7E9F | pdb_00007e9f

Cryo-EM structure of the 2:1 Orc1 BAH domain in complex with nucleosome

• PDB DOI: https://doi.org/10.2210/pdb7E9F/pdb
• NAKB: 7E9F
• EM Map EMD-31030: EMDB EMDataResource

• Classification: STRUCTURAL PROTEIN
• Organism(s): Saccharomyces cerevisiae S288C, Escherichia coli
• Expression System: Escherichia coli, Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2021-03-04 Released: 2022-09-07 
• Deposition Author(s): Jiang, H., Yu, C., Liu, C.P., Han, X., Yu, Z., Xu, R.M.
• Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental

Literature

Nucleosome binding relinquishes the association of the BAH domain of Orc1 with Sir1

Jiang, H., Yu, C., Liu, C.P., Han, X., Yu, Z., Xu, R.M.

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 - A8B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: cross-linking

Macromolecule Content

• Total Structure Weight: 251.24 kDa 
• Atom Count: 13,279 
• Modelled Residue Count: 1,308 
• Deposited Residue Count: 1,732 
• Unique protein chains: 5
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	A, E	134	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749
UniProt
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P61830  Go to UniProtKB:  P61830

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B, F	103	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752
UniProt
Find proteins for P02309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P02309  Go to UniProtKB:  P02309

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A.2	C, G	132	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: HTA2, H2A2, YBL003C, YBL0103
UniProt
Find proteins for P04912 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04912  Go to UniProtKB:  P04912

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B.2	D, H	131	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: HTB2, H2B2, YBL002W, YBL0104
UniProt
Find proteins for P02294 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P02294  Go to UniProtKB:  P02294

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Origin recognition complex subunit 1	K, L	219	Saccharomyces cerevisiae S288C	Mutation(s): 1  Gene Names: ORC1, YML065W
UniProt
Find proteins for P54784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P54784  Go to UniProtKB:  P54784

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (147-mer)	I	147	Escherichia coli

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (147-mer)	J	147	Escherichia coli

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.00 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.0
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-07 
Deposition Author(s): Jiang, H., Yu, C., Liu, C.P., Han, X., Yu, Z., Xu, R.M.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2019YFA0508900, 2018YFE0203300
National Natural Science Foundation of China (NSFC)	China	31991162, 91853204, 31521002

Revision History  

• Version 1.0: 2022-09-07
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Refinement description, Structure summary