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(-) Description

Title :  STRUCTURE OF MDM2-MDMX-UBCH5B-UBIQUITIN COMPLEX
 
Authors :  M. Klejnot, D. T. Huang
Date :  13 Dec 16  (Deposition) - 31 May 17  (Release) - 07 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.16
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Ubiquitin Ligase, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Nomura, M. Klejnot, D. Kowalczyk, A. K. Hock, G. J. Sibbet, K. H. Vousden, D. T. Huang
Structural Analysis Of Mdm2 Ring Separates Degradation From Regulation Of P53 Transcription Activity.
Nat. Struct. Mol. Biol. 2017
PubMed-ID: 28553961  |  Reference-DOI: 10.1038/NSMB.3414

(-) Compounds

Molecule 1 - UBIQUITIN-CONJUGATING ENZYME E2 D2
    Chains: A, E
    EC Number: 2.3.2.23, 2.3.2.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: K85 IN CHAINS A AND E FORM ISOPEPTIDE LINKAGE WITH THE CARBONYL CARBON OF G76 IN CHAINS B AND F, RESPECTIVELY.
    Synonym: (E3-INDEPENDENT) E2 UBIQUITIN-CONJUGATING ENZYME D2,E2 UBIQUITIN-CONJUGATING ENZYME D2,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
 
Molecule 2 - POLYUBIQUITIN-B
    Chains: B, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: UBB
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: GSGGS LINKER AT THE N-TERMINUS RESULTED FROM CLONING. G76 IN CHAIN B IS COVALENTLY LINKED TO K85 SIDE CHAIN IN CHAIN A.
 
Molecule 3 - E3 UBIQUITIN-PROTEIN LIGASE MDM2
    Chains: C, G
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MDM2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CONTAINS N-TERMINAL HIS-TAG FOLLOWED BY TEV PROTEASE CLEAVAGE SITE THAT WAS NOT REMOVED DURING PURIFICATION. MDM2 CONTAINS 428-491.
    Synonym: DOUBLE MINUTE 2 PROTEIN,HDM2,ONCOPROTEIN MDM2,P53-BINDING PROTEIN MDM2
 
Molecule 4 - PROTEIN MDM4
    Chains: D, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MDM4, MDMX
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: MDMX CONTAINS 427-490
    Synonym: DOUBLE MINUTE 4 PROTEIN,MDM2-LIKE P53-BINDING PROTEIN, PROTEIN MDMX,P53-BINDING PROTEIN MDM4

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2ZN8Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS C:438 , CYS C:441 , CYS C:461 , CYS C:464binding site for residue ZN C 501
02AC2SOFTWAREHIS C:452 , HIS C:457 , CYS C:475 , CYS C:478binding site for residue ZN C 502
03AC3SOFTWARECYS D:437 , CYS D:440 , CYS D:460 , CYS D:463binding site for residue ZN D 501
04AC4SOFTWAREHIS D:451 , HIS D:456 , CYS D:474 , CYS D:477binding site for residue ZN D 502
05AC5SOFTWAREALA D:472 , SER D:473 , LYS D:478 , ARG E:139 , ALA H:472 , SER H:473 , LYS H:478binding site for residue SO4 D 503
06AC6SOFTWARECYS G:438 , CYS G:441 , CYS G:461 , CYS G:464binding site for residue ZN G 501
07AC7SOFTWAREHIS G:452 , HIS G:457 , CYS G:475 , CYS G:478binding site for residue ZN G 502
08AC8SOFTWAREHIS H:451 , HIS H:456 , CYS H:474 , CYS H:477binding site for residue ZN H 501
09AC9SOFTWARECYS H:437 , CYS H:440 , CYS H:460 , CYS H:463binding site for residue ZN H 502
10AD1SOFTWARELYS D:442 , ARG D:443 , ARG D:466 , LYS H:442 , ARG H:443 , ARG H:466binding site for residue SO4 H 503
11AD2SOFTWAREHIS E:75 , ASN E:77 , ILE E:78 , ILE E:84 , LEU E:86 , ASP E:117 , LEU E:119 , VAL E:120 , TYR E:134 , GLY F:75binding site for Di-peptide GLY F 76 and LYS E 85

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5MNJ)

(-) 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................hhhhh.......hhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mnj 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:75
                                                                                                           
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeee......hhhhhhhhhhhhhh.hhh.eeeee..ee................eeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 5mnj B   2 QIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                    11        21        31        41        51        61        71     


Chain C from PDB  Type:PROTEIN  Length:63
                                                                                               
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh...........eeeee..eeeeeehhhhhhhhhhh............eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 5mnj C 429 SLPLNAIEPCVICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVLTYFP 491
                                   438       448       458       468       478       488   


Chain D from PDB  Type:PROTEIN  Length:63
                                                                                               
               SCOP domains --------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh...........eeeee..eeeeeehhhhhhhhhhh............eeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------- Transcript
                 5mnj D 428 EDCQNLLKPCSLCEKRPRDGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQLVIKVFIA 490
                                   437       447       457       467       477       487   


Chain E from PDB  Type:PROTEIN  Length:146
                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh....eeeee......eeeeeee..........eeeeeee..........eeee................hhhhh.......hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mnj E   2 ALKRIHKELNDLARDPPAQCRAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSIKLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDREKYNRIAREWTQKYAM 147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141      


