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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF THE SR CALCIUM PUMP WITH BOUND ALUMINIUM FLUORIDE, ADP AND CALCIUM

Authors :   C. Toyoshima, H. Nomura, T. Tsuda, H. Ogawa, Y. Norimatsu

Date :   20 Oct 07 (Deposition) - 20 Nov 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A

Keywords :   Membrane Protein, P-Type Atpase, Had Fold, Alternative Splicing, Atp-Binding, Calcium, Calcium Transport, Endoplasmic Reticulum, Hydrolase, Ion Transport, Magnesium, Metal-Binding, Nucleotide-Binding, Phosphorylation, Sarcoplasmic Reticulum, Transmembrane, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Toyoshima, H. Nomura, T. Tsuda
Lumenal Gating Mechanism Revealed In Calcium Pump Crystal Structures With Phosphate Analogues
Nature V. 432 361 2004
PubMed-ID: 15448704 | Reference-DOI: 10.1038/NATURE02981
(for further references see the PDB file header)

Molecule 1 - SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
	Chains	:	A
	EC Number	:	3.6.3.8
	Organism Common	:	RABBIT
	Organism Scientific	:	ORYCTOLAGUS CUNICULUS
	Organism Taxid	:	9986
	Synonym	:	CALCIUM PUMP 1, SERCA1, SR CA(2+)-ATPASE 1, CALCIUM-TRANSPORTING ATPASE SARCOPLASMIC RETICULUM TYPE, FAST TWITCH SKELETAL MUSCLE ISOFORM, ENDOPLASMIC RETICULUM CLASS 1/2 CA(2+) ATPASE
	Tissue	:	SKELETAL MUSCLE (WHITE)

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 9)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	ALF	1	Ligand/Ion	TETRAFLUOROALUMINATE ION
4	CA	2	Ligand/Ion	CALCIUM ION
5	MG	2	Ligand/Ion	MAGNESIUM ION
6	PC1	2	Ligand/Ion	1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:768 , GLU A:771 , THR A:799 , ASP A:800 , GLU A:908 , HOH A:1014 , HOH A:1015	BINDING SITE FOR RESIDUE CA A 995
2	AC2	SOFTWARE	VAL A:304 , ALA A:305 , ILE A:307 , GLU A:309 , ASN A:796 , ASP A:800	BINDING SITE FOR RESIDUE CA A 996
3	AC3	SOFTWARE	ALF A:998 , ADP A:1002 , HOH A:1041 , HOH A:1046 , HOH A:1059	BINDING SITE FOR RESIDUE MG A 997
4	AC4	SOFTWARE	ASP A:351 , LYS A:352 , THR A:353 , THR A:625 , GLY A:626 , LYS A:684 , ASN A:706 , MG A:997 , MG A:1001 , ADP A:1002 , HOH A:1038 , HOH A:1041	BINDING SITE FOR RESIDUE ALF A 998
5	AC5	SOFTWARE	ASP A:351 , THR A:353 , ASP A:703 , ALF A:998 , HOH A:1038 , HOH A:1041	BINDING SITE FOR RESIDUE MG A 1001
6	AC6	SOFTWARE	THR A:353 , GLU A:439 , GLU A:442 , PHE A:487 , ARG A:489 , MET A:494 , LYS A:515 , GLY A:516 , ALA A:517 , ARG A:560 , THR A:625 , GLY A:626 , ASP A:627 , ARG A:678 , MG A:997 , ALF A:998 , HOH A:1046 , HOH A:1059 , HOH A:1062 , HOH A:1077	BINDING SITE FOR RESIDUE ADP A 1002
7	AC7	SOFTWARE	VAL A:104 , GLN A:108 , ARG A:324 , PHE A:809 , TRP A:932 , SER A:936 , LEU A:946 , VAL A:950	BINDING SITE FOR RESIDUE PC1 A 1011
8	AC8	SOFTWARE	SER A:830 , GLY A:831 , PHE A:834	BINDING SITE FOR RESIDUE PC1 A 1012

Asymmetric/Biological Unit

No.	Residues
1	A:876	-	A:888

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

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ATPASE_E1_E2	PS00154	E1-E2 ATPases phosphorylation site.	AT2A1_RABIT	351-357	1	A:351-357

(no "Exon" information available for 2ZBD)

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
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Chain A from PDB  Type:PROTEIN  Length:995
 aligned with AT2A1_RABIT | P04191 from UniProtKB/Swiss-Prot  Length:1001

