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(-) Description

Title :  STRUCTURE OF MITOCHONDRIAL HSP90 (TRAP1) WITH ADP-BEF3
 
Authors :  J. R. Partridge, L. A. Lavery, D. A. Agard
Date :  30 Jan 13  (Deposition) - 22 Jan 14  (Release) - 27 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Chaperone, Atpase, Atp Binding, Mitochondria, Atpase Chaperone (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
    Fragment: UNP RESIDUES 73-719
    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  (4, 10)

Asymmetric/Biological Unit (4, 10)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2BEF2Ligand/IonBERYLLIUM TRIFLUORIDE ION
3CO4Ligand/IonCOBALT (II) ION
4MG2Ligand/IonMAGNESIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:95BINDING SITE FOR RESIDUE CO A 801
2AC2SOFTWARELEU A:202 , ASN A:204BINDING SITE FOR RESIDUE CO A 802
3AC3SOFTWAREASN A:134 , ALA A:138 , LYS A:141 , 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 , BEF A:804 , MG A:805 , HOH A:902 , HOH A:905 , HOH A:910 , HOH A:917 , HOH A:923 , HOH A:966 , HOH A:972BINDING SITE FOR RESIDUE ADP A 803
4AC4SOFTWAREGLU A:130 , GLY A:214 , GLN A:215 , PHE A:216 , GLY A:217 , VAL A:218 , GLY A:219 , ARG A:417 , ADP A:803 , MG A:805 , HOH A:917 , HOH A:918 , HOH A:960 , HOH A:970BINDING SITE FOR RESIDUE BEF A 804
5AC5SOFTWAREASN A:134 , ADP A:803 , BEF A:804 , HOH A:917 , HOH A:960BINDING SITE FOR RESIDUE MG A 805
6AC6SOFTWAREASP B:92BINDING SITE FOR RESIDUE CO B 802
7AC7SOFTWAREASN B:134 , ALA B:138 , LYS B:141 , ASP B:173 , MET B:178 , ASN B:186 , 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 , BEF B:804 , MG B:805 , HOH B:903 , HOH B:905 , HOH B:906 , HOH B:907 , HOH B:919 , HOH B:954 , HOH B:975BINDING SITE FOR RESIDUE ADP B 803
8AC8SOFTWAREGLU B:130 , GLY B:214 , GLN B:215 , PHE B:216 , GLY B:217 , VAL B:218 , GLY B:219 , ARG B:417 , ADP B:803 , MG B:805 , HOH B:906 , HOH B:919 , HOH B:933 , HOH B:948BINDING SITE FOR RESIDUE BEF B 804
9AC9SOFTWAREASN B:134 , ADP B:803 , BEF B:804 , HOH B:906 , HOH B:919BINDING SITE FOR RESIDUE MG B 805

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:516 -A:542
2B:516 -B:542

(-) Cis Peptide Bonds  (11, 11)

Asymmetric/Biological Unit
No.Residues
1Gly A:150 -Gly A:151
2Ser A:260 -Gly A:261
3Ala A:350 -Pro A:351
4Phe A:636 -Leu A:637
5Leu A:637 -Arg A:638
6Ala B:237 -Glu B:238
7Glu B:238 -Ala B:239
8Asp B:249 -Gly B:250
9Ala B:350 -Pro B:351
10Gly B:493 -Gln B:494
11Ala B:507 -Gly B:508

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J0B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J0B)

(-) Exons   (0, 0)

(no "Exon" information available for 4J0B)

(-) 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:594
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................eeee.eehhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeee....eeeeee.....hhhhhhhhhhee..hhhhhhhh......hhhhhh.....hhhhhhhhheeeeeeeee.......eeeeee....eeeeeeee....eeeeeeee.hhhhhhhhhhhhhhhhhhhh......eee..ee.....hhhhh.....hhhhhhhhhhhhhh....eeeeeeeee.....eeeeeeee........eeeee..eeee.......hhhhh..eeeee...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..ee..........hhhhhh.......eeeeee..hhhhhh.hhhhhhh.....eee...hhhhhhhhhhee..eeeee.......hhhhhhhhhhh........eeee........eeeee.hhhhhh..........eeeee...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4j0b A  85 TLHNIITDTENVQGSFSKHEFQAETKKLLDIVARSLYSEKEVFIRELISNGSDALEKLRHRMITAGGDTAPMEIHLQTDSVKGTFTIQDTGVGMNKEDLVSNLGTIARSGSKAFLDALQNQAEASSSIIGQFGVGFYSAFMVADKVEVYSQSAEADAPGYKWSSDGSGVFEVAEASGVRQGTKIVLHLKDDCKEFSSEDRVKEVVTKYSNFVSFPIFLNGRRLNTLQALWMMEPKDISEWQHEEFYRYVAQAYDKPRYTLHYRADAPLNIRSIFYVPEMKPMGSSVALYSRKILIQTKATDILPKWLRFLRGVVDSEDIPLNLSRELLQESALIRKLRDVLQQRVIRFLLDQSKKDPEKYARFFEDYGLFMREGIVTTGEQSVKEDIAKLLRFESSALPAGQQTSLMEYSSRMKAGTRNIYYLCAPNRHLAEHSPYFEAMKDMEVLFCFEQFDELTLLHLREFDRKKLISAETRLSSEQAEDLLAWMRNALVQRVTNIKVTPRLDTHPAMITVLEMGAARHFLRTQQILQPTLEINTGHDLIKKLHALKDSNPELAQLLLEQIYDNAMIAAGLNEDPRPMISRLNQLLTRALEK 718
                                    94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364||     382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532||     544       554       564  ||   594       604       614       624       634      |654       664       674       684       694       704       714    
                                                                                                                                                                                                                                                                                                                  365|                                                                                                                                                            533|                            567|                                                  641|                                                                  
                                                                                                                                                                                                                                                                                                                   374                                                                                                                                                             536                             588                                                   652                                                                  


