8UBI | pdb_00008ubi

Cryo-EM structure of NRCAM nucleosome aided by scFv (Class_A)

• PDB DOI: https://doi.org/10.2210/pdb8UBI/pdb
• EM Map EMD-42089: EMDB EMDataResource

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


• Deposited: 2023-09-23 Released: 2026-01-21 
• Deposition Author(s): Zhou, B.R., Bai, Y.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of NRCAM nucleosome aided by scFv

Zhou, B.R., Bai, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E2 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Hetero 10-mer - A6B2C2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 245.45 kDa 
• Atom Count: 16,288 
• Modeled Residue Count: 1,546 
• Deposited Residue Count: 1,632 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	A, E	97	Homo sapiens	Mutation(s): 0  Gene Names: CR201_G0042554
UniProt
Find proteins for H2PI50 (Pongo abelii) Explore H2PI50  Go to UniProtKB:  H2PI50

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	83	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for A0A9J8D176 (Cyprinus carpio carpio) Explore A0A9J8D176  Go to UniProtKB:  A0A9J8D176

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	C, G	109	Homo sapiens	Mutation(s): 0  Gene Names: E5288_WYG010732
UniProt
Find proteins for L8IQP7 (Bos mutus) Explore L8IQP7  Go to UniProtKB:  L8IQP7

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B type 1-J	D, H	95	Homo sapiens	Mutation(s): 0  Gene Names: H2BC11
UniProt & NIH Common Fund Data Resources
Find proteins for P06899 (Homo sapiens) Explore P06899  Go to UniProtKB:  P06899
PHAROS:  P06899 GTEx:  ENSG00000124635

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv	K [auth M], L [auth N]	270	Mus musculus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Length	Organism	Image
NRCAM DNA (162-MER)	I	162	Mus musculus

Entity ID: 6
Molecule	Chains	Length	Organism	Image
NRCAM DNA (162-MER)	J	162	Mus musculus

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	4.1

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-01-21 
Deposition Author(s): Zhou, B.R., Bai, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	Intramural Research Program

Revision History  

• Version 1.0: 2026-01-21
  Type: Initial release