Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE UNLIGANDED FORM OF GRP94, THE ER HSP90: BASIS FOR NUCLEOTIDE-INDUCED CONFORMATIONAL CHANGE, GRP94N(DELTA)41 APO CRYSTAL
 
Authors :  D. E. Dollins, R. M. Immormino, D. T. Gewirth
Date :  09 Feb 05  (Deposition) - 14 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Grp94, Gp96, Hsp90, Bergerat, Chaperone, Endoplasmic Reticulum, Htpg (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. E. Dollins, R. M. Immormino, D. T. Gewirth
Structure Of Unliganded Grp94, The Endoplasmic Reticulum Hsp90: Basis For Nucleotide-Induced Conformational Change
J. Biol. Chem. V. 280 30438 2005
PubMed-ID: 15951571  |  Reference-DOI: 10.1074/JBC.M503761200
(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
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN OF GRP94 RESIDUES (69-337)
    Gene: TRA1
    Mutation: YES
    Organism Common: DOG
    Organism Scientific: CANIS LUPUS FAMILIARIS
    Organism Taxid: 9615
    Other Details: DELETION OF 287-327 REPLACED BY 4 GLYCINES
    Strain: FAMILIARIS
    Synonym: 94 KDA GLUCOSE-REGULATED PROTEIN, GRP94

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2PG411Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
2PG44Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2PG47Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:212 , ARG A:237 , THR A:240 , THR A:248 , HOH A:614 , HOH A:657 , HOH A:682 , HOH A:702BINDING SITE FOR RESIDUE PG4 A 501
02AC2SOFTWARELYS A:137 , HIS A:146 , TRP A:282 , HOH A:603 , HOH A:672 , HOH A:684BINDING SITE FOR RESIDUE PG4 A 502
03AC3SOFTWAREALA A:111 , ASP A:149 , MET A:154 , HOH A:505 , HOH A:595 , HOH A:683BINDING SITE FOR RESIDUE PG4 A 503
04AC4SOFTWAREASP A:110 , LYS A:114 , HOH A:592 , HOH A:594BINDING SITE FOR RESIDUE PG4 A 504
05AC5SOFTWARETHR B:212 , ARG B:237 , THR B:248 , PG4 B:509 , HOH B:621 , HOH B:662 , HOH B:710 , HOH B:804 , HOH B:817BINDING SITE FOR RESIDUE PG4 B 508
06AC6SOFTWARELYS B:137 , THR B:148 , PG4 B:508 , HOH B:667 , HOH B:675 , HOH B:792BINDING SITE FOR RESIDUE PG4 B 509
07AC7SOFTWAREASN B:129 , ASN B:239 , GLY B:242BINDING SITE FOR RESIDUE PG4 B 511
08AC8SOFTWAREASP B:262 , THR B:263 , ASN B:266 , HOH B:712 , HOH B:797 , HOH B:824 , HOH B:833BINDING SITE FOR RESIDUE PG4 B 512
09AC9SOFTWAREASN A:83 , LYS A:87 , ILE A:90 , SER A:227 , ASN B:83 , LYS B:87 , ILE B:90 , SER B:227 , HOH B:670BINDING SITE FOR RESIDUE 1PE B 606
10BC1SOFTWAREASN B:107 , ALA B:111 , ASP B:149 , MET B:154 , HOH B:617BINDING SITE FOR RESIDUE PG4 B 613
11BC2SOFTWAREASP B:110 , LYS B:114 , PG4 B:615BINDING SITE FOR RESIDUE PG4 B 614
12BC3SOFTWARELYS B:114 , PG4 B:614 , HOH B:755BINDING SITE FOR RESIDUE PG4 B 615

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1YT1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1YT1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1YT1)

(-) PROSITE Motifs  (1, 2)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YT1)

(-) Sequences/Alignments

Asymmetric 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:227
 aligned with ENPL_CANLF | P41148 from UniProtKB/Swiss-Prot  Length:804

