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- EMDB-31029: Cryo-EM structure of the 1:1 Orc1 BAH domain in complex with nucl... -

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Basic information

Entry
Database: EMDB / ID: EMD-31029
TitleCryo-EM structure of the 1:1 Orc1 BAH domain in complex with nucleosome
Map data
Sample
  • Complex: yeast Orc1 BAH domain in complex with 147-bp nucleosome
    • Complex: Histone
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A.2
      • Protein or peptide: Histone H2B.2
    • Complex: DNA
      • DNA: DNA (147-mer)
      • DNA: DNA (147-mer)
    • Complex: Origin recognition complex subunit 1
      • Protein or peptide: Origin recognition complex subunit 1
Keywordsnucleosome / transcriptional silencing / chromatin / STRUCTURAL PROTEIN
Function / homology
Function and homology information


CDC6 association with the ORC:origin complex / Assembly of the ORC complex at the origin of replication / Orc1 removal from chromatin / HDMs demethylate histones / sexual sporulation resulting in formation of a cellular spore / HATs acetylate histones / cupric reductase (NADH) activity / Condensation of Prophase Chromosomes / global genome nucleotide-excision repair / maintenance of rDNA ...CDC6 association with the ORC:origin complex / Assembly of the ORC complex at the origin of replication / Orc1 removal from chromatin / HDMs demethylate histones / sexual sporulation resulting in formation of a cellular spore / HATs acetylate histones / cupric reductase (NADH) activity / Condensation of Prophase Chromosomes / global genome nucleotide-excision repair / maintenance of rDNA / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / nuclear origin of replication recognition complex / CENP-A containing nucleosome / Activation of the pre-replicative complex / nuclear pre-replicative complex / nucleosome organization / Activation of ATR in response to replication stress / SUMOylation of chromatin organization proteins / DNA replication preinitiation complex / mitotic DNA replication checkpoint signaling / RMTs methylate histone arginines / rRNA transcription / silent mating-type cassette heterochromatin formation / kinetochore assembly / positive regulation of transcription by RNA polymerase I / DNA replication origin binding / intracellular copper ion homeostasis / DNA replication initiation / nucleolar large rRNA transcription by RNA polymerase I / mitotic metaphase chromosome alignment / nucleosome binding / aerobic respiration / nucleosomal DNA binding / kinetochore / structural constituent of chromatin / nucleosome / nucleosome assembly / heterochromatin formation / 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 H2A conserved site / Histone H2A signature. / Histone H2B 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
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) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsJiang H / Yu C
Funding support China, 2 items
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 CP / Han X / Yu Z / Xu RM
History
DepositionMar 4, 2021-
Header (metadata) releaseSep 7, 2022-
Map releaseSep 7, 2022-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_31029.png

Downloads & links

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Map

FileDownload / File: emd_31029.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 192 pix.
= 192. Å		1 Å/pix.
x 192 pix.
= 192. Å		1 Å/pix.
x 192 pix.
= 192. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.8932904 - 1.6651977
Average (Standard dev.)0.0076045822 (±0.07924741)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 192.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_31029_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_31029_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : yeast Orc1 BAH domain in complex with 147-bp nucleosome

EntireName: yeast Orc1 BAH domain in complex with 147-bp nucleosome
Components
  • Complex: yeast Orc1 BAH domain in complex with 147-bp nucleosome
    • Complex: Histone
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A.2
      • Protein or peptide: Histone H2B.2
    • Complex: DNA
      • DNA: DNA (147-mer)
      • DNA: DNA (147-mer)
    • Complex: Origin recognition complex subunit 1
      • Protein or peptide: Origin recognition complex subunit 1

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Supramolecule #1: yeast Orc1 BAH domain in complex with 147-bp nucleosome

SupramoleculeName: yeast Orc1 BAH domain in complex with 147-bp nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #2: Histone

SupramoleculeName: Histone / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Escherichia coli (E. coli)

