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

(-) Description

Title :  CRYSTAL STRUCTURE OF RABBIT RYANODINE RECEPTOR 1 (RESIDUES 1-536) DISEASE MUTANT R402G
 
Authors :  L. Kimlicka, F. Van Petegem
Date :  25 Nov 12  (Deposition) - 20 Feb 13  (Release) - 06 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Calcium Channel, Sr/Er Membrane, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Kimlicka, K. Lau, C. C. Tung, F. Van Petegem
Disease Mutations In The Ryanodine Receptor N-Terminal Region Couple To A Mobile Intersubunit Interface.
Nat Commun V. 4 1506 2013
PubMed-ID: 23422674  |  Reference-DOI: 10.1038/NCOMMS2501

(-) Compounds

Molecule 1 - RYANODINE RECEPTOR 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA
    Expression System Taxid: 511693
    Fragment: N-TERMINAL DISEASE HOT SPOT, RESIDUES 1-536
    Gene: RYR1
    Mutation: YES
    Organism Common: RABBIT
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
    Synonym: RYR-1, RYR1, SKELETAL MUSCLE CALCIUM RELEASE CHANNEL, SKELETAL MUSCLE RYANODINE RECEPTOR, SKELETAL MUSCLE-TYPE RYANODINE RECEPTOR, TYPE 1 RYANODINE RECEPTOR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4I37)

(-) Sites  (0, 0)

(no "Site" information available for 4I37)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I37)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4I37)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I37)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I37)

(-) Exons   (0, 0)

(no "Exon" information available for 4I37)

(-) 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:466
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeee..eeeeeeee.........eeee...............eeeeeeehhhhhhhhhhh.........eeeeee.....eeeee......eeeeee........eeeeee...............eeeeee.....eeeee..eeeee.....eeeeeee............eeeeee..eeeee...........eeeehhhhhhhhhh.eeeee...............eeeee.....eeeee...eeeeehhhhhhhhhhheeee.......................eeeeee.....eeee...eeeeee........eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i37 A  10 EVQFLRTDDEVVLQCSATVLKEQLKLCLAAEGFGNRLCFLEPTSNAQNVPPDLAICCFTLEQSLSVRALQEMLANGHRTLLYGHAILLRHAHSRMYLSCLTTSRSAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVGDDLILVSVSSERYLHLSTLQVDASFMQTLWNMNPICSCCEEGYVTGGHVLRLFHGDECLTISAADSDDQRRLVYYEGGAVCTHARSLWRLEPLRISWSGSHLRWGQPLRIRHVTTGRYLALTEDQGLVVVDACKAHTKATSFCFRVSKEKLKRDVEGMGPPEIKYGESLCFVQHVASGLWLTYAAKKKAILHQEGHMDDALFLTRCQQEESQAAGMIHSTAGLYNQFIKGLDSFSALPIEAVILSLQDLIGYFEPPSEELQHEEKQSKLRSLRNRQSLFQEEGMLSLVLNCIDRLNVYTTAAHFAAESWKEIVNLLYELLASLIRG 532
                                    19        29        39        49        59        69        79    || 101       111       121    || 136       146       156       166       176       190       200       210       220    || 232       242       252       262       272       282       292       302       312       322||     336       346       356    || 377       387       397       407       417    || 439       449       459       469       479       489       499    || 516       526      
                                                                                                     84|                          126|                                                 184|                                 225|                                                                                            323|                              361|                                              422|                                                                  504|                    
                                                                                                      97                           132                                                  189                                  228                                                                                             328                               373                                               435                                                                   512
   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 4I37)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I37)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I37)

(-) Gene Ontology  (30, 30)

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
(no "Ligands, Modified Residues, Ions" information available for 4i37)
 
  Sites
(no "Sites" information available for 4i37)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4i37)
 

(-) 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 ](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
  4i37
    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
  RYR1_RABIT | P11716
    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)
  (no 'Enzyme Classificator' available)
    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
  RYR1_RABIT | P11716
    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
        RYR1_RABIT | P11716: 2bcx 2xoa 3hsm 3ila 3j8h 3rqr 4ert 4esu 4ett 4etu 4i0y 4i1e 4i2s 4i3n 4i6i 4i7i 4i8m 4i96 4p9j 4uwa 4uwe 5c30 5gky 5gkz 5gl0 5gl1 5j8v 5t15 5t9m 5t9n 5t9r 5t9s 5t9v 5ta3 5tal 5tam 5tan 5tap 5taq 5tas 5tat 5tau 5tav 5taw 5tax 5tay 5taz 5tb0 5tb1 5tb2 5tb3 5tb4

(-) Related Entries Specified in the PDB File

2xoa CRYSTAL STRUCTURE OF THE N-TERMINAL THREE DOMAINS OF THE SKELETAL MUSCLE RYANODINE
4i0y CRYSTAL STRUCTURE OF RABBIT RYANODINE RECEPTOR 1 (RESIDUES 1-536) MUTANT C36R
4i1e CRYSTAL STRUCTURE OF RABBIT RYANODINE RECEPTOR 1 (RESIDUES 1-536) MUTANT G249R
4i2s CRYSTAL STRUCTURE OF RABBIT RYANODINE RECEPTOR 1 (RESIDUES 1-536) MUTANT I404M
4i3n CRYSTAL STRUCTURE OF RABBIT RYANODINE RECEPTOR 1 (RESIDUES 1-536) MUTANT D61N
4i6i CRYSTAL STRUCTURE OF RABBIT RYANODINE RECEPTOR 1 (RESIDUES 1-536) MUTANT R45C
4i7i CRYSTAL STRUCTURE OF RABBIT RYANODINE RECEPTOR 1 (RESIDUES 1-536) MUTANT L14R
4i8m CRYSTAL STRUCTURE OF RABBIT RYANODINE RECEPTOR 1 (RESIDUES 1-536) MUTANT V219I
4i96 CRYSTAL STRUCTURE OF RABBIT RYANODINE RECEPTOR 1 (RESIDUES 217-536)