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(-) Description

Title :  N-DOMAIN OF GRP94 IN COMPLEX WITH THE 2-IODO-NECA
 
Authors :  R. M. Immormino, D. T. Gewirth
Date :  07 Jun 06  (Deposition) - 24 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Grp94, Hsp82, Hsp90, Htpg, Chaperone, Ligand, Neca, Npca, Adenosine (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. M. Immormino, D. T. Gewirth
N-Domain Of Grp94 In Complex With The 2-Iodo-Neca
To Be Published
PubMed: search
(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: HSP90B1, TRA1
    Mutation: YES
    Organism Common: DOG
    Organism Scientific: CANIS LUPUS FAMILIARIS
    Organism Taxid: 9615
    Strain: FAMILIARIS
    Synonym: HEAT SHOCK PROTEIN 90 KDA BETA MEMBER 1, 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  (3, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2NEI2Ligand/Ion(2S,3S,4R,5R)-5-(6-AMINO-2-IODO-9H-PURIN-9-YL)-N-ETHYL-3,4-DIHYDROXYTETRAHYDROFURAN-2-CARBOXAMIDE
3PG49Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
2NEI1Ligand/Ion(2S,3S,4R,5R)-5-(6-AMINO-2-IODO-9H-PURIN-9-YL)-N-ETHYL-3,4-DIHYDROXYTETRAHYDROFURAN-2-CARBOXAMIDE
3PG45Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
11PE2Ligand/IonPENTAETHYLENE GLYCOL
2NEI1Ligand/Ion(2S,3S,4R,5R)-5-(6-AMINO-2-IODO-9H-PURIN-9-YL)-N-ETHYL-3,4-DIHYDROXYTETRAHYDROFURAN-2-CARBOXAMIDE
3PG44Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:111 , ASP A:149 , VAL A:152 , GLY A:153 , MET A:154 , ASN A:162 , LEU A:163 , PHE A:199 , HOH A:522 , HOH A:524 , HOH A:631 , HOH A:689BINDING SITE FOR RESIDUE NEI A 401
02AC2SOFTWAREALA B:111 , ASP B:149 , VAL B:152 , GLY B:153 , MET B:154 , ASN B:162 , LEU B:163 , PHE B:199 , HOH B:604 , HOH B:605 , HOH B:607 , HOH B:608 , HOH B:693 , HOH B:699BINDING SITE FOR RESIDUE NEI B 402
03AC3SOFTWARETHR B:212 , ARG B:237 , HOH B:675 , HOH B:720BINDING SITE FOR RESIDUE PG4 B 501
04AC4SOFTWARELYS B:137 , HIS B:146 , THR B:148 , LEU B:241 , HOH B:708BINDING SITE FOR RESIDUE PG4 B 502
05AC5SOFTWARETHR A:212 , ARG A:237 , THR A:240 , THR A:248 , HOH A:534 , HOH A:554 , HOH A:585 , HOH A:651 , HOH A:686BINDING SITE FOR RESIDUE PG4 A 504
06AC6SOFTWARELYS A:137 , HIS A:146 , TRP A:282 , HOH A:590 , HOH A:597BINDING SITE FOR RESIDUE PG4 A 505
07AC7SOFTWAREASN A:162 , HOH A:668BINDING SITE FOR RESIDUE PG4 A 506
08AC8SOFTWAREASP A:110 , ASP A:113 , LYS A:114 , LEU A:117BINDING SITE FOR RESIDUE PG4 A 507
09AC9SOFTWAREASN B:107 , ALA B:108 , ASP B:149BINDING SITE FOR RESIDUE PG4 B 508
10BC1SOFTWAREASP B:110 , LYS B:114 , LEU B:117 , HOH B:711BINDING SITE FOR RESIDUE PG4 B 509
11BC2SOFTWARETHR A:263 , ASN A:266BINDING SITE FOR RESIDUE PG4 A 510
12BC3SOFTWAREASN A:83 , LYS A:87 , ILE A:90 , SER A:227 , ASN B:83 , LYS B:87 , ILE B:90 , SER B:227BINDING SITE FOR RESIDUE 1PE B 601
13BC4SOFTWARELYS A:75 , ALA A:77 , PHE A:78 , LYS B:75 , PHE B:76 , ALA B:77 , HOH B:724BINDING SITE FOR RESIDUE 1PE B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2H8M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2H8M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H8M)

(-) 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 2H8M)

(-) 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:215
 aligned with ENPL_CANLF | P41148 from UniProtKB/Swiss-Prot  Length:804

