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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC CORE OF E3 LIGASE HOIP
 
Authors :  B. Stieglitz, R. R. Rana, M. G. Koliopoulos, A. C. Morris-Davies, E. Christodoulou, S. Howell, N. R. Brown, K. Rittinger
Date :  05 Jul 13  (Deposition) - 16 Oct 13  (Release) - 18 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  B,C  (1x)
Biol. Unit 6:  A (1x),D (1x)
Keywords :  Rnf31, Zibra, Ring Domain, Zinc Finger, Ibr Domain, Rbr Ligase, E3 Ligase, Ligase, Ubiquitin, Hoil-1, Sharpin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Stieglitz, R. R. Rana, M. G. Koliopoulos, A. C. Morris-Davies, V. Schaeffer, E. Christodoulou, S. Howell, N. R. Brown, I. Dikic, K. Rittinger
Structural Basis For Ligase-Specific Conjugation Of Linear Ubiquitin Chains By Hoip.
Nature V. 503 422 2013
PubMed-ID: 24141947  |  Reference-DOI: 10.1038/NATURE12638

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE RNF31
    Chains: B, A, C, D
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET49B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN (UNP RESIDUES 853-1072)
    Gene: RNF31, ZIBRA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HOIL-1-INTERACTING PROTEIN, HOIP, RING FINGER PROTEIN 31, ZINC IN-BETWEEN-RING-FINGER UBIQUITIN-ASSOCIATED DOMAIN PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x):  B  
Biological Unit 2 (1x): A   
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D
Biological Unit 5 (1x):  BC 
Biological Unit 6 (1x): A (1x)  D (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 30)

Asymmetric Unit (2, 30)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2ZN18Ligand/IonZINC ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION
Biological Unit 5 (1, 6)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION
Biological Unit 6 (1, 3)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2ZN-1Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS B:871 , CYS B:874 , CYS B:890 , CYS B:893BINDING SITE FOR RESIDUE ZN B 1101
02AC2SOFTWARECYS B:898 , CYS B:901 , HIS B:926 , CYS B:930BINDING SITE FOR RESIDUE ZN B 1102
03AC3SOFTWARECYS B:911 , CYS B:916 , HIS B:923 , HIS B:925BINDING SITE FOR RESIDUE ZN B 1103
04AC4SOFTWARECYS B:969 , CYS B:986 , CYS B:998 , HIS B:1001BINDING SITE FOR RESIDUE ZN B 1104
05AC5SOFTWAREHIS B:887 , HIS B:889 , HIS C:887 , HIS C:889BINDING SITE FOR RESIDUE ZN B 1105
06AC6SOFTWARECYS A:871 , CYS A:874 , CYS A:890 , CYS A:893BINDING SITE FOR RESIDUE ZN A 1101
07AC7SOFTWARECYS A:898 , CYS A:901 , HIS A:926 , CYS A:930BINDING SITE FOR RESIDUE ZN A 1102
08AC8SOFTWARECYS A:911 , CYS A:916 , HIS A:923 , HIS A:925BINDING SITE FOR RESIDUE ZN A 1103
09AC9SOFTWARECYS A:969 , CYS A:986 , CYS A:998 , HIS A:1001BINDING SITE FOR RESIDUE ZN A 1104
10BC1SOFTWAREHIS A:887 , HIS A:889 , HIS D:887 , HIS D:889BINDING SITE FOR RESIDUE ZN A 1105
11BC2SOFTWARECYS C:871 , CYS C:874 , CYS C:890 , CYS C:893BINDING SITE FOR RESIDUE ZN C 1101
12BC3SOFTWARECYS C:898 , CYS C:901 , HIS C:926 , CYS C:930BINDING SITE FOR RESIDUE ZN C 1102
13BC4SOFTWARECYS C:911 , CYS C:916 , HIS C:923 , HIS C:925BINDING SITE FOR RESIDUE ZN C 1103
14BC5SOFTWARECYS C:969 , CYS C:986 , CYS C:998 , HIS C:1001BINDING SITE FOR RESIDUE ZN C 1104
15BC6SOFTWARECYS D:871 , CYS D:874 , CYS D:890 , CYS D:893BINDING SITE FOR RESIDUE ZN D 1101
16BC7SOFTWARECYS D:898 , CYS D:901 , HIS D:926 , CYS D:930BINDING SITE FOR RESIDUE ZN D 1102
17BC8SOFTWARECYS D:911 , CYS D:916 , HIS D:923 , HIS D:925BINDING SITE FOR RESIDUE ZN D 1103
18BC9SOFTWARECYS D:969 , VAL D:971 , CYS D:986 , CYS D:998 , HIS D:1001BINDING SITE FOR RESIDUE ZN D 1104

