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(-) Description

Title :  COMPLETE STRUCTURE FACTORS AND AN ATOMIC MODEL OF THE CALCIUM PUMP (SERCA1A) AND ASSOCIATED PHOSPHOLIPIDS IN THE E2(TG) CRYSTALS
 
Authors :  Y. Norimatsu, K. Hasegawa, N. Shimizu, C. Toyoshima
Date :  11 Mar 17  (Deposition) - 07 Jun 17  (Release) - 07 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A
Keywords :  P-Type Atpase, Hydrolase, Calcium Transport, Calcium Binding, Atp Binding, Endoplasmic Reticulum, Sarcoplasmic Reticulum, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Norimatsu, K. Hasegawa, N. Shimizu, C. Toyoshima
Protein-Phospholipid Interplay Revealed With Crystals Of A Calcium Pump.
Nature V. 545 193 2017
PubMed-ID: 28467821  |  Reference-DOI: 10.1038/NATURE22357

(-) Compounds

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: SR CA(2+)-ATPASE 1,CALCIUM PUMP 1,CALCIUM-TRANSPORTING ATPASE SARCOPLASMIC RETICULUM TYPE,FAST TWITCH SKELETAL MUSCLE ISOFORM,ENDOPLASMIC RETICULUM CLASS 1/2 CA(2+) ATPASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 33)

Asymmetric/Biological Unit (4, 33)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2NA1Ligand/IonSODIUM ION
3PCW30Ligand/Ion1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
4TG11Ligand/IonOCTANOIC ACID [3S-[3ALPHA, 3ABETA, 4ALPHA, 6BETA,6ABETA, 7BETA, 8ALPHA(Z), 9BALPHA]]-6-(ACETYLOXY)-2,3,-3A,4,5,6,6A,7,8,9B-DECAHYDRO-3,3A-DIHYDROXY-3,6,9-TRIMETHYL-8-[(2-METHYL-1-OXO-2-BUTENYL)OXY]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL ESTER

(-) Sites  (31, 31)

Asymmetric Unit (31, 31)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:244 , LEU A:711 , LYS A:712 , ALA A:714 , GLU A:732 , HOH A:1101 , HOH A:1134binding site for residue NA A 1001
02AC2SOFTWAREGLU A:255 , PHE A:256 , GLN A:259 , LEU A:260 , VAL A:263 , ALA A:306 , ILE A:765 , ASN A:768 , VAL A:769 , VAL A:772 , LEU A:828 , ILE A:829 , PHE A:834 , MET A:838binding site for residue TG1 A 1002
03AC3SOFTWAREGLU A:255 , VAL A:263 , PCW A:1019 , PCW A:1030 , PCW A:1032binding site for residue PCW A 1003
04AC4SOFTWAREGLY A:831 , TRP A:832binding site for residue PCW A 1004
05AC5SOFTWARESER A:921 , MET A:923 , ARG A:924 , GLU A:982 , PHE A:986 , ARG A:989 , ASN A:990 , PCW A:1020binding site for residue PCW A 1005
06AC6SOFTWAREARG A:324 , PCW A:1016binding site for residue PCW A 1006
07AC7SOFTWARETRP A:107 , THR A:316 , PCW A:1018binding site for residue PCW A 1007
08AC8SOFTWAREPCW A:1030binding site for residue PCW A 1008
09AC9SOFTWARELEU A:60 , ARG A:63 , SER A:261binding site for residue PCW A 1009
10AD1SOFTWARETRP A:77binding site for residue PCW A 1010
11AD2SOFTWAREILE A:103 , TRP A:107 , ARG A:110 , SER A:287 , TRP A:288 , ILE A:289binding site for residue PCW A 1011
12AD3SOFTWAREMET A:857 , TYR A:858 , THR A:866 , TYR A:867binding site for residue PCW A 1012
13AD4SOFTWARETRP A:50 , GLU A:51 , PCW A:1027binding site for residue PCW A 1013
14AD5SOFTWAREILE A:274 , TYR A:867 , TRP A:928 , VAL A:929 , PCW A:1023binding site for residue PCW A 1014
15AD6SOFTWARETRP A:77binding site for residue PCW A 1015
16AD7SOFTWAREMET A:969 , LYS A:972 , PCW A:1006 , PCW A:1022 , PCW A:1025binding site for residue PCW A 1016
17AD8SOFTWAREPCW A:1029binding site for residue PCW A 1017
18AD9SOFTWAREGLN A:56 , ASN A:101 , VAL A:104 , GLN A:108 , PRO A:312 , ALA A:313 , THR A:316 , PCW A:1007binding site for residue PCW A 1018
19AE1SOFTWARELYS A:262 , PCW A:1003 , PCW A:1029binding site for residue PCW A 1019
20AE2SOFTWAREASP A:951 , ASN A:990 , PCW A:1005 , PCW A:1026binding site for residue PCW A 1020
21AE3SOFTWAREARG A:324binding site for residue PCW A 1021
22AE4SOFTWARETYR A:858 , PCW A:1016 , PCW A:1025binding site for residue PCW A 1022
23AE5SOFTWARELEU A:273 , ASN A:275 , ALA A:780 , LEU A:922 , MET A:923 , TRP A:928 , PCW A:1014binding site for residue PCW A 1023
24AE6SOFTWAREPCW A:1030binding site for residue PCW A 1024
25AE7SOFTWARETRP A:932 , PCW A:1016 , PCW A:1022binding site for residue PCW A 1025
26AE8SOFTWAREPRO A:952 , PCW A:1020binding site for residue PCW A 1026
27AE9SOFTWAREILE A:276 , GLY A:277 , ASN A:280 , ARG A:924 , PCW A:1013binding site for residue PCW A 1027
28AF1SOFTWAREMET A:941 , LEU A:962 , ASP A:963 , LEU A:964 , TRP A:967 , LEU A:971binding site for residue PCW A 1028
29AF2SOFTWARELYS A:262 , PCW A:1017 , PCW A:1019binding site for residue PCW A 1029
30AF3SOFTWAREPCW A:1003 , PCW A:1008 , PCW A:1024binding site for residue PCW A 1030
31AF4SOFTWARESER A:830 , GLY A:831 , PCW A:1003binding site for residue PCW A 1032

