9CG9 | pdb_00009cg9

Cryo-EM structure of an HMGB1 box bound to nucleosome at SHL-2

• PDB DOI: https://doi.org/10.2210/pdb9CG9/pdb
• EM Map EMD-45578: EMDB EMDataResource
• NAKB: 9CG9

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Xenopus laevis, synthetic construct, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-06-28 Released: 2025-07-02 
• Deposition Author(s): Chio, U.S., Saunders, H.S., Narlikar, G.J., Cheng, Y.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.94 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Competition between HMGB1 and H1 on nucleosomes tunes dynamics within condensed chromatin

Saunders, H.S., Chio, U.S., Moore, C.M., Ramani, V., Cheng, Y., Narlikar, G.J.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 9-mer - A2B2C2D2E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 9-mer - A6B2C1 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: 228.24 kDa 
• Atom Count: 12,706 
• Modeled Residue Count: 1,132 
• Deposited Residue Count: 1,501 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	A, E	135	Xenopus laevis	Mutation(s): 2
UniProt
Find proteins for P84233 (Xenopus laevis) Explore P84233  Go to UniProtKB:  P84233

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	102	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799  Go to UniProtKB:  P62799

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1	C, G	129	Xenopus laevis	Mutation(s): 2
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897  Go to UniProtKB:  P06897

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	D, H	122	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281  Go to UniProtKB:  P02281

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
High mobility group protein B1	K	217	Homo sapiens	Mutation(s): 0  Gene Names: HMGB1, HMG1
UniProt & NIH Common Fund Data Resources
Find proteins for P09429 (Homo sapiens) Explore P09429  Go to UniProtKB:  P09429
PHAROS:  P09429 GTEx:  ENSG00000189403

Entity ID: 5
Molecule	Chains	Length	Organism	Image
Widom 601 DNA reverse strand (147-mer)	I	154	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
Widom 601 DNA forward strand (147-mer)	J	154	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.94 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.1.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Chio, U.S., Saunders, H.S., Narlikar, G.J., Cheng, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM127020
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM140847
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	F32GM137463
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release