9IPU

cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome

• PDB DOI: https://doi.org/10.2210/pdb9IPU/pdb
• EM Map EMD-60781: EMDB EMDataResource

• Classification: NUCLEAR PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-11 Released: 2024-10-02 
• Deposition Author(s): Ai, H.S., Deng, Z.H., Liu, L.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Chemically and Site-specifically Ubiquitylated Linker Histone H1 Facilitates RNF168-Mediated Nucleosomal H2A Ubiquitylation

Shi, Q., Deng, Z.H., Zhang, L.Y., Tong, Z.B., Chu, G.-C., Ai, H.S., Liu, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A2B2C2D2E1F1G1H1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A5B2C1D1E1F1G1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Hetero 8-mer - A2B2C2D2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 282.99 kDa 
• Atom Count: 15,750 
• Modelled Residue Count: 1,470 
• Deposited Residue Count: 1,933 
• Unique protein chains: 8
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H1.0	A [auth I]	194	Homo sapiens	Mutation(s): 0  Gene Names: H1-0, H1F0, H1FV
UniProt & NIH Common Fund Data Resources
Find proteins for P07305 (Homo sapiens) Explore P07305  Go to UniProtKB:  P07305
PHAROS:  P07305 GTEx:  ENSG00000189060

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	B [auth A], F [auth E]	135	Homo sapiens	Mutation(s): 0  Gene Names: H3C15, HIST2H3A, H3C14, H3F2, H3FM, HIST2H3C, H3C13, HIST2H3D
UniProt & NIH Common Fund Data Resources
Find proteins for Q71DI3 (Homo sapiens) Explore Q71DI3  Go to UniProtKB:  Q71DI3
PHAROS:  Q71DI3 GTEx:  ENSG00000183598 ENSG00000203811 ENSG00000203852

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	C [auth B], G [auth F]	102	Homo sapiens	Mutation(s): 0  Gene Names:  H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4C16, H4-16, HIST4H4
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805 GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1-B/E	D [auth C], H [auth G]	129	Homo sapiens	Mutation(s): 0  Gene Names: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE
UniProt & NIH Common Fund Data Resources
Find proteins for P04908 (Homo sapiens) Explore P04908  Go to UniProtKB:  P04908
PHAROS:  P04908 GTEx:  ENSG00000277075 ENSG00000278463

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-K	E [auth D], I [auth H]	125	Homo sapiens	Mutation(s): 0  Gene Names: H2BC12, H2BFT, HIRIP1, HIST1H2BK
UniProt & NIH Common Fund Data Resources
Find proteins for O60814 (Homo sapiens) Explore O60814  Go to UniProtKB:  O60814
PHAROS:  O60814 GTEx:  ENSG00000197903

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 D3	J [auth K]	147	Homo sapiens	Mutation(s): 0  Gene Names: UBE2D3, UBC5C, UBCH5C EC: 2.3.2.23 (PDB Primary Data), 2.3.2.24 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P61077 (Homo sapiens) Explore P61077  Go to UniProtKB:  P61077
PHAROS:  P61077 GTEx:  ENSG00000109332

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RNF168	K [auth L]	193	Homo sapiens	Mutation(s): 0  Gene Names: RNF168 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IYW5 (Homo sapiens) Explore Q8IYW5  Go to UniProtKB:  Q8IYW5
PHAROS:  Q8IYW5 GTEx:  ENSG00000163961

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	L [auth M]	75	Homo sapiens	Mutation(s): 0  Gene Names: RPS27A, UBA80, UBCEP1
UniProt & NIH Common Fund Data Resources
Find proteins for P62979 (Homo sapiens) Explore P62979  Go to UniProtKB:  P62979
PHAROS:  P62979 GTEx:  ENSG00000143947

Entity ID: 9
Molecule	Chains	Length	Organism	Image
DNA (171-MER)	M [auth J]	171	Homo sapiens

Entity ID: 10
Molecule	Chains	Length	Organism	Image
DNA (171-MER)	N	171	Homo sapiens

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN (Subject of Investigation/LOI)	O [auth L], P [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.30 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-02 
Deposition Author(s): Ai, H.S., Deng, Z.H., Liu, L.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22137005, 92253302, 22227810

Revision History  

• Version 1.0: 2024-10-02
  Type: Initial release