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(-) Description

Title :  CRYSTAL STRUCTURE OF USP7 UBIQUITIN-LIKE DOMAINS IN EXTENDED CONFORMATION
 
Authors :  R. Pfoh, I. K. L. Lacdao, V. Saridakis
Date :  18 Oct 14  (Deposition) - 17 Jun 15  (Release) - 17 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Deubiquitinating (Dub) Enzyme, Ubiquitin-Like (Ubl) Domains, Icp0 Binding Site, Hausp (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Pfoh, I. K. Lacdao, A. A. Georges, A. Capar, H. Zheng, L. Frappier, V. Saridakis
Crystal Structure Of Usp7 Ubiquitin-Like Domains With An Icp0 Peptide Reveals A Novel Mechanism Used By Viral And Cellular Proteins To Target Usp7.
Plos Pathog. V. 11 04950 2015
PubMed-ID: 26046769  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1004950

(-) Compounds

Molecule 1 - UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 7
    Chains: A, B
    EC Number: 3.4.19.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TV-L
    Expression System Strain: BL21(DE3)MGK
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UBIQUITIN-LIKE DOMAIN (UNP RESIDUES 535-888)
    Gene: USP7, HAUSP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DEUBIQUITINATING ENZYME 7,HERPESVIRUS-ASSOCIATED UBIQUITIN- SPECIFIC PROTEASE,UBIQUITIN THIOESTERASE 7,UBIQUITIN-SPECIFIC- PROCESSING PROTEASE 7
 
Molecule 2 - ICP0
    Chains: C, D
    Engineered: YES
    Fragment: USP7 BINDING SEQUENCE
    Organism Scientific: HERPES SIMPLEX VIRUS (TYPE 1 / STRAIN 17)
    Organism Taxid: 10299
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 27)

Asymmetric Unit (2, 27)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 13)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE13Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 11)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MSE11Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:697binding site for residue CL A 2002
2AC2SOFTWAREARG B:788 , HIS B:792 , ARG B:816binding site for residue CL B 2001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WPI)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asn A:656 -Pro A:657
2Asn B:656 -Pro B:657

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WPI)

(-) 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:341
                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhh...............eeeeee...hhhhhhhhhhhhhh.....eeeeeeee.....eee...........hhhhhh.....eeeeeee.hhhhhhh...........eeeeeeeeee....eeeeeeeeeee...hhhhhhhhhhhhhh......eeeeeeee..eeee......hhhhhh......eeeeeee.hhhhhh....hhhhhhhhhhheeeeeeee........eeeeee...hhhhhhhhhhhhh..hhh.eeeeee......eeeee......hhhhhhh........eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wpi A 543 RLQEEKRIEAQKRKERQEAHLYmQVQIVAEDQFCGHQGNDmYDEEKVKYTVFKVLKNSSLAEFVQSLSQTmGFPQDQIRLWPmQARSNGTKRPAmLDNEADGNKTmIELSDNENPWTIFLETVDPELAASGATLPKFDKDHDVmLFLKmYDPKTRSLNYCGHIYTPISCKIRDLLPVmCDRAGFIQDTSLILYEEVKPNLTERIQDYDVSLDKALDELmDGDIIVFQKDDPENDNSELPTAKEYFRDLYHRVDVIFCDKTIPNDPGFVVTLSNRmNYFQVAKTVAQRLNTDPmLLQFFKSQGYRDGPGNPLRHNYEGTLRDLLQFFKPRQPKKLYYQQLKm 883
                                   552       562  |    572       582|      592       602       612|      622  |    632    |  642     | 652       662       672       682   |   692       702       712       722       732       742       752       762       772       782       792       802       812    |  822       832  |    842       852       862       872       882|
                                                565-MSE           583-MSE                       613-MSE     625-MSE     637-MSE    648-MSE                               686-MSE|                          720-MSE                                  761-MSE                                                 817-MSE           835-MSE                                         883-MSE
                                                                                                                                                                              691-MSE                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:340
                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhh...............eeeeee...hhhhhhhhhhhhhh.....eeeeeeee.....eee......hhhhhh.....eeeeeee.hhhhhhh...........eeeeeeeeee....eeeeeeeeeee....hhhhhhhhhhhhh......eeeeeeee..eeee......hhhhhh......eeeeeee.hhhhhh....hhhhhhhhhhheeeeeeee........eeeeee...hhhhhhhhhhhhh..hhh.eeeeee......eeeee......hhhhhhh........eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wpi B 538 QQLVERLQEEKRIEAQKRKERQEAHLYmQVQIVAEDQFCGHQGNDmYDEEKVKYTVFKVLKNSSLAEFVQSLSQTmGFPQDQIRLWPmQARSNGTKRPAADGNKTmIELSDNENPWTIFLETVDPELAASGATLPKFDKDHDVmLFLKmYDPKTRSLNYCGHIYTPISCKIRDLLPVmCDRAGFIQDTSLILYEEVKPNLTERIQDYDVSLDKALDELmDGDIIVFQKDDPENDNSELPTAKEYFRDLYHRVDVIFCDKTIPNDPGFVVTLSNRmNYFQVAKTVAQRLNTDPmLLQFFKSQGYRDGPGNPLRHNYEGTLRDLLQFFKPRQPKKLYYQQLK 882
                                   547       557       567       577     | 587       597       607     | 617       627       642     | 652       662       672       682   |   692       702       712       722       732       742       752       762       772       782       792       802       812    |  822       832  |    842       852       862       872       882
                                                     565-MSE           583-MSE                       613-MSE     625-MSE    636|     |                                   686-MSE|                          720-MSE                                  761-MSE                                                 817-MSE           835-MSE                                           
                                                                                                                             642     |                                        691-MSE                                                                                                                                                                                           
                                                                                                                                   648-MSE                                                                                                                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4wpi C 617 GPRKCARKTR 626
                                   626


Chain D from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4wpi D 617 GPRKCARKTR 626
                                   626
   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 4WPI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (51, 53)

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  UBP7_HUMAN | Q93009
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 Related Entries

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

UniProtKB/Swiss-Prot
        ICP0_HHV11 | P08393: 4wph 5c56
        UBP7_HUMAN | Q93009: 1nb8 1nbf 1yy6 1yze 2f1w 2f1x 2f1y 2f1z 2foj 2foo 2fop 2kvr 2xxn 2ylm 3mqr 3mqs 4jjq 4kg9 4m5w 4m5x 4pyz 4wph 4yoc 4ysi 4z96 4z97 5c56 5c6d 5fwi 5gg4 5j7t 5jtj 5jtv

(-) Related Entries Specified in the PDB File

4wph