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:885 -D:885
2B:885 -C:885

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Lys B:908 -Asn B:909
2Gln A:858 -Gly A:859
3Gln A:865 -Glu A:866
4Lys A:908 -Asn A:909
5Lys C:908 -Asn C:909
6Cys C:916 -Arg C:917
7Lys D:908 -Asn D:909
8Cys D:916 -Arg D:917

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LJQ)

(-) 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:190
                                                                                                                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..ee......ee...eee......eee......ee..........hhhhh.ee.....hhhhhh..hhhhhhhhhhhh...............................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ljq A  858 QGLAmYLQEGIDCPKCKFSYACmHFHCTQCRHQFCSGCYNAFYAKNKCPEPNCRVKKSLHGHHPRDCLFYLRDWTALRLQKLLQDNNVmFNTEPPGGCRVIEDEACGKETPAGYAGLCQAHYKEYLVSLINAHSLDPATLYEVEELETATERYLHVRPQPLAGEDPPAYQARLLQKLTEEVPLGQSIPRR 1070
                                |  868       878|||    893       903       913       923       933       943       953    || 971 ||    990      1000      1010      1020      1030      1040      1050      1060      1070
                                | 866|        879||                                                               952-MSE58|   973|                                                                                       
                              862-MSE8         885|                                                                      967    983                                                                                       
                                                886-MSE                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhh...............eee......eee......ee................ee.....hhhhhh..hhhhhhhhhhhh.............ee...ee............hhhhhhhhhhhh.hh...hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4ljq B  858 QGLAmYLQEGIDCPKCKFSYALCmHFHCTQCRHQFCSGCYNAFYAKNKCPEPNCRVKKSLHGHHPRDCLFYLRDWTALRLQKLLQDNNVmFNTEPPGCRVIEQKDEACGKETPAGYAGLCQAHYKEYLVSLINAHSLDPATLYEVEELETATERYLHVRPQPLAGEDPPAYQARLLQKLTEEVPLGQSIPRR 1070
                                |  868       878 |||   892       902       912       922       932       942       952     ||971   ||  988       998      1008      1018      1028      1038      1048      1058      1068  
                              862-MSE|         880||                                                               952-MSE58|    975|                                                                                       
                                   868          885|                                                                      968     983                                                                                       
                                                 886-MSE                                                                                                                                                                    


Chain C from PDB  Type:PROTEIN  Length:192
                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhh.ee......ee.....eee......eee......ee................ee.....hhhhhh..hhhhhhhhhhhh...............................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4ljq C  858 QGLAmYLQEGIDCPKCKFSYALGCmHFHCTQCRHQFCSGCYNAFYAKNKCPEPNCRVKKSLHGHHPRDCLFYLRDWTALRLQKLLQDNNVmFNTEPPGGCRVIEDEACGKETPAGYAGLCQAHYKEYLVSLINAHSLDPATLYEVEELETATERYLHVRPQPLAGEDPPAYQARLLQKLTEEVPLGQSIPRR 1070
                                |  868       878 || |  891       901       911       921       931       941       951|     |969   ||  988       998      1008      1018      1028      1038      1048      1058      1068  
                              862-MSE|         880| |                                                               952-MSE58|   973|                                                                                       
                                   868          884 |                                                                      967    983                                                                                       
                                                  886-MSE                                                                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:190
                                                                                                                                                                                                                               
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.ee......ee....eee......eee......ee................ee.....hhhhhh..hhhhhhhhhhhh...............................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4ljq D  859 GLAmYLQEGIDCPKCKFSYAGCmHFHCTQCRHQFCSGCYNAFYAKNKCPEPNCRVKKSLHGHHPRDCLFYLRDWTALRLQKLLQDNNVmFNTEPPGGCRVIEDEACGKETPAGYAGLCQAHYKEYLVSLINAHSLDPATLYEVEELETATERYLHVRPQPLAGEDPPAYQARLLQKLTEEVPLGQSIPRR 1070
                               |   869       879| |    893       903       913       923       933       943       953    || 971 ||    990      1000      1010      1020      1030      1040      1050      1060      1070
                             862-MSE|        879| |                                                               952-MSE58|   973|                                                                                       
                                  868         884 |                                                                      967    983                                                                                       
                                                886-MSE
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  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 4LJQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        RNF31_HUMAN | Q96EP0: 2ct7 4dbg 4juy 4ljo 4ljp 4owf 4oyj 4oyk 4p09 4p0a 4p0b 5edv 5ljn

(-) Related Entries Specified in the PDB File

4ljo 4ljp