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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

8X7I

Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy

Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A, EHistone H3.2polymer9811530.42UniProt (Q71DI3)
Pfam (PF00125)
In PDB		Homo sapiens (human)H3-clustered histone 13,H3-clustered histone 14,H3-clustered histone 15,Histone H3/m,Histone H3/o
2B, FHistone H4polymer839509.22UniProt (P62805)
Pfam (PF15511)
In PDB		Homo sapiens (human)
3CHistone H2A type 1-B/Epolymer11112141.21UniProt (P04908)
Pfam (PF00125)
Pfam (PF16211)
In PDB		Homo sapiens (human)Histone H2A.2,Histone H2A/a,Histone H2A/m
4GHistone H2A type 1-B/Epolymer10911936.91UniProt (P04908)
Pfam (PF00125)
Pfam (PF16211)
In PDB		Homo sapiens (human)Histone H2A.2,Histone H2A/a,Histone H2A/m
5IDNA (147-MER)polymer14745604.01Homo sapiens (human)
6JDNA (147-MER)polymer14745145.81Homo sapiens (human)
7D, HHistone H2B type 1-Kpolymer9410478.02UniProt (O60814)
Pfam (PF00125)
In PDB		Homo sapiens (human)
8KUbiquitin-conjugating enzyme E2 D3polymer14716657.91UniProt (P61077)
Pfam (PF00179)
In PDB		Homo sapiens (human)(E3-independent) E2 ubiquitin-conjugating enzyme D3,E2 ubiquitin-conjugating enzyme D3,Ubiquitin carrier protein D3,Ubiquitin-conjugating enzyme E2(17)KB 3,Ubiquitin-conjugating enzyme E2-17 kDa 3,Ubiquitin-protein ligase D3
9LE3 ubiquitin-protein ligase RNF168polymer11312987.11UniProt (Q8IYW5)
Pfam (PF14447)
In PDB		Homo sapiens (human)hRNF168,RING finger protein 168,RING-type E3 ubiquitin transferase RNF168
10MUbiquitinpolymer768622.91UniProt (P62979)
Pfam (PF00240)
In PDB		Homo sapiens (human)
11LZINC IONnon-polymer65.42Chemie (ZN)
Sequence modifications
A, E: 37 - 134 (UniProt: Q71DI3)
PDBExternal DatabaseDetails
Ser 110Cys 111conflict
C: 10 - 120 (UniProt: P04908)
PDBExternal DatabaseDetails
Cys 15Lys 16conflict
K: 1 - 147 (UniProt: P61077)
PDBExternal DatabaseDetails
Ser 21Cys 21conflict
Ser 107Cys 107conflict
Ser 111Cys 111conflict
M: 1 - 75 (UniProt: P62979)
PDBExternal DatabaseDetails
Cys 76-expression tag
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains13
Total formula weight216131.2
Non-Polymers*Number of molecules2
Total formula weight130.8
All*Total formula weight216262.0
*Water molecules are not included.

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PDB entries from 2024-09-11

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