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(-) Description

Title :  CRYSTAL STRUCTURE OF NDP52 ZF2 IN COMPLEX WITH MONO-UBIQUITIN
 
Authors :  X. Xie, F. Li, Y. Wang, Z. Lin, X. Chen, J. Liu, L. Pan
Date :  12 Jan 15  (Deposition) - 11 Nov 15  (Release) - 11 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Ndp52, Ubiquitin, Zinc Finger, Autophagy Receptor, Complex, Protein Binding-Metal Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Xie, F. Li, Y. Wang, Y. Wang, Z. Lin, X. Cheng, J. Liu, C. Chen, L. Pan
Molecular Basis Of Ubiquitin Recognition By The Autophagy Receptor Calcoco2
Autophagy V. 11 1775 2015
PubMed-ID: 26506893  |  Reference-DOI: 10.1080/15548627.2015.1082025

(-) Compounds

Molecule 1 - UBIQUITIN
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3C
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: UBA52
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - CALCIUM-BINDING AND COILED-COIL DOMAIN-CONTAINING PROTEIN 2
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3C
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ZINC FINGER, UNP RESIDUES 414-446
    Gene: CALCOCO2, NDP52
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ANTIGEN NUCLEAR DOT 52 KDA PROTEIN,NUCLEAR DOMAIN 10 PROTEIN NDP52,NUCLEAR DOMAIN 10 PROTEIN 52,NUCLEAR DOT PROTEIN 52

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2GOL2Ligand/IonGLYCEROL
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2GOL1Ligand/IonGLYCEROL
3ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:7 , LEU A:8 , THR A:9 , LEU A:69 , VAL A:70 , LEU A:71 , HOH A:213 , LEU C:71 , HOH D:601binding site for residue GOL A 101
2AC2SOFTWAREASP B:426 , LYS B:427 , ILE B:428 , HOH B:615binding site for residue ACT B 502
3AC3SOFTWARECYS B:422 , CYS B:425 , HIS B:440 , HIS B:444binding site for residue ZN B 503
4AC4SOFTWARETHR C:7 , LEU C:8 , THR C:9 , LEU C:69 , VAL C:70 , LEU C:71 , HOH C:207 , HOH C:208binding site for residue GOL C 101
5AC5SOFTWARELYS C:11 , THR C:12binding site for residue ACT C 102
6AC6SOFTWARECYS D:419binding site for residue ACT D 501
7AC7SOFTWARECYS D:422 , CYS D:425 , HIS D:440 , HIS D:444binding site for residue ZN D 502

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:419 -D:419

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XKL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XKL)

(-) 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:78
                                                                                                              
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee....eeeeee....hhhhhhhhhhhhhh.hhh.eeeee..ee......hhhhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 4xkl A  -1 GSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                     8        18        28        38        48        58        68        


Chain B from PDB  Type:PROTEIN  Length:30
                                                              
               SCOP domains ------------------------------ SCOP domains
               CATH domains ------------------------------ CATH domains
               Pfam domains ------------------------------ Pfam domains
         Sec.struct. author ..eee......eee..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------ PROSITE
                 Transcript ------------------------------ Transcript
                 4xkl B 417 PLCFNCPICDKIFPATEKQIFEDHVFCHSL 446
                                   426       436       446


Chain C from PDB  Type:PROTEIN  Length:78
                                                                                                              
               SCOP domains ------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee....eeeeee....hhhhhhhhhhhhhh.hhh.eeee...........hhhhh.....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------ Transcript
                 4xkl C  -1 GSMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG  76
                                     8        18        28        38        48        58        68        


Chain D from PDB  Type:PROTEIN  Length:31
                                                               
               SCOP domains ------------------------------- SCOP domains
               CATH domains ------------------------------- CATH domains
               Pfam domains ------------------------------- Pfam domains
         Sec.struct. author ...eee......eee..hhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------- PROSITE
                 Transcript ------------------------------- Transcript
                 4xkl D 416 QPLCFNCPICDKIFPATEKQIFEDHVFCHSL 446
                                   425       435       445
   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 4XKL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (104, 108)

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  4xkl
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 Related Entries

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

UniProtKB/Swiss-Prot
        CACO2_HUMAN | Q13137: 2mxp 3vvv 3vvw 4gxl 4han 5aaq
        RL40_HUMAN | P62987: 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 2lj5 2mbh 2mjb 2mur 2n3u 2n3v 2n3w 2nbd 2nbe 2nr2 2o6v 2ojr 2pe9 2pea 2rsu 2w9n 2wdt 2xew 2xk5 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 3phd 4hjk 4jio 4p4h 4pig 4pih 4pij 4rf0 4rf1 4s1z 4ug0 4v6x 5aj0 5go7 5go8 5gob 5goc 5god 5gog 5goh 5goi 5goj 5gok 5hpk 5hpl 5hps 5hpt 5j26 5j8p 5jbv 5jby 5t2c

(-) Related Entries Specified in the PDB File

2mxp