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(-) Description

Title :  COMPLETE STRUCTURE FACTORS AND AN ATOMIC MODEL OF THE CALCIUM PUMP (SERCA1A) AND ASSOCIATED PHOSPHOLIPIDS IN THE E1-ALF4-ADP-2CA2+ CRYSTALS
 
Authors :  Y. Norimatsu, K. Hasegawa, N. Shimizu, C. Toyoshima
Date :  11 Mar 17  (Deposition) - 17 May 17  (Release) - 17 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A
Keywords :  P-Type Atpase, Hydrolase, Calcium Transport, Calcium Binding, Endoplasmic Reticulum, Sarcoplasmic Reticulum, Met 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 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  (6, 53)

Asymmetric/Biological Unit (6, 53)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3ALF1Ligand/IonTETRAFLUOROALUMINATE ION
4CA2Ligand/IonCALCIUM ION
5MG2Ligand/IonMAGNESIUM ION
6PCW46Ligand/Ion1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE

(-) Sites  (50, 50)

Asymmetric Unit (50, 50)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:768 , GLU A:771 , THR A:799 , ASP A:800 , GLU A:908 , HOH A:1112 , HOH A:1139binding site for residue CA A 1001
02AC2SOFTWAREVAL A:304 , ALA A:305 , ILE A:307 , GLU A:309 , ASN A:796 , ASP A:800binding site for residue CA A 1002
03AC3SOFTWAREALF A:1004 , ADP A:1006 , HOH A:1127 , HOH A:1141 , HOH A:1211binding site for residue MG A 1003
04AC4SOFTWAREASP A:351 , LYS A:352 , THR A:353 , THR A:625 , GLY A:626 , LYS A:684 , ASN A:706 , MG A:1003 , MG A:1005 , ADP A:1006 , HOH A:1122 , HOH A:1141 , HOH A:1211binding site for residue ALF A 1004
05AC5SOFTWAREASP A:351 , THR A:353 , ASP A:703 , ALF A:1004 , HOH A:1122 , HOH A:1211binding site for residue MG A 1005
06AC6SOFTWARETHR A:353 , GLU A:439 , GLU A:442 , PHE A:487 , ARG A:489 , MET A:494 , LYS A:515 , GLY A:516 , ARG A:560 , LEU A:562 , THR A:625 , GLY A:626 , ASP A:627 , ARG A:678 , ASN A:706 , MG A:1003 , ALF A:1004 , HOH A:1111 , HOH A:1114 , HOH A:1127 , HOH A:1141binding site for residue ADP A 1006
07AC7SOFTWAREPCW A:1022 , PCW A:1023 , PCW A:1025 , PCW A:1044binding site for residue PCW A 1007
08AC8SOFTWAREARG A:63 , PCW A:1019 , PCW A:1037 , PCW A:1050binding site for residue PCW A 1008
09AC9SOFTWAREPCW A:1010 , PCW A:1020binding site for residue PCW A 1009
10AD1SOFTWARELYS A:262 , LEU A:266 , PCW A:1009 , PCW A:1028binding site for residue PCW A 1010
11AD2SOFTWAREILE A:289binding site for residue PCW A 1011
12AD3SOFTWAREGLY A:831 , PCW A:1020 , PCW A:1038binding site for residue PCW A 1012
13AD4SOFTWAREPCW A:1014 , PCW A:1031 , PCW A:1041binding site for residue PCW A 1013
14AD5SOFTWAREMET A:923 , PHE A:986 , ARG A:989 , ASN A:990 , PCW A:1013binding site for residue PCW A 1014
15AD6SOFTWARELEU A:968binding site for residue PCW A 1016
16AD7SOFTWARETRP A:107 , GLN A:108 , ARG A:324 , PHE A:809 , TRP A:932 , VAL A:950 , ASP A:951binding site for residue PCW A 1017
17AD8SOFTWARELEU A:49 , ARG A:110binding site for residue PCW A 1018
18AD9SOFTWAREPCW A:1008binding site for residue PCW A 1019
19AE1SOFTWAREPCW A:1009 , PCW A:1012 , PCW A:1048binding site for residue PCW A 1020
20AE2SOFTWAREILE A:931 , PHE A:945 , TYR A:949binding site for residue PCW A 1021
21AE3SOFTWAREPCW A:1007binding site for residue PCW A 1022
22AE4SOFTWAREPCW A:1007 , PCW A:1046binding site for residue PCW A 1023
23AE5SOFTWAREALA A:780 , PCW A:1032 , PCW A:1034 , PCW A:1037binding site for residue PCW A 1024
24AE6SOFTWAREPCW A:1007binding site for residue PCW A 1025
25AE7SOFTWARETYR A:867 , HIS A:868 , PCW A:1036binding site for residue PCW A 1026
26AE8SOFTWAREGLU A:45binding site for residue PCW A 1027
27AE9SOFTWAREPCW A:1010 , PCW A:1049binding site for residue PCW A 1028
28AF1SOFTWAREPCW A:1030 , PCW A:1043binding site for residue PCW A 1029
29AF2SOFTWARELYS A:972 , PCW A:1029 , PCW A:1042 , PCW A:1046binding site for residue PCW A 1030
30AF3SOFTWAREPCW A:1013 , PCW A:1051 , PCW A:1052binding site for residue PCW A 1031
31AF4SOFTWAREHIS A:278 , GLY A:782 , MET A:874 , PCW A:1024 , PCW A:1040binding site for residue PCW A 1032
32AF5SOFTWARELEU A:781 , THR A:871 , HIS A:872 , PCW A:1024 , PCW A:1036binding site for residue PCW A 1034
33AF6SOFTWARELEU A:273 , ILE A:276 , GLY A:277 , ASN A:280binding site for residue PCW A 1035
34AF7SOFTWAREPCW A:1026 , PCW A:1034 , PCW A:1049binding site for residue PCW A 1036
35AF8SOFTWAREPCW A:1008 , PCW A:1024 , PCW A:1040 , PCW A:1041binding site for residue PCW A 1037
36AF9SOFTWARESER A:830 , GLY A:831 , TRP A:832 , PHE A:835 , PCW A:1012 , PCW A:1039binding site for residue PCW A 1038
37AG1SOFTWARETRP A:288 , PCW A:1038binding site for residue PCW A 1039
38AG2SOFTWAREPCW A:1032 , PCW A:1037 , PCW A:1045binding site for residue PCW A 1040
39AG3SOFTWAREPCW A:1013 , PCW A:1037binding site for residue PCW A 1041
40AG4SOFTWAREPCW A:1030binding site for residue PCW A 1042
41AG5SOFTWAREPCW A:1029binding site for residue PCW A 1043
42AG6SOFTWAREPCW A:1007binding site for residue PCW A 1044
43AG7SOFTWARETYR A:991 , PCW A:1040binding site for residue PCW A 1045
44AG8SOFTWARELEU A:968 , LYS A:972 , PCW A:1023 , PCW A:1030binding site for residue PCW A 1046
45AG9SOFTWAREPHE A:88binding site for residue PCW A 1047
46AH1SOFTWAREPCW A:1020binding site for residue PCW A 1048
47AH2SOFTWAREPCW A:1028 , PCW A:1036binding site for residue PCW A 1049
48AH3SOFTWAREILE A:54 , PCW A:1008 , PCW A:1052binding site for residue PCW A 1050
49AH4SOFTWARETRP A:50 , PCW A:1031binding site for residue PCW A 1051
50AH5SOFTWAREPCW A:1031 , PCW A:1050binding site for residue PCW A 1052

