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- PDB-5zr1: Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 72... -

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Entry
Database: PDB / ID: 5zr1
TitleSaccharomyces Cerevisiae Origin Recognition Complex Bound to a 72-bp Origin DNA containing ACS and B1 element
Components
  • (72bp-oring DNA, ACS305, ...) x 2
  • (Origin recognition complex subunit ...) x 6
KeywordsDNA BINDING PROTEIN/DNA / Origin Recognition Complex / DNA replication initiation / 72-bp origin DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homologyOrigin recognition complex winged helix C-terminal / Origin recognition complex subunit 2 / Origin recognition complex subunit 4 / Origin recognition complex, subunit 1 / Origin recognition complex, subunit 3 / Origin recognition complex, subunit 5 / P-loop containing nucleoside triphosphate hydrolase / Origin recognition complex subunit 4, C-terminal / ATPase family associated with various cellular activities (AAA) / BAH domain ...Origin recognition complex winged helix C-terminal / Origin recognition complex subunit 2 / Origin recognition complex subunit 4 / Origin recognition complex, subunit 1 / Origin recognition complex, subunit 3 / Origin recognition complex, subunit 5 / P-loop containing nucleoside triphosphate hydrolase / Origin recognition complex subunit 4, C-terminal / ATPase family associated with various cellular activities (AAA) / BAH domain / Origin recognition complex subunit 6 (ORC6) / Origin recognition complex, subunit 2 / AAA domain / Origin recognition complex (ORC) subunit 4 C-terminus / Origin recognition complex (ORC) subunit 5 C-terminus / BAH domain profile. / Assembly of the ORC complex at the origin of replication / Orc1 removal from chromatin / Activation of the pre-replicative complex / AAA lid domain / Origin recognition complex, subunit 6 / Origin recognition complex, subunit 6, fungi / ATPase, AAA-type, core / AAA+ ATPase domain / Bromo adjacent homology (BAH) domain / nuclear origin of replication recognition complex / regulation of chromatin silencing at telomere / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / nuclear pre-replicative complex / DNA replication preinitiation complex / mitotic DNA replication checkpoint / chromatin silencing at silent mating-type cassette / histone H3-K4 methylation / chromatin silencing at telomere / DNA replication origin binding / DNA replication initiation / chromosome, telomeric region / mitotic cell cycle / nuclear chromosome, telomeric region / ATPase activity / chromatin binding / ATP binding / nucleus / metal ion binding / Origin recognition complex subunit 2 / Origin recognition complex subunit 6 / Origin recognition complex subunit 5 / Origin recognition complex subunit 1 / Origin recognition complex subunit 3 / Origin recognition complex subunit 4
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3 Å resolution
AuthorsLi, N. / Lam, W.H. / Zhai, Y. / Cheng, J. / Cheng, E. / Zhao, Y. / Gao, N. / Tye, B.K.
CitationJournal: Nature / Year: 2018
Title: Structure of the origin recognition complex bound to DNA replication origin.
Authors: Ningning Li / Wai Hei Lam / Yuanliang Zhai / Jiaxuan Cheng / Erchao Cheng / Yongqian Zhao / Ning Gao / Bik-Kwoon Tye
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 21, 2018 / Release: Jul 11, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 11, 2018Structure modelrepositoryInitial release
1.1Jul 25, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

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Assembly

Deposited unit
A: Origin recognition complex subunit 1
B: Origin recognition complex subunit 2
C: Origin recognition complex subunit 3
D: Origin recognition complex subunit 4
E: Origin recognition complex subunit 5
F: Origin recognition complex subunit 6
G: 72bp-oring DNA, ACS305, T-rich
H: 72bp-oring DNA, ACS305, A-rich
hetero molecules


Theoretical massNumber of molelcules
Total (without water)460,55914
Polyers458,9178
Non-polymers1,6436
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)55020
ΔGint (kcal/M)-321
Surface area (Å2)120160

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Components

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Origin recognition complex subunit ... , 6 types, 6 molecules ABCDEF

#1: Protein/peptide Origin recognition complex subunit 1 / / Origin recognition complex 120 kDa subunit


Mass: 104546.164 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ORC1, YML065W / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P54784
#2: Protein/peptide Origin recognition complex subunit 2 / / Origin recognition complex 71 kDa subunit


Mass: 71342.180 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ORC2, RRR1, SIR5, YBR060C, YBR0523 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P32833
#3: Protein/peptide Origin recognition complex subunit 3 / / Origin recognition complex 62 kDa subunit


Mass: 72161.766 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ORC3, OAF1, OIF1, YLL004W, L1365 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P54790
#4: Protein/peptide Origin recognition complex subunit 4 / / Origin recognition complex 56 kDa subunit


Mass: 60772.152 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ORC4, YPR162C, P9325.5 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P54791
#5: Protein/peptide Origin recognition complex subunit 5 / / Origin recognition complex 53 kDa subunit


Mass: 55347.168 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ORC5, YNL261W, N0834 / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P50874
#6: Protein/peptide Origin recognition complex subunit 6 / / ACS-associated protein 1 / Origin recognition complex 50 kDa subunit


Mass: 50369.531 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ORC6, AAP1, YHR118C / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P38826

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72bp-oring DNA, ACS305, ... , 2 types, 2 molecules GH

#7: DNA chain 72bp-oring DNA, ACS305, T-rich


Mass: 22203.266 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae (baker's yeast)
#8: DNA chain 72bp-oring DNA, ACS305, A-rich


Mass: 22174.412 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae (baker's yeast)

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Non-polymers , 2 types, 6 molecules

#9: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 3 / Formula: C10H16N5O12P3S
Comment: ATP-gamma-S (energy-carrying molecule analogue) *YM
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Formula: Mg / Magnesium

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Saccharomyces Cerevisiae Origin Recognition Complex Bound to a 72-bp Origin DNA containing ACS and B1 element
Type: COMPLEX
Details: Saccharomyces Cerevisiae Origin Recognition Complex (Orc1-6, chain A-F) Bound to a 72-bp Origin DNA (a 72-bp dsDNA chain G-H) containing ACS and B1 element
Entity ID: 1,2,3,4,5,6,7,8 / Source: RECOMBINANT
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (baker's yeast)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 52.3 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.12_2829: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 164857 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00622869
ELECTRON MICROSCOPYf_angle_d1.02331269
ELECTRON MICROSCOPYf_dihedral_angle_d14.04313539
ELECTRON MICROSCOPYf_chiral_restr0.0583547
ELECTRON MICROSCOPYf_plane_restr0.0123692

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