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Supramolecule #4: Origin recognition complex subunit 1

SupramoleculeName: Origin recognition complex subunit 1 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #7

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 15.146734 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LASKAARKSA PSTGGVKKPH RYKPGTVALR EIRRFQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA IGALQESVEA YLVSLFEDTN LAAIHAKRVT IQKKDIKLAR RLRGE

UniProtKB: Histone H3

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 11.39539 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KILRDNIQGI TKPAIRRLAR RGGVKRISGL IYEEVRAVLK SFLESVIRDS VTYTEHAKRK TVTSLDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A.2

MacromoleculeName: Histone H2A.2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 14.013177 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGGKGGKAG SAAKASQSRS AKAGLTFPVG RVHRLLRRGN YAQRIGSGAP VYLTAVLEYL AAEILELAGN AARDNKKTRI IPRHLQLAI RNDDELNKLL GNVTIAQGGV LPNIHQNLLP KKSAKTAKAS QEL

UniProtKB: Histone H2A.2

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Macromolecule #4: Histone H2B.2

MacromoleculeName: Histone H2B.2 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 14.264341 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSSAAEKKPA SKAPAEKKPA AKKTSTSVDG KKRSKVRKET YSSYIYKVLK QTHPDTGISQ KSMSILNSFV NDIFERIATE ASKLAAYNK KSTISAREIQ TAVRLILPGE LAKHAVSEGT RAVTKYSSST QA

UniProtKB: Histone H2B.2

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Macromolecule #7: Origin recognition complex subunit 1

MacromoleculeName: Origin recognition complex subunit 1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 25.439887 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: (AYA)KTLKDLQGW EIITTDEQGN IIDGGQKRLR RRGAKTEHYL KRSSDGIKLG RGDSVVMHNE AAGTYSVYMI QELRLN TLN NVVELWALTY LRWFEVNPLA HYRQFNPDAN ILNRPLNYYN KLFSETANKN ELYLTAELAE LQLFNFIRVA NVMDGSK WE VLKGNVDPER ...String:
(AYA)KTLKDLQGW EIITTDEQGN IIDGGQKRLR RRGAKTEHYL KRSSDGIKLG RGDSVVMHNE AAGTYSVYMI QELRLN TLN NVVELWALTY LRWFEVNPLA HYRQFNPDAN ILNRPLNYYN KLFSETANKN ELYLTAELAE LQLFNFIRVA NVMDGSK WE VLKGNVDPER DFTVRYICEP TGEKFVDINI EDVKAYIKKV EPREAQEYLK DLTLPSKKKE

UniProtKB: Origin recognition complex subunit 1

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Macromolecule #5: DNA (147-mer)

MacromoleculeName: DNA (147-mer) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 45.145754 KDa
SequenceString: (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT) ...String:
(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT)(DC) (DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG)(DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC)(DA) (DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT)(DA) (DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC)(DT) (DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT)(DT) (DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC)(DG) (DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG)(DT) (DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG)(DT) (DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC)(DC) (DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT)(DT) (DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG)(DT) (DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT)(DC) (DC)(DT)(DG)(DT)

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Macromolecule #6: DNA (147-mer)

MacromoleculeName: DNA (147-mer) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 45.604047 KDa
SequenceString: (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC) ...String:
(DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA)(DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT)(DG) (DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG)(DG) (DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT)(DT) (DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG)(DG) (DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG)(DC) (DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC)(DG) (DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG)(DT) (DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT) (DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC)(DC) (DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC)(DG) (DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA)(DC) (DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC)(DT) (DC)(DC)(DA)(DG)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 251525
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6om3

source_name: PDB, initial_model_type: experimental model

1m4z

source_name: PDB, initial_model_type: experimental model

3lz0

source_name: PDB, initial_model_type: experimental model

1id3

source_name: PDB, initial_model_type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-7e9c:
Cryo-EM structure of the 1:1 Orc1 BAH domain in complex with nucleosome

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