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(-) Description

Title :  ATOMIC CRYOEM STRUCTURE OF HSP90-CDC37-CDK4 COMPLEX
 
Authors :  K. A. Verba, R. Y. R. Wang, A. Arakawa, Y. Liu, S. Yokoyama, D. A. Agard
Date :  18 Feb 16  (Deposition) - 06 Jul 16  (Release) - 19 Apr 17  (Revision)
Method :  ELECTRON MICROSCOPY
Resolution :  8.00
Chains :  Asym./Biol. Unit :  A,B,E,K
Keywords :  Hsp90, Cdc37, Cdk4, Chaperone, Kinase, Unfolding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. A. Verba, R. Y. Wang, A. Arakawa, Y. Liu, M. Shirouzu, S. Yokoyama, D. A. Agard
Atomic Structure Of Hsp90-Cdc37-Cdk4 Reveals That Hsp90 Traps And Stabilizes An Unfolded Kinase.
Science V. 352 1542 2016
PubMed-ID: 27339980  |  Reference-DOI: 10.1126/SCIENCE.AAF5023

(-) Compounds

Molecule 1 - HEAT SHOCK PROTEIN HSP 90 BETA
    Chains: A, B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFASTBACHT
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HSP 90, HEAT SHOCK 84 KDA, HSP 84, HSP84, HEAT SHOCK PROTEIN HSP 90 BETA
 
Molecule 2 - HSP90 CO-CHAPERONE CDC37
    Chains: E
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFASTBACHT
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HSP90 CHAPERONE PROTEIN KINASE-TARGETING SUBUNIT, P50CDC37
 
Molecule 3 - CYCLIN-DEPENDENT KINASE 4
    Chains: K
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PFASTBACHT
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABEK

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2MG2Ligand/IonMAGNESIUM ION
3SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:42 , ASN A:46 , ALA A:50 , ASP A:88 , MET A:93 , ASN A:101 , SER A:108 , GLY A:109 , THR A:110 , GLY A:127 , GLN A:128 , PHE A:129 , GLY A:130 , VAL A:131 , GLY A:132 , PHE A:133 , THR A:179 , MG A:1692BINDING SITE FOR RESIDUE ATP A 1691
2AC2SOFTWAREASN A:46 , ATP A:1691BINDING SITE FOR RESIDUE MG A 1692
3AC3SOFTWAREGLU B:42 , ASN B:46 , ALA B:50 , LYS B:53 , ASP B:88 , MET B:93 , ASN B:101 , SER B:108 , GLY B:109 , THR B:110 , GLY B:127 , GLN B:128 , PHE B:129 , GLY B:130 , VAL B:131 , GLY B:132 , PHE B:133 , THR B:179 , ARG B:392 , MG B:1693BINDING SITE FOR RESIDUE ATP B 1692
4AC4SOFTWAREASN B:46 , ATP B:1692BINDING SITE FOR RESIDUE MG B 1693

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FWM)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys E:132 -Pro E:133

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FWM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FWM)

(-) Exons   (0, 0)

(no "Exon" information available for 5FWM)

(-) 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:638
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.eehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee....eeeeee.....hhhhhhhh..ee...hhhhhhhhh.............hhhhhhhh.eeeeeeee.......eeeee....eeeeee.........eeeeeee...hhhhhhhhhhhhhhh.........eeeeee..............eee.hhhhh.......hhhhhhhhhhhhhhhhhh.......eeeeeee.....eeeeeee.................eeeee..eeee.hhhhhhhhhhh..eeeeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...eeee......eeehhhhhhh......eeeeee..hhhhhhhhhhhhhhhhh...eeee.hhhhhhhhhhh.ee..eeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee........eeee........hhhhhhhhhh...hhhhhhhh...eeee...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fwm A  10 EEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYESLTDPSKLDSGKELKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVVVITKHNDDEQYAWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQFIGYPITLYLEKEREKEISKKIKEKYIDQEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKKKKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFSELAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMKETQKSIYYITGESKEQVANSAFVERVRKRGFEVVYMTEPIDEYCVQQLKEFDGKSLVSVTKEGLELPEDEEEKKKMEESKAKFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMMAKKHLEINPDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLSSGFSLEDPQTHSNRIYRMIKLGLGI 690
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219      |272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682        
                                                                                                                                                                                                                                                  226|                                                                                                                                                                                                                                                                                                                                                                                                                                    
                                                                                                                                                                                                                                                   270                                                                                                                                                                                                                                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:630
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee.eehhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee....eeeeee.....hhhhhhhh..ee..hhhhhhhhhhhhh..........hhhhhhhh.eeeeeeeee.....eeeeee....eeeeee.........eeeeeee.hhhhhhhhhhhhhhhhhhhh......eeeeeee...eeeeehhhhh.......hhhhhhhhhhhhhhhhhhh......eeeeeeeee...eeeeeee.................eeeee..eeee.hhhhhhhhhhh..eeeeee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh..eeee.......eehhhhhhh......eeeeee..hhhhhhhhhhhhhhhhh...eeee...hhhhhhhhh.ee..eeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee........eeeee.....hhhhhhhhhh....hhhhhhhh...eeeee...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5fwm B  10 EEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNASDALDKIRYESLTDPSKLDSGKELKIDIIPNPQERTLTLVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVVVITKHNDDEQYAWESSAGGSFTVRADHGEPIGRGTKVILHLKEDQTEYLEERRVKEVVKKHSQFIGYPITLYLEKEKEKYIDQEELNKTKPIWTRNPDDITQEEYGEFYKSLTNDWEDHLAVKHFSVEGQLEFRALLFIPRRAPFDLFENKKKKNNIKLYVRRVFIMDSCDELIPEYLNFIRGVVDSEDLPLNISREMLQQSKILKVIRKNIVKKCLELFSELAEDKENYKKFYEAFSKNLKLGIHEDSTNRRRLSELLRYHTSQSGDEMTSLSEYVSRMKETQKSIYYITGESKEQVANSAFVERVRKRGFEVVYMTEPIDEYCVQQLKEFDGKSLVSVTKEGLELPEDEEEKKKMEESKAKFENLCKLMKEILDKKVEKVTISNRLVSSPCCIVTSTYGWTANMERIMKAQALRDNSTMGYMMAKKHLEINPDHPIVETLRQKAEADKNDKAVKDLVVLLFETALLSSGFSLEDPQTHSNRIYRMIKLGLGID 691
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219||     281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691
                                                                                                                                                                                                                                            220|                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                                                                                                                                                                                                                             273                                                                                                                                                                                                                                                                                                                                                                                                                                  