Chain F from PDB  Type:PROTEIN  Length:76
                                                                                                            
               SCOP domains ---------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeeee.....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------- Transcript
                 5mnj F   1 MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                    10        20        30        40        50        60        70      


Chain G from PDB  Type:PROTEIN  Length:65
                                                                                                 
               SCOP domains ----------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh...........eeeee..eeeeeehhhhhhhhhhh............eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------- Transcript
                 5mnj G 427 SSSLPLNAIEPCVICQGRPKNGCIVHGKTGHLMACFTCAKKLKKRNKPCPVCRQPIQMIVLTYFP 491
                                   436       446       456       466       476       486     


Chain H from PDB  Type:PROTEIN  Length:64
                                                                                                
               SCOP domains ---------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh...........eeeee..eeeeeehhhhhhhhhhhh...........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------- Transcript
                 5mnj H 427 MEDCQNLLKPCSLCEKRPRDGNIIHGRTGHLVTCFHCARRLKKAGASCPICKKEIQLVIKVFIA 490
                                   436       446       456       466       476       486
   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 5MNJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (175, 215)

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 Related Entries

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

UniProtKB/Swiss-Prot
        MDM2_HUMAN | Q00987: 1rv1 1t4e 1t4f 1ycr 1z1m 2axi 2c6a 2c6b 2f1y 2fop 2gv2 2hdp 2lzg 2m86 2mps 2ruh 2vje 2vjf 3eqs 3g03 3iux 3iwy 3jzk 3jzr 3jzs 3lbk 3lbl 3lnj 3lnz 3mqs 3tj2 3tpx 3tu1 3v3b 3vbg 3vzv 3w69 4dij 4ere 4erf 4hbm 4hfz 4hg7 4jv7 4jv9 4jve 4jvr 4jwr 4mdn 4mdq 4oas 4oba 4occ 4ode 4odf 4ogn 4ogt 4ogv 4oq3 4qo4 4qoc 4ud7 4ue1 4umn 4wt2 4xxb 4zfi 4zgk 4zyc 4zyf 4zyi 5afg 5c5a 5hmh 5hmi 5hmk 5j7f 5j7g 5lav 5law 5lay 5laz 5ln2 5trf
        MDM4_HUMAN | O15151: 2cr8 2mwy 2n06 2n0u 2n0w 2n14 2vje 2vjf 2vyr 3dab 3eqy 3fdo 3fe7 3fea 3jzo 3jzp 3jzq 3lbj 3mqr 3u15 4rxz
        UB2D2_HUMAN | P62837: 1ur6 1w4u 2clw 2esk 2eso 2esp 2esq 3a33 3jvz 3jw0 3l1y 3tgd 3zni 4a49 4a4b 4a4c 4auq 4ddg 4ddi 4ldt 4v3k 4v3l 4wz3 5d0k 5d0m 5d1k 5d1l 5d1m 5edv 5ulf 5ulh 5ulk
        UBB_HUMAN | P0CG47: 1c3t 1cmx 1d3z 1f9j 1fxt 1g6j 1gjz 1nbf 1q5w 1s1q 1sif 1tbe 1ubi 1ubq 1ud7 1uzx 1xd3 1yx5 1yx6 1zo6 2ayo 2bgf 2den 2fuh 2g45 2gbj 2gbk 2gbm 2gbn 2gbr 2hth 2ibi 2j7q 2jf5 2jzz 2k6d 2k8b 2k8c 2kdf 2khw 2kjh 2klg 2kn5 2kox 2ktf 2kwu 2kwv 2l0f 2l0t 2mbb 2mro 2msg 2n13 2nr2 2o6v 2ojr 2pe9 2pea 2w9n 2wdt 2xew 2xk5 2y5b 2zcb 3a33 3by4 3c0r 3dvg 3dvn 3eec 3efu 3ehv 3h7p 3h7s 3hm3 3i3t 3ifw 3ihp 3jsv 3jvz 3jw0 3k9p 3kvf 3kw5 3ldz 3mhs 3mtn 3n30 3n32 3n3k 3nhe 3nob 3ns8 3o65 3oj3 3oj4 3ons 3phd 3ptf 3zlz 3znh 4uel 4uf6 4whv 4wlr 4wur 4wzp 4xof 4zfr 4zft 4zpz 4zux 5bnb 5caw 5cra 5cvm 5cvn 5cvo 5d0k 5d0m 5dfl 5dk8 5e6j 5edv 5emz 5eya 5gjq 5go7 5go8 5gob 5goc 5god 5gog 5goh 5goi 5goj 5gok 5ibk 5ifr 5j8p 5jbv 5jby 5jg6 5jp3 5jtj 5jtv 5k9p 5kgf 5khy 5l8h 5l8w 5l9t 5ln1 5lrv 5lrw 5lrx 5m93 5n2w 5n38 5nl5 5nlj 5nvg 5tof 5tog 5ulf 5ulh 5ulk 5v1y 5v1z 5vey 5vf0 5w46 5x3m 5x3n 5x3o 5xbo 5xdp 5xk4 5xk5

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5MNJ)