    Alignment length:995
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929       939       949       959       969       979       989     
          AT2A1_RABIT     - -MEAAHSKSTEECLAYFGVSETTGLTPDQVKRHLEKYGHNELPAEEGKSLWELVIEQFEDLLVRILLLAACISFVLAWFEEGEETITAFVEPFVILLILIANAIVGVWQERNAENAIEALKEYEPEMGKVYRADRKSVQRIKARDIVPGDIVEVAVGDKVPADIRILSIKSTTLRVDQSILTGESVSVIKHTEPVPDPRAVNQDKKNMLFSGTNIAAGKALGIVATTGVSTEIGKIRDQMAATEQDKTPLQQKLDEFGEQLSKVISLICVAVWLINIGHFNDPVHGGSWIRGAIYYFKIAVALAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTNQMSVCKMFIIDKVDGDFCSLNEFSITGSTYAPEGEVLKNDKPIRSGQFDGLVELATICALCNDSSLDFNETKGVYEKVGEATETALTTLVEKMNVFNTEVRNLSKVERANACNSVIRQLMKKEFTLEFSRDRKSMSVYCSPAKSSRAAVGNKMFVKGAPEGVIDRCNYVRVGTTRVPMTGPVKEKILSVIKEWGTGRDTLRCLALATRDTPPKREEMVLDDSSRFMEYETDLTFVGVVGMLDPPRKEVMGSIQLCRDAGIRVIMITGDNKGTAIAICRRIGIFGENEEVADRAYTGREFDDLPLAEQREACRRACCFARVEPSHKSKIVEYLQSYDEITAMTGDGVNDAPALKKAEIGIAMGSGTAVAKTASEMVLADDNFSTIVAAVEEGRAIYNNMKQFIRYLISSNVGEVVCIFLTAALGLPEALIPVQLLWVNLVTDGLPATALGFNPPDLDIMDRPPRSPKEPLISGWLFFRYMAIGGYVGAATVGAAAWWFMYAEDGPGVTYHQLTHFMQCTEDHPHFEGLDCEIFEAPEPMTMALSVLVTIEMCNALNSLSENQSLMRMPPWVNIWLLGSICLSMSLHFLILYVDPLPMIFKLKALDLTQWLMVLKISLPVIGLDEILKFIARNYLED 994
               SCOP domains -d2zbda4 A:1-124,A:240-343,A:751-994 Calcium ATPase, transmembrane domain M                                                  d2zbda1 A:125-239 Calcium ATPase, transduction domain A                                                            d2zbda4 A:1-124,A:240-343,A:751-994 Calcium ATPase, transmembrane domain M                              d2zbda2          d2zbda3 A:361-599 Calcium ATPase                                                                                                                                                                                                               d2zbda2 A:344-360,A:600-750 Calcium ATPase, catalytic domain P                                                                                         d2zbda4 A:1-124,A:240-343,A:751-994 Calcium ATPase, transmembrane domain M                                                                                                                                                                           SCOP domains
               CATH domains -2zbdA01 A:1-53,A:121-242                             2zbdA02 A:54-120,A:243-345,A:746-994                               2zbdA01 A:1-53,A:121-242 Calcium-transporting ATPase, cytoplasmic transduction domain A                                   2zbdA02 A:54-120,A:243-345,A:746-994 Calcium-transporting ATPase, transmembrane domain                 2zbdA03      2zbdA04 A:359-602 Calcium-transporting ATPase, cytoplasmic domain N                                                                                                                                                                                 2zbdA03 A:346-358,A:603-745  [code=3.40.50.1000, no name defined]                                                                              2zbdA02 A:54-120,A:243-345,A:746-994 Calcium-transporting ATPase, transmembrane domain                                                                                                                                                                    CATH domains
               Pfam domains ----Cation_ATPase_N-2zbdA03 A:4-72                                       --------------------E1-E2_ATPase-2zbdA04 A:93-341                                                                                                                                                                                                                            ---Hydrolase-2zbdA01 A:345-715                                                                                                                                                                                                                                                                                                                                                        --------------------------------------------------------------------Cation_ATPase_C-2zbdA02 A:784-987                                                                                                                                                                           ------- Pfam domains
         Sec.struct. author ........hhhhhhhhhh.......hhhhhhhhhhhhh...........hhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.......eeee.hhh....eeeee.......eeeeeee.....eeehhhhhh....ee..................ee....eeee.eeeeeeeehhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.eee...hhhhhhhhh.eeee...........eeeeeeeeeeee..eeeeeeeee..........eee..ee.hhhhhhhhhhhhhhhhhh...eeeee....eeeee.hhhhhhhhhhhhhh..........hhhhhhhhhhhhhhh.eeeeeeeeee....eeeeeeee...hhhhh..eeeeeehhhhhhhheeeeee..eeee.hhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhh......hhhhhh..eeeeeeeeee.....hhhhhhhhhhhh..eeeee...hhhhhhhhhhhh............eeehhhhhh.hhhhhhhhhhhh.eee..hhhhhhhhhhhhhh....eeeee.hhhhhhhhhhh.eeeee...hhhhhhh..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhh...............................hhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATPASE_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zbd A   0 xMEAAHSKSTEECLAYFGVSETTGLTPDQVKRHLEKYGHNELPAEEGKSLWELVIEQFEDLLVRILLLAACISFVLAWFEEGEETITAFVEPFVILLILIANAIVGVWQERNAENAIEALKEYEPEMGKVYRADRKSVQRIKARDIVPGDIVEVAVGDKVPADIRILSIKSTTLRVDQSILTGESVSVIKHTEPVPDPRAVNQDKKNMLFSGTNIAAGKALGIVATTGVSTEIGKIRDQMAATEQDKTPLQQKLDEFGEQLSKVISLICVAVWLINIGHFNDPVHGGSWIRGAIYYFKIAVALAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTNQMSVCKMFIIDKVDGDFCSLNEFSITGSTYAPEGEVLKNDKPIRSGQFDGLVELATICALCNDSSLDFNETKGVYEKVGEATETALTTLVEKMNVFNTEVRNLSKVERANACNSVIRQLMKKEFTLEFSRDRKSMSVYCSPAKSSRAAVGNKMFVKGAPEGVIDRCNYVRVGTTRVPMTGPVKEKILSVIKEWGTGRDTLRCLALATRDTPPKREEMVLDDSSRFMEYETDLTFVGVVGMLDPPRKEVMGSIQLCRDAGIRVIMITGDNKGTAIAICRRIGIFGENEEVADRAYTGREFDDLPLAEQREACRRACCFARVEPSHKSKIVEYLQSYDEITAMTGDGVNDAPALKKAEIGIAMGSGTAVAKTASEMVLADDNFSTIVAAVEEGRAIYNNMKQFIRYLISSNVGEVVCIFLTAALGLPEALIPVQLLWVNLVTDGLPATALGFNPPDLDIMDRPPRSPKEPLISGWLFFRYMAIGGYVGAATVGAAAWWFMYAEDGPGVTYHQLTHFMQCTEDHPHFEGLDCEIFEAPEPMTMALSVLVTIEMCNALNSLSENQSLMRMPPWVNIWLLGSICLSMSLHFLILYVDPLPMIFKLKALDLTQWLMVLKISLPVIGLDEILKFIARNYLEG 994
                            |        9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849       859       869       879       889       899       909       919       929       939       949       959       969       979       989     
                            |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                            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 '\|'

