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PDBsum entry 9dde
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protein dna_rna metals Protein-protein interface(s) links
Gene regulation/DNA PDB id
9dde

 

 

 

 

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Contents
Protein chains
98 a.a.
84 a.a.
107 a.a.
93 a.a.
102 a.a.
101 a.a.
40 a.a.
74 a.a.
71 a.a.
DNA/RNA
Metals
_ZN ×5
PDB id:
9dde
Name: Gene regulation/DNA
Title: Ncprc1rybp bound to h2ak119ub/h1.4 chromatosome
Structure: Histone h3.2. Chain: a, e. Synonym: histone h3. Engineered: yes. Mutation: yes. Histone h4. Chain: b, f. Engineered: yes. Histone h2a type 1.
Source: Xenopus laevis. African clawed frog. Organism_taxid: 8355. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic construct. Organism_taxid: 32630. Homo sapiens. Human.
Authors: V.Godinez-Lopez,M.I.Valencia-Sanchez,J.P.Armache,K.-J.Armache
Key ref: V.Godinez-Lopez et al. Structural visualization of read-Write mechanisms of h2a lysine 119 mono-Ubiquitination by polycomb repres complex 1. To be published, . PubMed id: 39537923
Date:
28-Aug-24     Release date:   20-Nov-24    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P84233  (H32_XENLA) -  Histone H3.2 from Xenopus laevis
Seq:
Struc: 		136 a.a.
98 a.a.*
Protein chains
Pfam   ArchSchema ?
P62799  (H4_XENLA) -  Histone H4 from Xenopus laevis
Seq:
Struc: 		103 a.a.
84 a.a.
Protein chains
Pfam   ArchSchema ?
P06897  (H2A1_XENLA) -  Histone H2A type 1 from Xenopus laevis
Seq:
Struc: 		130 a.a.
107 a.a.*
Protein chains
Pfam   ArchSchema ?
P02281  (H2B11_XENLA) -  Histone H2B 1.1 from Xenopus laevis
Seq:
Struc: 		126 a.a.
93 a.a.*
Protein chain
Pfam   ArchSchema ?
P35226  (BMI1_HUMAN) -  Polycomb complex protein BMI-1 from Homo sapiens
Seq:
Struc: 		326 a.a.
102 a.a.
Protein chain
Pfam   ArchSchema ?
Q99496  (RING2_HUMAN) -  E3 ubiquitin-protein ligase RING2 from Homo sapiens
Seq:
Struc: 		336 a.a.
101 a.a.
Protein chain
Pfam   ArchSchema ?
Q8N488  (RYBP_HUMAN) -  RING1 and YY1-binding protein from Homo sapiens
Seq:
Struc: 		228 a.a.
40 a.a.
Protein chain
Pfam   ArchSchema ?
P0CG48  (UBC_HUMAN) -  Polyubiquitin-C from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		685 a.a.
74 a.a.
Protein chain
Pfam   ArchSchema ?
P10412  (H14_HUMAN) -  Histone H1.4 from Homo sapiens
Seq:
Struc: 		219 a.a.
71 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

DNA/RNA chains
  C-A-C-T-G-G-A-A-C-A-G-G-A-T-G-T-A-T-A-T-A-T-C-T-G-A-C-A-C-G-T-G-C-C-T-G-G-A-G- 162 bases
  C-C-G-A-T-C-C-C-C-T-G-G-A-G-A-A-T-C-C-C-G-G-T-G-C-C-G-A-G-G-C-C-G-C-T-C-A-A-T- 162 bases

 Enzyme reactions 
   Enzyme class: Chain L: E.C.2.3.2.27  - RING-type E3 ubiquitin transferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N6- ubiquitinyl-[acceptor protein]-L-lysine

 

 

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