Chain E from PDB  Type:PROTEIN  Length:259
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fwm E   2 VDYSVWDHIEVsDDEDETHPNIDTASLFRWRHQARVERMEQFQKEKEELDRGCRECKRKVAECQRKLKELEVAEGGKAELERLQAEAQQLRKEERSWEQKLEEMRKKEKSMPWNVDTLSKDGFSKSMVNTKPEKTEEDSEEVREQKHKTFVEKYEKQIKHFGMLRRWDDSQKYLSDNVHLVCEETANYLVIWCIDLEVEEKCALMEQVAHQTIVMQFILELAKSLKVDPRACFRQFFTKIKTADRQYMEGFNDELEAFK 260
                                    11 |      21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251         
                                      13-SEP                                                                                                                                                                                                                                                   


Chain K from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee..eeeeeee......eeee.................hhhhhhhhhhhhhhhh...............................hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee...hhhhh.................hhhhhh....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh........................hhhhhh...hhhhhhhhhhhhh.......hhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fwm K   5 RYEPVAEIGVGAYGTVYKARDPHSGHFVALKSVRVPNGGGGGGGLPISTVREVALLRRLEAFEHPNVVRLMDVCATSRTDREIKVTLVFEHVDQDLRTYLDKAPPPGLPAETIKDLMRQFLRGLDFLHANCIVHRDLKPENILVTSGGTVKLADFGLARIYSYQMALTPVVVTLWYRAPEVLLQSTYATPVDMWSVGCIFAEMFRRKPLFCGNSEADQLGKIFDLIGLPPEDDWPRDVSLPRGAFPPRGPRPVQSVVPEMEESGAQLLLEMLTFNPHKRISAFRALQHSYL 295
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294
   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 5FWM)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FWM)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FWM)

(-) Gene Ontology  (108, 130)

Asymmetric/Biological Unit(hide GO term definitions)

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    Lys E:132 - Pro E:133   [ RasMol ]  
 

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  5fwm
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Access by UniProt ID/Accession number
  CDC37_HUMAN | Q16543
    Comparative Protein Structure Models: ModBase
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  CDK4_HUMAN | P11802
    Comparative Protein Structure Models: ModBase
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  HS90B_HUMAN | P08238
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 Related Entries

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

UniProtKB/Swiss-Prot
        CDC37_HUMAN | Q16543: 1us7 2k5b 2n5x 2nca 2w0g 5fwk 5fwl 5fwp 5hpe
        CDK4_HUMAN | P11802: 1ld2 2w96 2w99 2w9f 2w9z 3g33 5fwk 5fwl 5fwp
        HS90B_HUMAN | P08238: 1qz2 1uym 2l6j 3fwv 3nmq 3pry 3uq3 5fwk 5fwl 5fwp

(-) Related Entries Specified in the PDB File

5fwk ATOMIC CRYOEM STRUCTURE OF HSP90-CDC37-CDK4 COMPLEX
5fwl ATOMIC CRYOEM STRUCTURE OF HSP90-CDC37-CDK4 COMPLEX
5fwp ATOMIC CRYOEM STRUCTURE OF HSP90-CDC37-CDK4 COMPLEX RELATED ID: EMD-3342 RELATED DB: EMDB ATOMIC CRYOEM STRUCTURE OF HSP90-CDC37-CDK4 COMPLEX