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(-) Description

Title :  STRUCTURE OF UHRF2-SRA IN COMPLEX WITH A 5MC-CONTAINING DNA
 
Authors :  T. Zhou, J. Xiong, M. Wang, N. Yang, J. Wong, B. Zhu, R. M. Xu
Date :  19 Mar 14  (Deposition) - 07 May 14  (Release) - 25 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
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 :  Sra, 5Hmc Binding, 5Hmc-Containing Dna, Methylation, Nuclear, Ligase- Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Zhou, J. Xiong, M. Wang, N. Yang, J. Wong, B. Zhu, R. M. Xu
Structural Basis For Hydroxymethylcytosine Recognition By The Sra Domain Of Uhrf2.
Mol. Cell V. 54 879 2014
PubMed-ID: 24813944  |  Reference-DOI: 10.1016/J.MOLCEL.2014.04.003

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE UHRF2
    Chains: A, B, E, F
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A-SMT
    Expression System Strain: BL21(DE3) CODON PLUS RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: UHRF2, NIRF, RNF107
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NP95/ICBP90-LIKE RING FINGER PROTEIN, NP95-LIKE RING FINGER PROTEIN, NUCLEAR PROTEIN 97, NUCLEAR ZINC FINGER PROTEIN NP97, RING FINGER PROTEIN 107, UBIQUITIN-LIKE PHD AND RING FINGER DOMAIN- CONTAINING PROTEIN 2, UBIQUITIN-LIKE-CONTAINING PHD AND RING FINGER DOMAINS PROTEIN 2
 
Molecule 2 - 5MC-CONTAINING DNA1
    Chains: C, G
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5MC-CONTAINING DNA2
    Chains: D, H
    Engineered: YES
    Synthetic: YES

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
15CM2Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
15CM1Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
15CM1Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE

(-) Sites  (0, 0)

(no "Site" information available for 4PW7)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PW7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PW7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PW7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PW7)

(-) Exons   (0, 0)

(no "Exon" information available for 4PW7)

(-) 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:197
                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................ee.hhhhhhhh.........eeee...eeeeeee............eeeee.................hhhhhhhhhh..........ee..hhhhh..eeeeee.hhhhh........eeeeeeeeeeeeeeee......eeeeeeeee........hhhhhhhhhhh...ee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pw7 A 441 IVPSNHYGPIPGIPVGSTWRFRVQVSEAGVHRPHVGGIHGRSNDGAYSLVLAGGFADEVDRGDEFTYTGSGGKKRIGAPSADQTLTNMNRALALNCDAPLDDKIGAESRNWRAGKPVRVIRSFKGRKISKYAPEEGNRYDGIYKVVKYWPEISSSHGFLVWRYLLRRDDVEPAPWTSEGIERSRRLCLRLQYPAGYP 642
                                   450       460       470       480       490       500       510  ||   525       535       545       555       565       575       585       595       605       615       625       635       
                                                                                                  513|                                                                                                                           
                                                                                                   519                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:189
                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................ee.hhhhhhhh.........eeee...eeeeeee............eeeee.........hhhhhhhhhh..........ee..hhhhh..eeeeee.hhhhh........eeeeeeeeeeeeeeee......eeeeeeeee........hhhhhhhhhhh...ee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pw7 B 441 IVPSNHYGPIPGIPVGSTWRFRVQVSEAGVHRPHVGGIHGRSNDGAYSLVLAGGFADEVDRGDEFTYTGSGSADQTLTNMNRALALNCDAPLDDKIGAESRNWRAGKPVRVIRSFKGRKISKYAPEEGNRYDGIYKVVKYWPEISSSHGFLVWRYLLRRDDVEPAPWTSEGIERSRRLCLRLQYPAGYP 642
                                   450       460       470       480       490       500       510||     533       543       553       563       573       583       593       603       613       623       633         
                                                                                                511|                                                                                                                     
                                                                                                 525                                                                                                                     


Chain C from PDB  Type:DNA  Length:12
                                            
                 4pw7 C   1 CTGGTCcGGATG  12
                                  | 10  
                                  7-5CM 


Chain D from PDB  Type:DNA  Length:12
                                            
                 4pw7 D   1 CCATCCGGACCA  12
                                    10  


Chain E from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...................ee.hhhhhhhh.........eeee...eeeeeee............eeeee................hhhhhhhhhh..........ee..hhhhh..eeeeee.hhhhh........eeeeeeeeeeeeeeee......eeeeeeeee........hhhhhhhhhhh...ee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pw7 E 439 CTIVPSNHYGPIPGIPVGSTWRFRVQVSEAGVHRPHVGGIHGRSNDGAYSLVLAGGFADEVDRGDEFTYTGSGGKRIGAPSADQTLTNMNRALALNCDAPLDDKIGAESRNWRAGKPVRVIRSFKGRKISKYAPEEGNRYDGIYKVVKYWPEISSSHGFLVWRYLLRRDDVEPAPWTSEGIERSRRLCLRLQYPAGYP 642
                                   448       458       468       478       488       498       508    || 524       534       544       554       564       574       584       594       604       614       624       634        
                                                                                                    513|                                                                                                                          
                                                                                                     520                                                                                                                          


Chain F from PDB  Type:PROTEIN  Length:191
                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...................ee.hhhhhhhh.........eeee...eeeeeee............eeeee.........hhhhhhhhhh..........ee..hhhhh..eeeeee.hhhhh........eeeeeeeeeeeeeeee......eeeeeeeee........hhhhhhhhhhh...ee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pw7 F 439 CTIVPSNHYGPIPGIPVGSTWRFRVQVSEAGVHRPHVGGIHGRSNDGAYSLVLAGGFADEVDRGDEFTYTGSGSADQTLTNMNRALALNCDAPLDDKIGAESRNWRAGKPVRVIRSFKGRKISKYAPEEGNRYDGIYKVVKYWPEISSSHGFLVWRYLLRRDDVEPAPWTSEGIERSRRLCLRLQYPAGYP 642
                                   448       458       468       478       488       498       508  ||   531       541       551       561       571       581       591       601       611       621       631       641 
                                                                                                  511|                                                                                                                     
                                                                                                   525                                                                                                                     


Chain G from PDB  Type:DNA  Length:12
                                            
                 4pw7 G   1 CTGGTCcGGATG  12
                                  | 10  
                                  7-5CM 


Chain H from PDB  Type:DNA  Length:12
                                            
                 4pw7 H   1 CCATCCGGACCA  12
                                    10
   Legend:   → Mismatch (orange background)
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    → 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 4PW7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PW7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PW7)

(-) Gene Ontology  (21, 21)

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 Related Entries

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

UniProtKB/Swiss-Prot
        UHRF2_HUMAN | Q96PU4: 1wy8 1z6u 2e6s 3oln 4pw5 4pw6 4tvr

(-) Related Entries Specified in the PDB File

4pw5 4pw6