9B2T | pdb_00009b2t

Haspin bound to nucleosome in position 2

• PDB DOI: https://doi.org/10.2210/pdb9B2T/pdb
• EM Map EMD-44114: EMDB EMDataResource
• NAKB: 9B2T

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


• Deposited: 2024-03-16 Released: 2025-01-22 
• Deposition Author(s): Hicks, C.W., Wolberger, C.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.99 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Haspin binds to nucleosomes using a unique DNA binding mechanism

Hicks, C.W., Gliech, C.R., Zhang, X., Rahman, S., Vasquez, S., Holland, A.J., Wolberger, C.

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 - A7B1C1 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 and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 264.14 kDa 
• Atom Count: 15,194 
• Modeled Residue Count: 1,412 
• Deposited Residue Count: 1,711 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	C [auth A], G [auth E]	136	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P84233 (Xenopus laevis) Explore P84233  Go to UniProtKB:  P84233

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	D [auth B], H [auth F]	103	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799  Go to UniProtKB:  P62799

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	E [auth C], I [auth G]	130	Xenopus laevis	Mutation(s): 0  Gene Names: hist1h2aj, LOC494591, XELAEV_18003602mg
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897  Go to UniProtKB:  P06897

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	F [auth D], J [auth H]	123	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
Serine/threonine-protein kinase haspin	K	357	Homo sapiens	Mutation(s): 0  Gene Names: HASPIN, GSG2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TF76 (Homo sapiens) Explore Q8TF76  Go to UniProtKB:  Q8TF76
PHAROS:  Q8TF76 GTEx:  ENSG00000177602

Entity ID: 1
Molecule	Chains	Length	Organism	Image
601 DNA (185-MER)	A [auth I]	185	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
601 DNA (185-MER)	B [auth J]	185	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.99 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Hicks, C.W., Wolberger, C.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R35GM130393

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release
  
• Version 1.1: 2025-05-28
  Changes: Data collection