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5XA8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5XA8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5XA8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5XA8)

(-) Exons   (0, 0)

(no "Exon" information available for 5XA8)

(-) 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 ........hhhhhhhhh........hhhhhhhhhhhh...........hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee.......eeee.hhh....eeee........eeeeeee.....eee..........ee...........hhhhh..ee....eeee..eeeeeeehhhhh................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.eee...hhhhhhhhh.eeee...........eeeeeeeeeee....eeeeeeee..........ee......hhhhhhhhhhhhhhhhhh...eeeee....eeeee.hhhhhhhhhhhhhh................hhhhhhhhh.eeeeeeeeee....eeeeeeee...hhhhh..eeeeeehhhhhhhheeeeee..eeee.hhhhhhhhhhhhhhhhhh....eeeeeeee....hhhhh...hhhhhhhhh..eeeeeeeeee....hhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh............eeehhhhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhh....eeeee....hhhhhhhh.eeeee...hhhhhhh..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...................hhhhhhhhhhhhhhhhhhhhhhhhhhhh...............................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5xa8 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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  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 5XA8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5XA8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5XA8)

(-) Gene Ontology  (24, 24)

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  5xa8
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  AT2A1_RABIT | P04191
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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 5xa9 5xaa 5xab

(-) Related Entries Specified in the PDB File

5xa7 5xa9 5xaa 5xab