Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  THE STRUCTURE OF PHOSPHOLAMBAN BOUND TO THE CALCIUM PUMP SERCA1A
 
Authors :  T. D. Hurley
Date :  10 Feb 15  (Deposition) - 25 Feb 15  (Release) - 25 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.51
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Ca-Atpase, Serca1A, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. L. Akin, T. D. Hurley, Z. Chen, L. R. Jones
The Structural Basis For Phospholamban Inhibition Of The Calcium Pump In Sarcoplasmic Reticulum.
J. Biol. Chem. V. 288 30181 2013
PubMed-ID: 23996003  |  Reference-DOI: 10.1074/JBC.M113.501585

(-) Compounds

Molecule 1 - SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1
    Chains: A
    EC Number: 3.6.3.8
    Organ: MUSCLE
    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
    Tissue: SKELETAL MUSCLE
 
Molecule 2 - CARDIAC PHOSPHOLAMBAN
    Chains: B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF21
    Expression System Plasmid: PVL1393
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: PLN
    Organism Common: DOG
    Organism Scientific: CANIS FAMILIARIS
    Organism Taxid: 9615
    Synonym: PLB
 
Molecule 3 - CARDIAC PHOSPHOLAMBAN
    Chains: C
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Gene: PLN
    Organism Common: DOG
    Organism Scientific: CANIS FAMILIARIS
    Organism Taxid: 9615
    Other Details: THIS IS A SECOND COPY OF PHOSPHOLAMBAN BOUND IN THIS STRUCTURE, BUT THE SIDE CHAIN ELECTRON DENSITY IS INSUFFICIENT TO ASSIGN THE CORRECT SEQUENCE REGISTER

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric/Biological Unit (2, 17)
No.NameCountTypeFull Name
1K1Ligand/IonPOTASSIUM ION
2UNK16Mod. Amino Acid

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:711 , LYS A:712 , ALA A:714 , GLU A:732binding site for residue K A 1001

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:876 -A:888

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4Y3U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Y3U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y3U)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y3U)

(-) 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:970
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh..hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.......eeee.hhh....eeeee.......eeeeeee.....eee..........ee..................ee....eeee.eeeeeeeehhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh..eee...hhhhhhhh..eeeee..........eeeeeeeeeeee..eeeeeeeee..........eee..ee.hhhhhhhhhhhhhhhhhh....eee......eee..hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.eeeeeee.......eeeeeeee.......eeeeeehhhhhhhheeeeee..eeee.hhhhhhhhhhhhhhhhhh....eeeeeeee............hhhhhhhhhh.eeeeeeeeee.....hhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhh............eeehhhhhh.hhhhhhhhhhhh.eee....hhhhhhhhhhhhh...eeeee.hhhhhhhhhhh.eeeee...hhhhhhh..eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..hhhhhhhhh....hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh......................hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y3u A   1 MEAAHSKSTEECLAYFGVSETTGLTPDQVKRHLEKYGHNELPAEESLWELVIEQFEDLLVRILLLAACISFVLAWFTAFVEPFVILLILIANAIVGVWQERNAENAIEALKEYEPEMGKVYRADRKSVQRIKARDIVPGDIVEVAVGDKVPADIRILSIKSTTLRVDQSILTGESVSVIKHTEPVPDPRAVNQDKKNMLFSGTNIAAGKALGIVATTGVSTEIGKIRDQMAQDKTPLQQKLDEFGEQLSKVISLICVAVWLINIGHFNDPRGAIYYFKIAVALAVAAIPEGLPAVITTCLALGTRRMAKKNAIVRSLPSVETLGCTSVICSDKTGTLTTNQMSVCKMFIIDKVDGDFCSLNEFSITGSTYAPEGEVLKNDKPIRSGQFDGLVELATICALCNDSSLDFNETKGVYEKVGEATETALTTLVEKMNVFNTEVRNLSKVERANACNSVIRQLMKKEFTLEFSRDRKSMSVYCSPAKSAVGNKMFVKGAPEGVIDRCNYVRVGTTRVPMTGPVKEKILSVIKEWGTGRDTLRCLALATRDTPPKREEMVLDDSSRFMEYETDLTFVGVVGMLDPPRKEVMGSIQLCRDAGIRVIMITGDNKGTAIAICRRIGIFGENEEVADRAYTGREFDDLPLAEQREACRRACCFARVEPSHKSKIVEYLQSYDEITAMTGDGVNDAPALKKAEIGIAMGSGTAVAKTASEMVLADDNFSTIVAAVEEGRAIYNNMKQFIRYLISSNVGEVVCIFLTAALGLPEALIPVQLLWVNLVTDGLPATALGFNPPDLDIMDRPPRSPKEPLISGWLFFRYMAIGGYVGAATVGAAAWWFMYAEDGPGVTYHQLTHFMQCTEDHPHFEGLDCEIFEAPEPMTMALSVLVTIEMCNALNSLSENQSLMRMPPWVNIWLLGSICLSMSLHFLILYVDPLPMIFKLKALDLTQWLMVLKISLPVIGLDEILKFIARNYL 992
                                    10        20        30        40    ||  52        62        72     || 89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239||     252       262       272       282|      299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499   ||  512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982       992
                                                                       45|                            78|                                                                                                                                                       240|                                   282|                                                                                                                                                                                                                  503|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
                                                                        48                             86                                                                                                                                                        244                                    290                                                                                                                                                                                                                   507                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:30
                                                              
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                 4y3u B  21 PQQARQNLQNLFINFCLILICLLLICIIVM  50
                                    30        40        50


Chain C from PDB  Type:PROTEIN  Length:16
                                                
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 4y3u C 101 xxxxxxxxxxxxxxxx 116
                            |||||||110||||||
                          101-UNK||110-UNK||
                           102-UNK||111-UNK|
                            103-UNK||112-UNK
                             104-UNK| 113-UNK
                              105-UNK  114-UNK
                               106-UNK  115-UNK
                                107-UNK  116-UNK
                                 108-UNK    
                                  109-UNK
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4Y3U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y3U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y3U)

(-) Gene Ontology  (52, 59)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

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
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UNK  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4y3u)
 

(-) Still Images

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)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4y3u
    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
  AT2A1_RABIT | P04191
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  PPLA_CANLF | P61012
    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)
  3.6.3.8
    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

(-) Analysis Tools

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
  AT2A1_RABIT | P04191
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PPLA_CANLF | P61012
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 4ycl 4ycm 4ycn 5a3q 5a3r 5a3s 5xa7 5xa8 5xa9 5xaa 5xab
        PPLA_CANLF | P61012: 4kyt

(-) Related Entries Specified in the PDB File

4kyt 4KYT CONTAINED A HIGH-AFFINITY MUTANT OF PHOSPHOLAMBAN. THIS ENTRY CONTAINS THE WILD-TYPE SEQUENCE FOR PHOSPHOLAMBAN