    Alignment length:264
                                    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333    
           ENPL_CANLF    74 EKFAFQAEVNRMMKLIINSLYKNKEIFLRELISNASDALDKIRLISLTDENALAGNEELTVKIKCDKEKNLLHVTDTGVGMTREELVKNLGTIAKSGTSEFLNKMTEAQEDGQSTSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLELDTIKNLVKKYSQFINFPIYVWSSKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKTVWDWELMN 337
               SCOP domains d2h8ma_ A: HSP90                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2h8mA00 A:74-337  [code=3.30.565.10, no name defined]                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...........eeeeeehhh.eeeeee.....hhhhhhhhhhh.---hhhhhhhhhhhhh-----hhhhhhhhhhhhhhhhh.eeeeeeeee......eeeee....eeeee.........eeeeeeee.hhhhhhhhhhhhhhhhhhhhh.....eeeeeee.-----------------------------------------..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------HSP90     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2h8m A  74 EKFAFQAEVNRMMKLIINSLYKNKEIFLRELISNASDALDKIRLISLTDENALAGNEELTVKIKCDKEKNLLHVTDTGVGMTREELVKNLGTI---GTSEFLNKMTEAQ-----TSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLELDTIKNLVKKYSQFINFPIYVWSSKT-----------------------------------------KTVWDWELMN 337
                                    83        93       103       113       123       133       143       153       163  |   |173        |-    |  193       203       213       223       233       243       253       263       273       283  |      -         -         -         -    |  333    
                                                                                                                      166 170         182   188                                                                                               286                                       328         


Chain B from PDB  Type:PROTEIN  Length:210
 aligned with ENPL_CANLF | P41148 from UniProtKB/Swiss-Prot  Length:804

    Alignment length:264
                                    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333    
           ENPL_CANLF    74 EKFAFQAEVNRMMKLIINSLYKNKEIFLRELISNASDALDKIRLISLTDENALAGNEELTVKIKCDKEKNLLHVTDTGVGMTREELVKNLGTIAKSGTSEFLNKMTEAQEDGQSTSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLELDTIKNLVKKYSQFINFPIYVWSSKTETVEEPMEEEEAAKEEKEDSDDEAAVEEEEEEKKPKTKKVEKTVWDWELMN 337
               SCOP domains d2h8mb_ B: HSP90                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 2h8mB00 B:74-337  [code=3.30.565.10, no name defined]                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh...........eeeeee....eeeeee.....hhhhhhhhhhh.------hhhhhhhh-------hhhhhhhhhhhhhhhhh.eeeeeeeee......eeeee....eeeee.........eeeeeeee.hhhhhhhhhhhhhhhhhhhh......eeeeeee.-----------------------------------------..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------HSP90     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2h8m B  74 EKFAFQAEVNRMMKLIINSLYKNKEIFLRELISNASDALDKIRLISLTDENALAGNEELTVKIKCDKEKNLLHVTDTGVGMTREELVKNLGTI------EFLNKMTE-------TSELIGQFGVGFYSAFLVADKVIVTSKHNNDTQHIWESDSNEFSVIADPRGNTLGRGTTITLVLKEEASDYLELDTIKNLVKKYSQFINFPIYVWSSKT-----------------------------------------KTVWDWELMN 337
                                    83        93       103       113       123       133       143       153       163  |    173      |  -    |  193       203       213       223       233       243       253       263       273       283  |      -         -         -         -    |  333    
                                                                                                                      166    173    180     188                                                                                               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 2H8M)

(-) 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.

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  2h8m
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  ENPL_CANLF | P41148
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 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 1yt1 1yt2 2esa 2exl 2fyp 2gfd 2gqp 2hch 2hg1 2o1t 2o1u 2o1v 2o1w 3o2f 5in9

(-) Related Entries Specified in the PDB File

1u0y N-DOMAIN OF GRP94, LACKING THE CHARGED DOMAIN, IN COMPLEX WITH THE NOVEL LIGAND N-PROPYL CARBOXYAMIDO ADENOSINE
1u2o CRYSTAL STRUCTURE OF THE N-DOMAIN OF GRP94 LACKING THE CHARGED DOMAIN IN COMPLEX WITH NECA
1yt1 CRYSTAL STRUCTURE OF THE UNLIGANDED FORM OF GRP94, THE ER HSP90: BASIS FOR NUCLEOTIDE-INDUCED CONFORMATIONAL CHANGE, GRP94N(DELTA)41 APO CRYSTAL