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 :  LIGAND INDUCED CONFORMATIONAL SHIFT IN THE N-TERMINAL DOMAIN OF GRP94, OPEN CONFORMATION
 
Authors :  D. T. Gewirth, R. M. Immormino, D. E. Dollins, P. L. Shaffer, M. A. Walker, K. L. Soldano
Date :  20 May 04  (Deposition) - 24 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Grp94, Hsp90, Amp, Bergrat, Chaperone, Endoplasmic Reticulum (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. M. Immormino, D. E. Dollins, P. L. Shaffer, K. L. Soldano, M. A. Walker, D. T. Gewirth
Ligand-Induced Conformational Shift In The N-Terminal Domain Of Grp94, An Hsp90 Chaperone.
J. Biol. Chem. V. 279 46162 2004
PubMed-ID: 15292259  |  Reference-DOI: 10.1074/JBC.M405253200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ENDOPLASMIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX-NB-GRP94 (69-337DELTA41)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN OF GRP94 RESIDUES 69-337, 287- 327 DELETED AND REPLACED WITH 4 GLYCINES
    Gene: TRA1
    Organism Common: DOG
    Organism Scientific: CANIS LUPUS FAMILIARIS
    Organism Taxid: 9615
    Strain: FAMILIARIS
    Synonym: 94 KDA GLUCOSE-REGULATED PROTEIN, GRP94

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3PG45Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:107 , AMP A:301 , HOH A:502 , HOH A:519 , HOH A:522 , HOH A:526BINDING SITE FOR RESIDUE MG A 501
2AC2SOFTWAREASN B:107 , AMP B:601 , HOH B:819 , HOH B:826 , HOH B:847 , HOH B:882BINDING SITE FOR RESIDUE MG B 802
3AC3SOFTWAREASN A:107 , ALA A:111 , ASP A:149 , MET A:154 , ASN A:162 , LEU A:163 , GLY A:198 , PHE A:199 , THR A:245 , MG A:501 , HOH A:502 , HOH A:503 , HOH A:504 , HOH A:536 , HOH A:549 , HOH A:628BINDING SITE FOR RESIDUE AMP A 301
4AC4SOFTWARETHR A:212 , ARG A:237 , THR A:240 , PG4 A:403 , HOH A:589BINDING SITE FOR RESIDUE PG4 A 401
5AC5SOFTWARETHR B:212 , ARG B:237 , HOH B:838BINDING SITE FOR RESIDUE PG4 B 402
6AC6SOFTWARETHR A:148 , LEU A:241 , THR A:246 , PG4 A:401 , HOH A:566BINDING SITE FOR RESIDUE PG4 A 403
7AC7SOFTWAREASN B:107 , ALA B:111 , ASP B:149 , MET B:154 , ASN B:162 , LEU B:163 , GLY B:198 , PHE B:199 , THR B:245 , MG B:802 , HOH B:806 , HOH B:810 , HOH B:826 , HOH B:847 , HOH B:890BINDING SITE FOR RESIDUE AMP B 601
8AC8SOFTWARELYS B:137 , TRP B:282 , TRP B:333BINDING SITE FOR RESIDUE PG4 B 701
9AC9SOFTWARELYS B:137BINDING SITE FOR RESIDUE PG4 B 702

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TBW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TBW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TBW)

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HSP90PS00298 Heat shock hsp90 proteins family signature.ENPL_CANLF94-103
 		  2A:94-103
B:94-103

(-) Exons   (0, 0)

(no "Exon" information available for 1TBW)

(-) 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:222
 aligned with ENPL_CANLF | P41148 from UniProtKB/Swiss-Prot  Length:804

    Alignment length:262
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335  
           ENPL_CANLF    76 FAFQAEVNRMMKLIINSLYKNKEIFLRELISNASDALDKIRLISLTDENALAGNEELTVKIKCDKEKNLLHVTDTGVGMTREELVKNLGTIAKSGTSEFLNKMTEAQEDGQSTSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLELDTIKNLVKKYSQFINFPIYVWSSKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKTVWDWELMN 337
               SCOP domains d1tbwa_ A: HSP90                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1tbwA00 A:76-337  [code=3.30.565.10, no name defined]                                                                                                                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee....eeeeee.....hhhhhhhhh......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.eeeeeeeee......eeeee....eeeee.........eeeeeeee.hhhhhhhhhhhhhhhhhhhh......eeeeeee.---.-------------------------------------..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------HSP90     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tbw A  76 FAFQAEVNRMMKLIINSLYKNKEIFLRELISNASDALDKIRLISLTDENALAGNEELTVKIKCDKEKNLLHVTDTGVGMTREELVKNLGTIAKSGTSEFLNKMTEAQEDGQSTSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLELDTIKNLVKKYSQFINFPIYVWSSKT---G-------------------------------------KTVWDWELMN 337
                                    85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285|   |    -         -         -         -  |    335  
                                                                                                                                                                                                                                            286 290                                   328         


