7E9C | pdb_00007e9c

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

PDB DOI: https://doi.org/10.2210/pdb7E9C/pdb
NAKB: 7E9C
EM Map EMD-31029: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Saccharomyces cerevisiae S288C, Escherichia coli
Expression System: Escherichia coli, Spodoptera frugiperda
Mutation(s): No

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)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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.

Macromolecule Content

Total Structure Weight: 225.83 kDa
Atom Count: 12,338
Modeled Residue Count: 1,158
Deposited Residue Count: 1,512
Unique protein chains: 5
Unique nucleic acid chains: 2

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61830
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02309
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04912
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02294
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Origin recognition complex subunit 1	K	218	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: ORC1, YML065W
UniProt
Find proteins for P54784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P54784 Go to UniProtKB: P54784
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P54784
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 5
DNA (147-mer)	I	147	Escherichia coli
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 6
DNA (147-mer)	J	147	Escherichia coli
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AYA Query on AYA	K	L-PEPTIDE LINKING	C₅ H₉ N O₃		ALA

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-09-07

Deposition Author(s):

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