8UX1 | pdb_00008ux1

Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle

• PDB DOI: https://doi.org/10.2210/pdb8UX1/pdb
• EM Map EMD-42685: EMDB EMDataResource
• NAKB: 8UX1

• Classification: NUCLEAR PROTEIN
• Organism(s): Drosophila melanogaster, synthetic construct, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-11-08 Released: 2023-11-22 
• Deposition Author(s): Huang, S.K., Rubinstein, J.L., Kay, L.E.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada), Canadian Institutes of Health Research (CIHR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle

Huang, S.K., Rubinstein, J.L., Kay, L.E.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A6B2C1D1 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: 272.23 kDa 
• Atom Count: 16,395 
• Modeled Residue Count: 1,623 
• Deposited Residue Count: 1,920 
• Unique protein chains: 6
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	A, E	136	Drosophila melanogaster	Mutation(s): 0  Gene Names: CALMAC_LOCUS17614
UniProt
Find proteins for P02299 (Drosophila melanogaster) Explore P02299  Go to UniProtKB:  P02299

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	104	Drosophila melanogaster	Mutation(s): 0  Gene Names:  His4, H4, His4r, H4r, CG3379, His4:CG31611, CG31611, His4:CG33869, CG33869, His4:CG33871, CG33871, His4:CG33873, CG33873, His4:CG33875, CG33875, His4:CG33877, CG33877, His4:CG33879, CG33879, His4:CG33881, CG33881, His4:CG33883, CG33883, His4:CG33885, CG33885, His4:CG33887, CG33887, His4:CG33889, CG33889, His4:CG33891, CG33891, His4:CG33893, CG33893, His4:CG33895, CG33895, His4:CG33897, CG33897, His4:CG33899, CG33899, His4:CG33901, CG33901, His4:CG33903, CG33903, His4:CG33905, CG33905, His4:CG33907, CG33907, His4:CG33909, CG33909
UniProt
Find proteins for P84040 (Drosophila melanogaster) Explore P84040  Go to UniProtKB:  P84040

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A	C, G	124	Drosophila melanogaster	Mutation(s): 0  Gene Names:  His2A, H2a, His2A:CG31618, CG31618, His2A:CG33808, CG33808, His2A:CG33814, CG33814, His2A:CG33817, CG33817, His2A:CG33820, CG33820, His2A:CG33823, CG33823, His2A:CG33826, CG33826, His2A:CG33829, CG33829, His2A:CG33832, CG33832, His2A:CG33835, CG33835, His2A:CG33838, CG33838, His2A:CG33841, CG33841, His2A:CG33844, CG33844, His2A:CG33847, CG33847, His2A:CG33850, CG33850, His2A:CG33862, CG33862, His2A:CG33865, CG33865
UniProt
Find proteins for P84051 (Drosophila melanogaster) Explore P84051  Go to UniProtKB:  P84051

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B	D, H	125	Drosophila melanogaster	Mutation(s): 0  Gene Names: His2B
UniProt
Find proteins for P02283 (Drosophila melanogaster) Explore P02283  Go to UniProtKB:  P02283

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding nuclear protein Ran	K	216	Homo sapiens	Mutation(s): 0  Gene Names: RAN, ARA24, OK/SW-cl.81 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P62826 (Homo sapiens) Explore P62826  Go to UniProtKB:  P62826
PHAROS:  P62826 GTEx:  ENSG00000132341

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Regulator of chromosome condensation	L	420	Homo sapiens	Mutation(s): 0  Gene Names: RCC1
UniProt & NIH Common Fund Data Resources
Find proteins for P18754 (Homo sapiens) Explore P18754  Go to UniProtKB:  P18754
PHAROS:  P18754 GTEx:  ENSG00000180198

Entity ID: 5
Molecule	Chains	Length	Organism	Image
153-bp Widom 601 DNA forward strand	I	153	synthetic construct

Entity ID: 6
Molecule	Chains	Length	Organism	Image
153-bp Widom 601 DNA reverse strand	J	153	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-22 
Deposition Author(s): Huang, S.K., Rubinstein, J.L., Kay, L.E.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	2015-04347
Canadian Institutes of Health Research (CIHR)	Canada	FND-50357

Revision History  

• Version 1.0: 2023-11-22
  Type: Initial release
  
• Version 1.1: 2025-05-28
  Changes: Data collection, Structure summary