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(-) Description

Title :  STRUCTURE OF UHRF2-SRA IN COMPLEX WITH A 5HMC-CONTAINING DNA, COMPLEX I
 
Authors :  T. Zhou, J. Xiong, M. Wang, N. Yang, J. Wong, B. Zhu, R. M. Xu
Date :  18 Mar 14  (Deposition) - 07 May 14  (Release) - 25 Jun 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
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, Hydroxymethylation, 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: 469008
    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 - 5HMC-CONTAINING DNA1
    Chains: C, G
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - 5HMC-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
15HC2Mod. Nucleotide2'-DEOXY-5-(HYDROXYMETHYL)CYTIDINE 5'-(DIHYDROGENPHOSPHATE)
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
15HC1Mod. Nucleotide2'-DEOXY-5-(HYDROXYMETHYL)CYTIDINE 5'-(DIHYDROGENPHOSPHATE)
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
15HC1Mod. Nucleotide2'-DEOXY-5-(HYDROXYMETHYL)CYTIDINE 5'-(DIHYDROGENPHOSPHATE)

(-) Sites  (0, 0)

(no "Site" information available for 4PW5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PW5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PW5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PW5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PW5)

(-) Exons   (0, 0)

(no "Exon" information available for 4PW5)

(-) 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: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
                 4pw5 A 441 IVPSNHYGPIPGIPVGSTWRFRVQVSEAGVHRPHVGGIHGRSNDGAYSLVLAGGFADEVDRGDEFTYTGSGGSADQTLTNMNRALALNCDAPLDDKIGAESRNWRAGKPVRVIRSFKGRKISKYAPEEGNRYDGIYKVVKYWPEISSSHGFLVWRYLLRRDDVEPAPWTSEGIERSRRLCLRLQYPAGY 641
                                   450       460       470       480       490       500       510 ||    532       542       552       562       572       582       592       602       612       622       632         
                                                                                                 512|                                                                                                                    
                                                                                                  525                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               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.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pw5 B 441 IVPSNHYGPIPGIPVGSTWRFRVQVSEAGVHRPHVGGIHGRSNDGAYSLVLAGGFADEVDRGDEFTYTGSGSADQTLTNMNRALALNCDAPLDDKIGAESRNWRAGKPVRVIRSFKGRKISKYAPEEGNRYDGIYKVVKYWPEISSSHGFLVWRYLLRRDDVEPAPWTSEGIERSRRLCLRLQYPAGY 641
                                   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
                                            
                 4pw5 C   1 CTGGTCcGGATG  12
                                  | 10  
                                  7-5HC 


Chain D from PDB  Type:DNA  Length:11
                                           
                 4pw5 D   2 CATCCGGACCA  12
                                    11 


Chain E from PDB  Type:PROTEIN  Length:188
                                                                                                                                                                                                                            
               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
                 4pw5 E 442 VPSNHYGPIPGIPVGSTWRFRVQVSEAGVHRPHVGGIHGRSNDGAYSLVLAGGFADEVDRGDEFTYTGSGGSADQTLTNMNRALALNCDAPLDDKIGAESRNWRAGKPVRVIRSFKGRKISKYAPEEGNRYDGIYKVVKYWPEISSSHGFLVWRYLLRRDDVEPAPWTSEGIERSRRLCLRLQYPAGY 641
                                   451       461       471       481       491       501       511||     533       543       553       563       573       583       593       603       613       623       633        
                                                                                                512|                                                                                                                    
                                                                                                 525                                                                                                                    


Chain F from PDB  Type:PROTEIN  Length:187
                                                                                                                                                                                                                           
               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.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pw5 F 442 VPSNHYGPIPGIPVGSTWRFRVQVSEAGVHRPHVGGIHGRSNDGAYSLVLAGGFADEVDRGDEFTYTGSGSADQTLTNMNRALALNCDAPLDDKIGAESRNWRAGKPVRVIRSFKGRKISKYAPEEGNRYDGIYKVVKYWPEISSSHGFLVWRYLLRRDDVEPAPWTSEGIERSRRLCLRLQYPAGY 641
                                   451       461       471       481       491       501       511|      534       544       554       564       574       584       594       604       614       624       634       
                                                                                               511|                                                                                                                    
                                                                                                525                                                                                                                    


Chain G from PDB  Type:DNA  Length:12
                                            
                 4pw5 G   1 CTGGTCcGGATG  12
                                  | 10  
                                  7-5HC 


Chain H from PDB  Type:DNA  Length:11
                                           
                 4pw5 H   2 CATCCGGACCA  12
                                    11
   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 4PW5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PW5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PW5)

(-) 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 4pw6 4pw7 4tvr

(-) Related Entries Specified in the PDB File

4pw6 4pw7