Chain B from PDB  Type:PROTEIN  Length:195
 aligned with ENPL_CANLF | P41148 from UniProtKB/Swiss-Prot  Length:804

    Alignment length:259
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328         
           ENPL_CANLF    79 QAEVNRMMKLIINSLYKNKEIFLRELISNASDALDKIRLISLTDENALAGNEELTVKIKCDKEKNLLHVTDTGVGMTREELVKNLGTIAKSGTSEFLNKMTEAQEDGQSTSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLELDTIKNLVKKYSQFINFPIYVWSSKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKTVWDWELMN 337
               SCOP domains d1tbwb_ B: HSP90                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1tbwB00 B:79-337  [code=3.30.565.10, no name defined]                                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.............eeeeee....eeeeee.....hhhhhhhhh-----------------------hhhhhhhhhh.hhhhhhh.eeeeeeeee......eeeee....eeeee.........eeeeeeee.hhhhhhhhhhhhhhhhhhh.......eeeeeee----.-------------------------------------..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------HSP90     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tbw B  79 QAEVNRMMKLIINSLYKNKEIFLRELISNASDALDKIRLISLTDENALAGNEELTVKIKCDKEKNLLHVTDTGVGMTREELVKNL-----------------------STSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLELDTIKNLVKKYSQFINFPIYVWSSK----G-------------------------------------KTVWDWELMN 337
                                    88        98       108       118       128       138       148       158    |    -         -       188       198       208       218       228       238       248       258       268       278      |  - |       -         -         -       328         
                                                                                                              163                     187                                                                                               285  290                                   328
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1TBW)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (ENPL_CANLF | P41148)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    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:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
biological process
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0006950    response to stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
    GO:0030433    ubiquitin-dependent ERAD pathway    The series of steps necessary to target endoplasmic reticulum (ER)-resident proteins for degradation by the cytoplasmic proteasome. Begins with recognition of the ER-resident protein, includes retrotranslocation (dislocation) of the protein from the ER to the cytosol, protein ubiquitination necessary for correct substrate transfer, transport of the protein to the proteasome, and ends with degradation of the protein by the cytoplasmic proteasome.
cellular component
    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:0005788    endoplasmic reticulum lumen    The volume enclosed by the membranes of the endoplasmic reticulum.
    GO:0042470    melanosome    A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
    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.

 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
    AMP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1tbw)
 

(-) 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
  1tbw
    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
  ENPL_CANLF | P41148
    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
  ENPL_CANLF | P41148
    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
        ENPL_CANLF | P41148: 1qy5 1qy8 1qye 1tc0 1tc6 1u0y 1u0z 1u2o 1ysz 1yt0 1yt1 1yt2 2esa 2exl 2fyp 2gfd 2gqp 2h8m 2hch 2hg1 2o1t 2o1u 2o1v 2o1w 3o2f 5in9

(-) Related Entries Specified in the PDB File

1qy5 CRYSTAL STRUCTURE OF THE N-DOMAIN OF THE ER HSP90 CHAPERONE GRP94 IN COMPLEX WITH THE SPECIFIC LIGAND NECA
1qy8 CRYSTAL STRUCTURE OF THE N-DOMAIN OF THE ER HSP90 CHAPERONE GRP94 IN COMPLEX WITH RADICICOL
1qye CRYSTAL STRUCTURE OF THE N-DOMAIN OF THE ER HSP90 CHAPERONE GRP94 IN COMPLEX WITH RADICICOL
1qyh CRYSTAL STRUCTURE OF THE N-DOMAIN OF GRP94 LACKING THE CHARGED DOMAIN IN COMPLEX WITH NECA
1tc0 LIGAND INDUCED CONFORMATIONAL SHIFTS IN THE N-TERMINAL DOMAIN OF GRP94. OPEN CONFORMATION COMPLEXED WITH THE PHYSIOLOGICAL PARTNER ATP.
1tc6 LIGAND INDUCED CONFORMATIONAL SHIFT IN THE N-TERMINAL DOMAIN OF GRP94. OPEN CONFORMATION ADP-COMPLEX.