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (AT2A1_RABIT | P04191)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0005388	calcium-transporting ATPase activity	Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + Ca2+(cis) = ADP + phosphate + Ca2+(trans).
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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:0070588	calcium ion transmembrane transport	A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0006816	calcium ion transport	The directed movement of calcium (Ca) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0045988	negative regulation of striated muscle contraction	Any process that stops, prevents, or reduces the frequency, rate or extent of striated muscle contraction.
	GO:0031448	positive regulation of fast-twitch skeletal muscle fiber contraction	Any process that activates or increases the frequency, rate or extent of fast-twitch skeletal muscle contraction.
	GO:0006942	regulation of striated muscle contraction	Any process that modulates the frequency, rate or extent of striated muscle contraction.
	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.
cellular component
	GO:0031673	H zone	A relatively pale zone traversing the center of the A band of a sarcomere, visible in relaxed muscle fibers; consists of the central portion of thick (myosin) filaments that are not overlapped by thin (actin) filaments.
	GO:0031674	I band	A region of a sarcomere that appears as a light band on each side of the Z disc, comprising a region of the sarcomere where thin (actin) filaments are not overlapped by thick (myosin) filaments; contains actin, troponin, and tropomyosin; each sarcomere includes half of an I band at each end.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0005793	endoplasmic reticulum-Golgi intermediate compartment	A complex system of membrane-bounded compartments located between endoplasmic reticulum (ER) and the Golgi complex, with a distinctive membrane protein composition; involved in ER-to-Golgi and Golgi-to-ER transport.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	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:0016529	sarcoplasmic reticulum	A fine reticular network of membrane-limited elements that pervades the sarcoplasm of a muscle cell; continuous over large portions of the cell and with the nuclear envelope; that part of the endoplasmic reticulum specialized for calcium release, uptake and storage.
	GO:0033017	sarcoplasmic reticulum membrane	The lipid bilayer surrounding the sarcoplasmic reticulum.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2zbd)

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1iwo	THE SAME PROTEIN WITHOUT CALCIUM
1su4	THE SAME PROTEIN WITH BOUND CALCIUM
1vfp	THE SAME PROTEIN WITH BOUND AMPPCP AND CALCIUM
1wpg	THE SAME PROTEIN WITH BOUND MAGNESIUM FLUORIDE AND THAPSIGARGIN IN THE ABSENCE OF CALCIUM
2agv	THE SAME PROTEIN WITH BOUND BHQ AND THAPSIGARGIN IN THE ABSENCE OF CALCIUM
2dqs	THE SAME PROTEIN WITH BOUND AMPPCP IN THE ABSENCE OF CALCIUM
2ear	THE SAME PROTEIN WITH BOUND TG
2eas	THE SAME PROTEIN WITH BOUND CPA
2eat	THE SAME PROTEIN WITH BOUND CPA AND TG
2eau	THE SAME PROTEIN WITH BOUND CPA IN THE PRESENCE OF CURCUMIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 9)

Sites (8, 8)

SS Bonds (1, 1)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (4, 4)

CATH Domains (4, 4)

Pfam Domains (4, 4)

Gene Ontology (24, 24)

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Related Entries Specified in the PDB File