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(-) Description

Title :  RNF38-UBCH5B-UB COMPLEX
 
Authors :  L. Buetow, M. Gabrielsen, N. G. Anthony, H. Dou, A. Patel, H. Aitkenhead G. J. Sibbet, B. O. Smith, D. T. Huang
Date :  20 Oct 14  (Deposition) - 08 Apr 15  (Release) - 29 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  D,E,F  (1x)
Biol. Unit 2:  A,B,C  (1x)
Keywords :  Ring E3, E2, Ubiquitin, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Buetow, M. Gabrielsen, N. G. Anthony, H. Dou, A. Patel, H. Aitkenhead, G. J. Sibbet, B. O. Smith, D. T. Huang
Activation Of A Primed Ring E3-E2-Ubiquitin Complex By Non- Covalent Ubiquitin.
Mol. Cell V. 58 297 2015
PubMed-ID: 25801170  |  Reference-DOI: 10.1016/J.MOLCEL.2015.02.017

(-) Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 D2
    Chains: A, D
    EC Number: 6.3.2.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: RESIDUES 2-147
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: LYS85 IN CHAINS A AND D IS COVALENTLY LINKED TO GLY76 IN CHAINS B AND E, RESPECTIVELY.
    Synonym: UBIQUITIN CARRIER PROTEIN D2, UBIQUITIN-CONJUGATING ENZYME E2(17)KB 2, UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2, UBIQUITIN- PROTEIN LIGASE D2, P53-REGULATED UBIQUITIN-CONJUGATING ENZYME 1, UBCH5B
 
Molecule 2 - POLYUBIQUITIN-C
    Chains: B, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: RESIDUES 77-152
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: LYS85 IN CHAINS A AND D IS COVALENTLY LINKED TO GLY76 IN CHAINS B AND E, RESPECTIVELY.
    Synonym: UBIQUITIN
 
Molecule 3 - E3 UBIQUITIN-PROTEIN LIGASE RNF38
    Chains: C, F
    EC Number: 6.3.2.19
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: RESIDUES 439-515
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: RING FINGER PROTEIN 38, RNF38

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x):    DEF
Biological Unit 2 (1x): ABC   

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric Unit (3, 15)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO2Ligand/Ion1,2-ETHANEDIOL
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:2 , LEU A:3 , LYS A:4BINDING SITE FOR RESIDUE CL A1148
02AC2SOFTWAREARG A:90 , SER A:91BINDING SITE FOR RESIDUE CL A1149
03AC3SOFTWAREASN A:81 , SER A:83BINDING SITE FOR RESIDUE CL A1150
04AC4SOFTWAREARG A:131 , ASN A:135BINDING SITE FOR RESIDUE EDO A1151
05AC5SOFTWAREGLU B:18 , PRO B:19 , SER B:20 , HOH B:2010BINDING SITE FOR RESIDUE EDO B1077
06AC6SOFTWARELYS B:11 , THR B:12BINDING SITE FOR RESIDUE EDO B1078
07AC7SOFTWAREASN D:79 , ASN D:81 , SER D:83BINDING SITE FOR RESIDUE CL D1149
08AC8SOFTWARESER D:91BINDING SITE FOR RESIDUE CL D1150
09AC9SOFTWAREASN B:60 , HOH B:2035 , ARG D:131BINDING SITE FOR RESIDUE EDO D1151
10BC1SOFTWAREHOH D:2059 , ARG E:72 , ARG E:74BINDING SITE FOR RESIDUE EDO E1077
11BC2SOFTWARECYS C:413 , CYS C:416 , HIS C:436 , CYS C:439BINDING SITE FOR RESIDUE ZN C1465
12BC3SOFTWARECYS C:431 , HIS C:433 , CYS C:450 , CYS C:453BINDING SITE FOR RESIDUE ZN C1466
13BC4SOFTWARECYS F:413 , CYS F:416 , HIS F:436 , CYS F:439BINDING SITE FOR RESIDUE ZN F1460
14BC5SOFTWARECYS F:431 , HIS F:433 , CYS F:450 , CYS F:453BINDING SITE FOR RESIDUE ZN F1461

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4V3K)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:60 -Pro A:61
2Tyr D:60 -Pro D:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4V3K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4V3K)

(-) Exons   (0, 0)

(no "Exon" information available for 4V3K)

