and actin-related proteins signature.	ACTH_CHICK	105-117	1	A:103-115
3	DNASE_I_1	PS00919	Deoxyribonuclease I signature 1.	DNAS1_BOVIN	152-172	1	B:130-150
4	DNASE_I_2	PS00918	Deoxyribonuclease I signature 2.	DNAS1_BOVIN	189-196	1	B:167-174
5	ACTINS_2	PS00432	Actins signature 2.	ACTH_CHICK	357-365	1	A:355-363

Asymmetric/Biological Unit (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSBTAT00000026784	1	ENSBTAE00000293181	chr25:3564711-3564829	119	DNAS1_BOVIN	-	0	0	-	-
1.2	ENSBTAT00000026784	2	ENSBTAE00000218065	chr25:3565156-3565303	148	DNAS1_BOVIN	1-49	49	1	B:1-27	27
1.3	ENSBTAT00000026784	3	ENSBTAE00000420413	chr25:3565639-3565727	89	DNAS1_BOVIN	50-79	30	1	B:28-57	30
1.4	ENSBTAT00000026784	4	ENSBTAE00000410212	chr25:3565904-3565987	84	DNAS1_BOVIN	79-107	29	1	B:57-85	29
1.5	ENSBTAT00000026784	5	ENSBTAE00000218074	chr25:3566232-3566347	116	DNAS1_BOVIN	107-146	40	1	B:85-124	40
1.6	ENSBTAT00000026784	6	ENSBTAE00000407443	chr25:3566499-3566611	113	DNAS1_BOVIN	146-183	38	1	B:124-161	38
1.7	ENSBTAT00000026784	7	ENSBTAE00000398022	chr25:3566701-3566855	155	DNAS1_BOVIN	184-235	52	1	B:162-213	52
1.8	ENSBTAT00000026784	8	ENSBTAE00000425804	chr25:3567129-3567225	97	DNAS1_BOVIN	235-267	33	1	B:213-245	33
1.9	ENSBTAT00000026784	9	ENSBTAE00000293180	chr25:3567369-3567733	365	DNAS1_BOVIN	268-282	15	1	B:246-260	15

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:374
 aligned with ACTH_CHICK | P63270 from UniProtKB/Swiss-Prot  Length:376

    Alignment length:374
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372    
           ACTH_CHICK     3 EEETTALVCDNGSGLCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIITNWDDMEKIWHHSFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKPEYDEAGPSIVHRKCF 376
               SCOP domains d3w3da1 A:1-145 automated matches                                                                                                                d3w3da2 A:146-374 automated matches                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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....hhhhhhhhhhhhh..hhhhhhhh.eeee.hhhhh.hhhhhhhhhhhh.........ee......hhhhhhhhhhhhhhhhhhh.eehhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------ACTINS_1   ----------------------------------------ACTINS_ACT_LI-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ACTINS_2 ----------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3w3d A   1 EEETTALVCDNGSGLCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEhGIITNWDDMEKIWHHSFYNELRVAPEEHPTLLTEAPLNPKANREKMTQIMFETFNVPAMYVAIQAVLSLYASGRTTGIVLDSGDGVTHNVPIYEGYALPHAIMRLDLAGRDLTDYLMKILTERGYSFVTTAEREIVRDIKEKLCYVALDFENEMATAASSSSLEKSYELPDGQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSIMKCDIDIRKDLYANNVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDEAGPSIVHRKCF 374
                                    10        20        30        40        50        60        70 |      80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370    
                                                                                                  72-HIC

Chain B from PDB  Type:PROTEIN  Length:260
 aligned with DNAS1_BOVIN | P00639 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:260
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282
          DNAS1_BOVIN    23 LKIAAFNIRTFGETKMSNATLASYIVRIVRRYDIVLIQEVRDSHLVAVGKLLDYLNQDDPNTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQYDDGCESCGNDSFSREPAVVKFSSHSTKVKEFAIVALHSAPSDAVAEINSLYDVYLDVQQKWHLNDVMLMGDFNADCSYVTSSQWSSIRLRTSSTFQWLIPDSADTTATSTNCAYDRIVVAGSLLQSSVVPGSAAPFDFQAAYGLSNEMALAISDHYPVEVTLT 282
               SCOP domains d3w3db_ B: Deoxyribonuclease I                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeehhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhh......eeee...........eeeeee....eeeeeeee.....hhhhhhh.....eeeeeee......eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhhhhhhhh..eee.................eeeeeehhhhhhhh.....ee.hhhhhh..hhhhhhhhh....eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------P------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------DNASE_I_1            ----------------DNASE_I_-------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:1-27      Exon 1.3  PDB: B:28-57        ---------------------------Exon 1.5  PDB: B:85-124 UniProt: 107-146-------------------------------------Exon 1.7  PDB: B:162-213 UniProt: 184-235           --------------------------------Exon 1.9        Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.4  PDB: B:57-85       --------------------------------------Exon 1.6  PDB: B:124-161              ---------------------------------------------------Exon 1.8  PDB: B:213-245         --------------- Transcript 1 (2)
                 3w3d B   1 LKIAAFNIRTFGETKMSNATLASYIVRIVRRYDIVLIQEVRDSHLVAVGKLLDYLNQDDPNTYHYVVSEPLGRNSYKERYLFLFRPNKVSVLDTYQYDDGCESCGNDSFSREPAVVKFSSHSTKVKEFAIVALHSAPSDAVAEINSLYDVYLDVQQKWHLNDVMLMGDFNADCSYVTSSQWSSIRLRTSSTFQWLIPDSADTTATSTNCAYDRIVVAGSLLQSSVVPGSAAPFDFQAAYGLSNEMALAISDHYPVEVTLT 260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

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 3W3D)

(no "Pfam Domain" information available for 3W3D)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ACTH_CHICK | P63270)

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.
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.

Chain B (DNAS1_BOVIN | P00639)

molecular function
	GO:0003779	actin binding	Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
	GO:0004530	deoxyribonuclease I activity	Catalysis of the endonucleolytic cleavage of DNA to 5'-phosphodinucleotide and 5'-phosphooligonucleotide end products.
	GO:0004536	deoxyribonuclease activity	Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid.
	GO:0004519	endonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
biological process
	GO:0006308	DNA catabolic process	The cellular DNA metabolic process resulting in the breakdown of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005635	nuclear envelope	The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
	GO:0005634	nucleus	A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
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	DNAS1_BOVIN \| P00639	:	1atn 1dnk 2a3z 2a40 2a41 2a42 2d1k 2dnj 3cjc 3dni

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Description

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Chains, Units

Ligands, Modified Residues, Ions (6, 11)

Sites (4, 4)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

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