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(-) Description

Title :  CRYSTAL STRUCTURE OF MITOCHONDRIAL HSP90 (TRAP1) WITH AMPPNP
 
Authors :  J. R. Partridge, L. A. Lavery, D. A. Agard
Date :  09 Jan 13  (Deposition) - 22 Jan 14  (Release) - 27 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.29
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Chaperone, Atpase, Atp Binding, Mitochondria (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. A. Lavery, J. R. Partridge, T. A. Ramelot, D. Elnatan, M. A. Kennedy, D. A. Agard
Structural Asymmetry In The Closed State Of Mitochondrial Hsp90 (Trap1) Supports A Two-Step Atp Hydrolysis Mechanism.
Mol. Cell V. 53 330 2014
PubMed-ID: 24462206  |  Reference-DOI: 10.1016/J.MOLCEL.2013.12.023

(-) Compounds

Molecule 1 - TNF RECEPTOR-ASSOCIATED PROTEIN 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET151/D-TOPO
    Expression System Strain: BL21(DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TRAP1
    Organism Common: LEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955
    Synonym: TRAP1 PROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2CO4Ligand/IonCOBALT (II) ION
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:130 , ASN A:134 , ALA A:138 , ASP A:173 , MET A:178 , ASN A:186 , SER A:193 , GLY A:194 , SER A:195 , GLY A:214 , GLN A:215 , PHE A:216 , GLY A:217 , VAL A:218 , GLY A:219 , PHE A:220 , THR A:266 , ARG A:417 , MG A:802 , HOH A:902 , HOH A:905 , HOH A:907 , HOH A:910 , HOH A:911 , HOH A:912 , HOH A:935 , HOH A:948 , HOH A:956 , HOH A:958 , HOH A:1006BINDING SITE FOR RESIDUE ANP A 801
2AC2SOFTWAREASN A:134 , ANP A:801 , HOH A:956 , HOH A:958BINDING SITE FOR RESIDUE MG A 802
3AC3SOFTWAREASP A:92 , ASN A:95BINDING SITE FOR RESIDUE CO A 803
4AC4SOFTWARELEU A:202 , ASN A:204 , HOH A:990BINDING SITE FOR RESIDUE CO A 804
5AC5SOFTWAREGLU B:130 , ASN B:134 , ALA B:138 , ASP B:173 , MET B:178 , ASN B:186 , LEU B:187 , SER B:193 , GLY B:194 , SER B:195 , GLY B:214 , GLN B:215 , PHE B:216 , GLY B:217 , VAL B:218 , GLY B:219 , PHE B:220 , THR B:266 , ARG B:417 , MG B:803 , HOH B:901 , HOH B:905 , HOH B:908 , HOH B:933 , HOH B:968 , HOH B:1015 , HOH B:1027 , HOH B:1029BINDING SITE FOR RESIDUE ANP B 802
6AC6SOFTWAREASN B:134 , ANP B:802 , HOH B:968 , HOH B:1027BINDING SITE FOR RESIDUE MG B 803
7AC7SOFTWAREHOH B:1007BINDING SITE FOR RESIDUE CO B 804

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:516 -A:542

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ser A:260 -Gly A:261
2Ala A:350 -Pro A:351
3Ile B:147 -Thr B:148
4Leu B:199 -Asp B:200
5Ala B:237 -Glu B:238
6Glu B:238 -Ala B:239
7Asp B:240 -Ala B:241
8Ala B:350 -Pro B:351

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IPE)