(-) 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:146
                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh....eeee.......eeeeeee..........eeeeeee..........eeee.................hhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4v3k A   2 ALKRIHKELNDLARDPPAQCRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM 147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      


Chain B from PDB  Type:PROTEIN  Length:77
                                                                                                             
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 4v3k B   0 SMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                     9        19        29        39        49        59        69       


Chain C from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh.eee...........ee....ee.....eeee.....eeehhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 4v3k C 390 KADIEQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADASEVHRDS 464
                                   399       409       419       429       439       449       459     


Chain D from PDB  Type:PROTEIN  Length:146
                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee.................hhhh.......hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4v3k D   2 ALKRIHKELNDLARDPPAQCRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM 147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      


Chain E from PDB  Type:PROTEIN  Length:77
                                                                                                             
               SCOP domains ----------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeeee....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------- Transcript
                 4v3k E   0 SMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                     9        19        29        39        49        59        69       


Chain F from PDB  Type:PROTEIN  Length:70
                                                                                                      
               SCOP domains ---------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh.eee...........ee....ee.....eeee.....eeehhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 4v3k F 390 KADIEQLPSYRFNPNNHQSEQTLCVVCMCDFESRQLLRVLPCNHEFHAKCVDKWLKANRTCPICRADASE 459
                                   399       409       419       429       439       449       459
   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 4V3K)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4V3K)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4V3K)

(-) Gene Ontology  (100, 116)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        RNF38_HUMAN | Q9H0F5: 1x4j 4v3l
        UB2D2_HUMAN | P62837: 1ur6 1w4u 2clw 2esk 2eso 2esp 2esq 3a33 3jvz 3jw0 3l1y 3tgd 3zni 4a49 4a4b 4a4c 4auq 4ddg 4ddi 4ldt 4v3l 4wz3 5d0k 5d0m 5d1k 5d1l 5d1m 5edv 5mnj 5ulf 5ulh 5ulk
        UBC_HUMAN | P0CG48: 1c3t 1cmx 1d3z 1f9j 1fxt 1g6j 1gjz 1nbf 1ogw 1q5w 1s1q 1sif 1tbe 1ubi 1ubq 1ud7 1uzx 1xd3 1xqq 1yx5 1yx6 1zgu 1zo6 2ayo 2bgf 2den 2fuh 2g45 2gbj 2gbk 2gbm 2gbn 2gbr 2gmi 2hth 2ibi 2j7q 2jf5 2jri 2jy6 2jzz 2k25 2k6d 2k8b 2k8c 2kdf 2khw 2kjh 2klg 2kn5 2kox 2ktf 2kwu 2kwv 2kx0 2l0f 2l0t 2l3z 2ld9 2lvo 2lvp 2lvq 2lz6 2mbo 2mbq 2mcn 2mi8 2mj5 2mor 2mre 2mws 2n2k 2nr2 2o6v 2ojr 2pe9 2pea 2rr9 2rsu 2ru6 2w9n 2wdt 2xew 2xk5 2y5b 2z59 2zcb 2zvn 2zvo 3a33 3alb 3aul 3b08 3b0a 3by4 3c0r 3dvg 3dvn 3eec 3efu 3ehv 3h7p 3h7s 3hm3 3i3t 3ifw 3ihp 3jsv 3jvz 3jw0 3k9o 3k9p 3kvf 3kw5 3ldz 3mhs 3mtn 3n30 3n32 3n3k 3nhe 3nob 3ns8 3o65 3ofi 3oj3 3oj4 3ons 3phd 3prm 3pt2 3ptf 3q3f 3rul 3tmp 3u30 3ugb 3v6c 3v6e 3vfk 3vuw 3vux 3vuy 3wxe 3wxf 3zlz 3znh 3zni 3znz 4ap4 4auq 4bos 4boz 4bvu 4ddg 4ddi 4dhj 4dhz 4fjv 4hk2 4hxd 4i6l 4i6n 4ig7 4ium 4jqw 4k1r 4k7s 4k7u 4k7w 4ksk 4ksl 4lcd 4ldt 4mdk 4mm3 4msm 4msq 4nqk 4un2 4v3l 4wzp 4xok 4xol 4zqs 5a5b 5af4 5af5 5af6 5ait 5aiu 5b83 5c7j 5c7m 5e6j 5h07 5nl4 5nlf 5nli 5nmc

(-) Related Entries Specified in the PDB File

4v3l E3-E2-UB