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PDBsum entry 8u13
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protein dna_rna metals Protein-protein interface(s) links
Structural protein/DNA/transferase PDB id
8u13

 

 

 

 

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Contents
Protein chains
99 a.a.
83 a.a.
95 a.a.
88 a.a.
109 a.a.
DNA/RNA
Metals
_ZN ×2
PDB id:
8u13
Name: Structural protein/DNA/transferase
Title: Cryo-em structure of the human nucleosome core particle ubiquitylated at histone h2a lysine 15 in complex with rnf168-ubch5c (class 1)
Structure: Histone h3.1. Chain: a, e. Synonym: histone h3/a,histone h3/b,histone h3/c,histone h3/d,histone h3/f,histone h3/h,histone h3/i,histone h3/j,histone h3/k,histone h3/l. Engineered: yes. Histone h4. Chain: b, f. Engineered: yes.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: h3c1, h3fa, hist1h3a, h3c2, h3fl, hist1h3b, h3c3, h3fc hist1h3c, h3c4, h3fb, hist1h3d, h3c6, h3fd, hist1h3e, h3c7, h3fi, hist1h3f, h3c8, h3fh, hist1h3g, h3c10, h3fk, hist1h3h, h3c11, h3ff, hist1h3i, h3c12, h3fj, hist1h3j. Expressed in: escherichia coli. Expression_system_taxid: 562.
Authors: Q.Hu,M.V.Botuyan,D.Zhao,G.Cui,G.Mer
Key ref: Q.Hu et al. Cryo-Em structure of the human nucleosome core partic ubiquitylated at histone h2a lysine 15 in complex wit rnf168-Ubch5c (class 1). To be published, . PubMed id: 38242129
Date:
30-Aug-23     Release date:   17-Jan-24    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P68431  (H31_HUMAN) -  Histone H3.1 from Homo sapiens
Seq:
Struc: 		136 a.a.
99 a.a.
Protein chains
Pfam   ArchSchema ?
P62805  (H4_HUMAN) -  Histone H4 from Homo sapiens
Seq:
Struc: 		103 a.a.
83 a.a.
Protein chains
Pfam   ArchSchema ?
P62807  (H2B1C_HUMAN) -  Histone H2B type 1-C/E/F/G/I from Homo sapiens
Seq:
Struc: 		126 a.a.
95 a.a.*
Protein chain
Pfam   ArchSchema ?
Q8IYW5  (RN168_HUMAN) -  E3 ubiquitin-protein ligase RNF168 from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		571 a.a.
88 a.a.
Protein chains
Pfam   ArchSchema ?
P04908  (H2A1B_HUMAN) -  Histone H2A type 1-B/E from Homo sapiens
Seq:
Struc: 		130 a.a.
109 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DNA/RNA chains
  A-T-C-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-T-G-G-T-C-G-T-A- 147 bases
  T-C-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-A-C-T-A-G-G-G-A- 146 bases

 Enzyme reactions 
   Enzyme class: Chain K: 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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