Chain B from PDB  Type:PROTEIN  Length:609
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeeee.eehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh........eeeeee....eeeeee.....hhhhhhhhhhee..hhhhhhhhh...........hhhhhhhh.eeeeeeeee.......eeeeee....eeeeeee.....eeeeeeee.hhhhhhhhhhhhhhhhhhhh......eee..ee.....hhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeee.....eeeeeeee....hhhhhhh...eeeee..eee......hhhhh..eeeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh....ee.........hhhhhhhhh.....eeeeee..hhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhee..eeeeehhhhhhhhhhh........hhhhh.hhhhhhhhhhhhhhhh.....eeee........eeee..hhhhhhhhh......eeee...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j0b B  85 TLHNIITDTENVQGSFSKHEFQAETKKLLDIVARSLYSEKEVFIRELISNGSDALEKLRHRMITAGAPMEIHLQTDSVKGTFTIQDTGVGMNKEDLVSNLGTIARSGSKAFLDALQSSSIIGQFGVGFYSAFMVADKVEVYSQSAEADAPGYKWSSDGSGVFEVAEASGVRQGTKIVLHLKDDCKEFSSEDRVKEVVTKYSNFVSFPIFLNGRRLNTLQALWMMEPKDISEWQHEEFYRYVAQAYDKPRYTLHYRADAPLNIRSIFYVPEMKPSMFDVSREMSVALYSRKILIQTKDILPKWLRFLRGVVDSEDIPLNLSRELLQESALIRKLRDVLQQRVIRFLLDQSKKDPEKYARFFEDYGLFMREGIVTTGEQSVKEDIAKLLRFESSALPAGQQTSLMEYSSRMKAGTRNIYYLCAPNRHLAEHSPYFEAMKQKDMEVLFCFEQFDELTLLHLREFDRKKLISAETDIVVDHYKEEKFQDSKPASERLSSEQAEDLLAWMRNALVQRVTNIKVTPRLDTHPAMITVLEMGAARHFLRTILQPTLEINTGHDLIKKLHALKDSNPELAQLLLEQIYDNAMIAAGLNEDPRPMISRLNQLLTRALE 717
                                    94       104       114       124       134       144     ||157       167       177       187       197     ||212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372 ||    384     ||396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636  ||   658       668       678       688       698       708         
                                                                                           150|                                              203|                                                                                                                                                                  374|          390|                                                                                                                                                                                                                                                   639|                                                                 
                                                                                            154                                               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 4J0B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J0B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J0B)

(-) 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 ]  
    Ala B:507 - Gly B:508   [ RasMol ]  
    Asp B:249 - Gly B:250   [ RasMol ]  
    Glu B:238 - Ala B:239   [ RasMol ]  
    Gly A:150 - Gly A:151   [ RasMol ]  
    Gly B:493 - Gln B:494   [ RasMol ]  
    Leu A:637 - Arg A:638   [ RasMol ]  
    Phe A:636 - Leu A:637   [ RasMol ]  
    Ser A:260 - Gly A:261   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        A8WFV1_DANRE | A8WFV1: 4ipe 4ivg 4iyn

(-) Related Entries Specified in the PDB File

4ipe CRYSTAL STRUCTURE OF MITOCHONDRIAL HSP90 (TRAP1) WITH AMPPNP
4ivg CRYSTAL STRUCTURE OF MITOCHONDRIAL HSP90 (TRAP1) NTD-MIDDLE DOMAIN DIMER WITH AMPPNP
4iyn FULL LENGTH TRAP1 WITH ADP-ALF4-