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- PDB-7e9f: Cryo-EM structure of the 2:1 Orc1 BAH domain in complex with nucl... -

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Basic information

Entry
Database: PDB / ID: 7e9f
TitleCryo-EM structure of the 2:1 Orc1 BAH domain in complex with nucleosome
Components
  • (DNA (147-mer)) x 2
  • Histone H2A.2
  • Histone H2B.2
  • Histone H3
  • Histone H4
  • Origin recognition complex subunit 1
KeywordsSTRUCTURAL PROTEIN / nucleosome / transcriptional silencing / chromatin
Function / homology
Function and homology information


CDC6 association with the ORC:origin complex / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / maintenance of rDNA / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 ...CDC6 association with the ORC:origin complex / sexual sporulation resulting in formation of a cellular spore / cupric reductase (NADH) activity / HATs acetylate histones / global genome nucleotide-excision repair / RNA polymerase I upstream activating factor complex / maintenance of rDNA / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / nuclear origin of replication recognition complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / Activation of the pre-replicative complex / nuclear pre-replicative complex / Activation of ATR in response to replication stress / nucleosome organization / DNA replication preinitiation complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / mitotic DNA replication checkpoint signaling / Oxidative Stress Induced Senescence / RMTs methylate histone arginines / SUMOylation of chromatin organization proteins / silent mating-type cassette heterochromatin formation / Orc1 removal from chromatin / RNA Polymerase I Promoter Escape / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / Estrogen-dependent gene expression / rRNA transcription / DNA replication origin binding / intracellular copper ion homeostasis / DNA replication initiation / Ub-specific processing proteases / nucleosome binding / CENP-A containing nucleosome / aerobic respiration / structural constituent of chromatin / nucleosome / heterochromatin formation / nucleosome assembly / chromatin organization / protein heterodimerization activity / DNA repair / chromatin binding / regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / metal ion binding / identical protein binding / nucleus
Similarity search - Function
: / Origin recognition complex subunit 1 C-terminal winged HTH domain / AAA lid domain / AAA lid domain / : / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. ...: / Origin recognition complex subunit 1 C-terminal winged HTH domain / AAA lid domain / AAA lid domain / : / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain / Bromo adjacent homology (BAH) domain superfamily / BAH domain profile. / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B.2 / Histone H4 / Histone H2A.2 / Origin recognition complex subunit 1 / Histone H3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsJiang, H. / Yu, C. / Liu, C.P. / Han, X. / Yu, Z. / Xu, R.M.
Funding support China, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFA0508900, 2018YFE0203300 China
National Natural Science Foundation of China (NSFC)31991162, 91853204, 31521002 China
CitationJournal: To Be Published
Title: Nucleosome binding relinquishes the association of the BAH domain of Orc1 with Sir1
Authors: Jiang, H. / Yu, C. / Liu, C.P. / Han, X. / Yu, Z. / Xu, R.M.
History
DepositionMar 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone H3
B: Histone H4
C: Histone H2A.2
D: Histone H2B.2
E: Histone H3
F: Histone H4
G: Histone H2A.2
H: Histone H2B.2
I: DNA (147-mer)
J: DNA (147-mer)
K: Origin recognition complex subunit 1
L: Origin recognition complex subunit 1


Theoretical massNumber of molelcules
Total (without water)251,23712
Polymers251,23712
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 10 molecules AEBFCGDHKL

#1: Protein Histone H3


Mass: 15146.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HHT1, YBR010W, YBR0201, HHT2, SIN2, YNL031C, N2749 / Production host: Escherichia coli (E. coli) / References: UniProt: P61830
#2: Protein Histone H4


Mass: 11395.390 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HHF1, YBR009C, YBR0122, HHF2, YNL030W, N2752 / Production host: Escherichia coli (E. coli) / References: UniProt: P02309
#3: Protein Histone H2A.2


Mass: 14013.177 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HTA2, H2A2, YBL003C, YBL0103 / Production host: Escherichia coli (E. coli) / References: UniProt: P04912
#4: Protein Histone H2B.2


Mass: 14264.341 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: HTB2, H2B2, YBL002W, YBL0104 / Production host: Escherichia coli (E. coli) / References: UniProt: P02294
#7: Protein Origin recognition complex subunit 1 / Origin recognition complex 120 kDa subunit


Mass: 25423.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ORC1, YML065W / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P54784

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (147-mer)


Mass: 45145.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
#6: DNA chain DNA (147-mer)


Mass: 45604.047 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Yeast Orc1 BAH domain in complex with 147-bp nucleosomeCOMPLEXall0MULTIPLE SOURCES
2HistoneRIBOSOME#1-#41RECOMBINANT
3DNARIBOSOME#5-#61NATURAL
4Origin recognition complex subunit 1RIBOSOME#71RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Saccharomyces cerevisiae S288C (yeast)559292
32Escherichia coli (E. coli)562
43Saccharomyces cerevisiae S288C (yeast)559292
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Spodoptera frugiperda (fall armyworm)7108
42Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3247: / Classification: refinement
EM software
IDNameVersionCategory
4GctfCTF correction
7UCSF Chimeramodel fitting
12RELION33D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 119206 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
16OM3

6om3

16OM31PDBexperimental model
21M4Z

1m4z

11M4Z2PDBexperimental model
33LZ0

3lz0

13LZ03PDBexperimental model
41ID3

1id3

11ID34PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00414005
ELECTRON MICROSCOPYf_angle_d0.71620007
ELECTRON MICROSCOPYf_dihedral_angle_d22.9857526
ELECTRON MICROSCOPYf_chiral_restr0.0442316
ELECTRON MICROSCOPYf_plane_restr0.0051668

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