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

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Basic information

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 / homology
Function and homology information


Assembly of the ORC complex at the origin of replication / maintenance of rDNA / nuclear origin of replication recognition complex / Activation of the pre-replicative complex / : / nuclear pre-replicative complex / mitotic DNA replication checkpoint signaling / DNA replication preinitiation complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / silent mating-type cassette heterochromatin assembly ...Assembly of the ORC complex at the origin of replication / maintenance of rDNA / nuclear origin of replication recognition complex / Activation of the pre-replicative complex / : / nuclear pre-replicative complex / mitotic DNA replication checkpoint signaling / DNA replication preinitiation complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / silent mating-type cassette heterochromatin assembly / nucleosome binding / histone H3-K4 methylation / subtelomeric heterochromatin assembly => GO:0031509 / DNA replication origin binding / DNA replication initiation / Orc1 removal from chromatin / ATP hydrolysis activity / chromosome, telomeric region / chromatin binding / ATP binding / metal ion binding / nucleus
Similarity search - Function
Origin recognition complex, subunit 6, fungi / Origin recognition complex, subunit 6 / Origin recognition complex subunit 6 (ORC6) / AAA domain / Origin recognition complex winged helix C-terminal / Origin recognition complex (ORC) subunit 5 C-terminus / Origin recognition complex (ORC) subunit 4 C-terminus / Origin recognition complex subunit 3, winged helix C-terminal / Origin recognition complex subunit 4, C-terminal / Origin recognition complex, subunit 5 ...Origin recognition complex, subunit 6, fungi / Origin recognition complex, subunit 6 / Origin recognition complex subunit 6 (ORC6) / AAA domain / Origin recognition complex winged helix C-terminal / Origin recognition complex (ORC) subunit 5 C-terminus / Origin recognition complex (ORC) subunit 4 C-terminus / Origin recognition complex subunit 3, winged helix C-terminal / Origin recognition complex subunit 4, C-terminal / Origin recognition complex, subunit 5 / Origin recognition complex subunit 4 / Origin recognition complex, subunit 3 / Origin recognition complex subunit 2 / Origin recognition complex, subunit 2 / Origin recognition complex, subunit 1 / AAA lid domain / AAA lid domain / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology domain / BAH domain / BAH domain profile. / Bromo adjacent homology (BAH) domain / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / EF-Hand 1, calcium-binding site / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Origin recognition complex subunit 1 / Origin recognition complex subunit 3 / Origin recognition complex subunit 5 / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Origin recognition complex subunit 6 / Origin recognition complex subunit 2 / DNA (> 10) / DNA / Origin recognition complex subunit 4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
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 /
Abstract: The six-subunit origin recognition complex (ORC) binds to DNA to mark the site for the initiation of replication in eukaryotes. Here we report a 3 Å cryo-electron microscopy structure of the ...The six-subunit origin recognition complex (ORC) binds to DNA to mark the site for the initiation of replication in eukaryotes. Here we report a 3 Å cryo-electron microscopy structure of the Saccharomyces cerevisiae ORC bound to a 72-base-pair origin DNA sequence that contains the ARS consensus sequence (ACS) and the B1 element. The ORC encircles DNA through extensive interactions with both phosphate backbone and bases, and bends DNA at the ACS and B1 sites. Specific recognition of thymine residues in the ACS is carried out by a conserved basic amino acid motif of Orc1 in the minor groove, and by a species-specific helical insertion motif of Orc4 in the major groove. Moreover, similar insertions into major and minor grooves are also embedded in the B1 site by basic patch motifs from Orc2 and Orc5, respectively, to contact bases and to bend DNA. This work pinpoints a conserved role of ORC in modulating DNA structure to facilitate origin selection and helicase loading in eukaryotes.
History
DepositionApr 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._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
Polymers458,9178
Non-polymers1,6436
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area55020 Å2
ΔGint-321 kcal/mol
Surface area120160 Å2

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Components

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

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


Mass: 104546.164 Da / Num. of mol.: 1
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: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P54784
#2: Protein Origin recognition complex subunit 2 / / Origin recognition complex 71 kDa subunit


Mass: 71342.180 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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 Origin recognition complex subunit 3 / / Origin recognition complex 62 kDa subunit


Mass: 72161.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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 Origin recognition complex subunit 4 / / Origin recognition complex 56 kDa subunit


Mass: 60772.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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 Origin recognition complex subunit 5 / / Origin recognition complex 53 kDa subunit


Mass: 55347.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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 Origin recognition complex subunit 6 / / ACS-associated protein 1 / Origin recognition complex 50 kDa subunit


Mass: 50369.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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 method: obtained synthetically / 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 method: obtained synthetically / 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 / Source method: obtained synthetically / 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 / Source method: obtained synthetically / Formula: Mg

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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

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-#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
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 52.3 e/Å2 / 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 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. 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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