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5XAB)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5XAB)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5XAB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5XAB)

(-) Exons   (0, 0)

(no "Exon" information available for 5XAB)

(-) Sequences/Alignments

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:995
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhh.......hhhhhhhhhhhhh..........hhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh...eeeee.......eeee.hhh....eeeee.......eeeeeee.....eee..........ee...........hhhhh..ee....eeee.eeeeeeeehhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.eee...hhhhhhhh..eeeee..........eeeeeeeeeeee..eeeeeeeee..........eee..ee.hhhhhhhhhhhhhhhhhh...eeee......eeee.hhhhhhhhhhhhhhh................hhhhhhhh.eeeeeee.......eeeeeeee..........eeeeeehhhhhhhheeeeee..eeee.hhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhh...hhhhhhhhh..eeeeeeeeee.....hhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhh...........eeehhhhhh.hhhhhhhhhh...eee....hhhhhhhhhhhh....eeeee.hhhhhhhhhhh.eeeee...hhhhhhh..eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.hhhhhhhhhhh....hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5xab 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)
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    → 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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5XAB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5XAB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5XAB)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)

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  AT2A1_RABIT | P04191
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 Related Entries

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UniProtKB/Swiss-Prot
        AT2A1_RABIT | P04191: 1fqu 1iwo 1kju 1su4 1t5s 1t5t 1vfp 1wpg 1xp5 2agv 2by4 2c88 2c8k 2c8l 2c9m 2dqs 2ear 2eat 2eau 2o9j 2oa0 2voy 2yfy 2zbd 2zbe 2zbf 2zbg 3ar2 3ar3 3ar4 3ar5 3ar6 3ar7 3ar8 3ar9 3b9b 3b9r 3ba6 3fgo 3fpb 3fps 3j7t 3n5k 3n8g 3w5a 3w5b 3w5c 3w5d 4bew 4h1w 4j2t 4kyt 4nab 4uu0 4uu1 4xou 4y3u 4ycl 4ycm 4ycn 5a3q 5a3r 5a3s 5xa7 5xa8 5xa9 5xaa

(-) Related Entries Specified in the PDB File

5xa7 5xa8 5xa9 5xaa