(-) 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:588
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeeeeeeee.eehhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee....eeeeee.....hhhhhhhhhhee..hhhhhhhhh.....hhhhhh.....hhhhhhhhheeeeeeeee.....eeeeee....eeeeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhhhh......eee..ee.....hhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeeeee..........eeeee..eeee.......hhhhh..eeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..ee.........hhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhhhh....eee...hhhhhhhhhhee..eeeee......hhhhhhhhhhhhhh......eee.......eeee..hhhhhhhhhh...eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ipe A  85 TLHNIITDTENVQGSFSKHEFQAETKKLLDIVARSLYSEKEVFIRELISNGSDALEKLRHRMITAGGDAPMEIHLQTDSVKGTFTIQDTGVGMNKEDLVSNLGTIARSGSKAFLDALQNQAEASSSIIGQFGVGFYSAFMVADKVEVYSQSAEAPGYKWSSDGSGVFEVAEASGVRQGTKIVLHLKDDCKEFSSEDRVKEVVTKYSNFVSFPIFLNGRRLNTLQALWMMEPKDISEWQHEEFYRYVAQAYDKPRYTLHYRADAPLNIRSIFYVPEMKPSMFDSSVALYSRKILIQTKATDILPKWLRFLRGVVDSEDIPLNLSRELLQESALIRKLRDVLQQRVIRFLLDQSKKDPEKYARFFEDYGLFMREGIVTTGEQSVKEDIAKLLRFESSALPAGQQTSLMEYSSRMKAGTRNIYYLCAPNRHLAEHSPYFEAMKQKDMEVLFCFEQFDELTLLHLREFDRKKLISAERLSSEQAEDLLAWMRNALVQRVTNIKVTPLDTHPAMITVLEMGAARHFLRLQPTLEINTGHDLIKKLHALKDSNPELAQLLLEQIYDNAMIAAGLNEDPRPMISRLNQLLTRALE 717
                                    94       104       114       124       134       144       155       165       175       185       195       205       215       225       235   ||  247       257       267       277       287       297       307       317       327       337       347       357       367 ||    383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563  ||   594       604       614 ||    625       635  ||   659       669       679       689       699       709        
                                                                                             152|                                                                                  239|                                                                                                                            369|                                                                                                                                                                                           566|                         616|                 638|                                                                
                                                                                              154                                                                                   242                                                                                                                             376                                                                                                                                                                                            588                          618                  653                                                                


Chain B from PDB  Type:PROTEIN  Length:601
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeeee.eehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......eeeeee....eeeeee.....hhhhhhhhhhee..hhhhhh...........hhhhhhhh.eeeeeeeee.......eeeeee....eeeeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhhhh......eee..ee.....hhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee.....eeeeeeee....hhhhhhh.eeeee..eee....hhhhh..eeeee................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh....ee.........hhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhee..eeeeehhhhhhhhhh.........hhhhh.hhhhhhhhhhhhhhhh.....eeee........eeee..hhhhhhhhhh.....eeee...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ipe B  85 TLHNIITDTENVQGSFSKHEFQAETKKLLDIVARSLYSEKEVFIRELISNGSDALEKLRHRMITTAPMEIHLQTDSVKGTFTIQDTGVGMNKEDLVSNLGTIARSGSKAFLDSSSIIGQFGVGFYSAFMVADKVEVYSQSAEADAPGYKWSSDGSGVFEVAEASGVRQGTKIVLHLKDDCKEFSSEDRVKEVVTKYSNFVSFPIFLNGRRLNTLQALWMMEPKDISEWQHEEFYRYVAQAYDKPRYTLHYRADAPLNIRSIFYVPEMKPSMFDVSRSVALYSRKILIQDILPKWLRFLRGVVDSEDIPLNLSRELLQESALIRKLRDVLQQRVIRFLLDQSKKDPEKYARFFEDYGLFMREGIVTTGEQSVKEDIAKLLRFESSALPAGQQTSLMEYSSRMKAGTRNIYYLCAPNRHLAEHSPYFEAMKQKDMEVLFCFEQFDELTLLHLREFDRKKLISAETDIVVDHYKEEKFQDSKPASERLSSEQAEDLLAWMRNALVQRVTNIKVTPRLDTHPAMITVLEMGAARHFLRTILQPTLEINTGHDLIKKLHALKDSNPELAQLLLEQIYDNAMIAAGLNEDPRPMISRLNQLLTRALE 717
                                    94       104       114       124       134       144   ||  158       168       178       188       198 ||    216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366     ||380       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634    || 656       666       676       686       696       706       716 
                                                                                         148|                                            200|                                                                                                                                                                372|        388|                                                                                                                                                                                                                                                   639|                                                                 
                                                                                          153                                             209                                                                                                                                                                 377         393                                                                                                                                                                                                                                                    652
   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 4IPE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:350 - Pro A:351   [ RasMol ]  
    Ala B:237 - Glu B:238   [ RasMol ]  
    Ala B:350 - Pro B:351   [ RasMol ]  
    Asp B:240 - Ala B:241   [ RasMol ]  
    Glu B:238 - Ala B:239   [ RasMol ]  
    Ile B:147 - Thr B:148   [ RasMol ]  
    Leu B:199 - Asp B:200   [ RasMol ]  
    Ser A:260 - Gly A:261   [ RasMol ]  
 

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        A8WFV1_DANRE | A8WFV1: 4ivg 4iyn 4j0b

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