    Alignment length:297
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       
           ENPL_CANLF    41 GSRTDDEVVQREEEAIQLDGLNASQIRELREKSEKFAFQAEVNRMMKLIINSLYKNKEIFLRELISNASDALDKIRLISLTDENALAGNEELTVKIKCDKEKNLLHVTDTGVGMTREELVKNLGTIAKSGTSEFLNKMTEAQEDGQSTSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLELDTIKNLVKKYSQFINFPIYVWSSKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKTVWDWELMN 337
               SCOP domains d1                        yt1a_ A: HSP90                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1y                        t1A00 A:65-337  [code=3.30.565.10, no name defined]                                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..------------------------........ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeeee....eeeeee.....hhhhhhhhhhh.---hhhhhhhhhhhh..--..hhhhhhhhhhhhhhhhh.eeeeeeeee......eeeee....eeeee.........eeeeeeee.hhhhhhhhhhhhhhhhhhhhh.....eeeeeee.-----------------------------------------..eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------HSP90     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yt1 A  65 GS------------------------HMLREKSEKFAFQAEVNRMMKLIINSLYKNKEIFLRELISNASDALDKIRLISLTDENALAGNEELTVKIKCDKEKNLLHVTDTGVGMTREELVKNLGTI---GTSEFLNKMTEAQE--QSTSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLELDTIKNLVKKYSQFINFPIYVWSSKT-----------------------------------------KTVWDWELMN 337
                             |       -         -      | 70        80        90       100       110       120       130       140       150       160     | 170       180  |  | 190       200       210       220       230       240       250       260       270       280     |   -         -         -         -       330       
                             |                       67                                                                                                166 170          183  |                                                                                                 286                                       328         
                            66                                                                                                                                             186                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:232
 aligned with ENPL_CANLF | P41148 from UniProtKB/Swiss-Prot  Length:804

    Alignment length:297
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       
           ENPL_CANLF    41 GSRTDDEVVQREEEAIQLDGLNASQIRELREKSEKFAFQAEVNRMMKLIINSLYKNKEIFLRELISNASDALDKIRLISLTDENALAGNEELTVKIKCDKEKNLLHVTDTGVGMTREELVKNLGTIAKSGTSEFLNKMTEAQEDGQSTSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLELDTIKNLVKKYSQFINFPIYVWSSKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKTVWDWELMN 337
               SCOP domains d1                        yt1b_ B: HSP90                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1y                        t1B00 B:65-337  [code=3.30.565.10, no name defined]                                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .h------------------------hhhhhh..ee..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh...........eeeeee....eeeeee.....hhhhhhhhhhh....hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.eeeeeeeee......eeeee....eeeee.........eeeeeeee.hhhhhhhhhhhhhhhhhhhhh.....eeeeeee.-----------------------------------------..eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------HSP90     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yt1 B  65 GS------------------------HMLREKSEKFAFQAEVNRMMKLIINSLYKNKEIFLRELISNASDALDKIRLISLTDENALAGNEELTVKIKCDKEKNLLHVTDTGVGMTREELVKNLGTIAKSGTSEFLNKMTEAQEDGQSTSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLELDTIKNLVKKYSQFINFPIYVWSSKT-----------------------------------------KTVWDWELMN 337
                             |       -         -      | 70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280     |   -         -         -         -       330       
                            66                       67                                                                                                                                                                                                                        286                                       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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1YT1)

(-) Gene Ontology  (10, 10)

Asymmetric 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 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
    1PE  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1yt1)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  1yt1
    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 1tbw 1tc0 1tc6 1u0y 1u0z 1u2o 1ysz 1yt0 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
1tbw LIGAND INDUCED CONFORMATIONAL SHIFT IN THE N-TERMINAL DOMAIN OF GRP94, OPEN CONFORMATION
1tc0 LIGAND INDUCED CONFORMATIONAL SHIFT 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
1u2o CRYSTAL STRUCTURE OF THE N-DOMAIN OF GRP94 LACKING THE CHARGED DOMAIN IN COMPLEX WITH NECA
1ysz
1yt0
1yt2