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- PDB-7jps: ORC-DNA: Human Origin Recognition Complex (ORC) with DNA bound in... -

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Basic information

Entry
Database: PDB / ID: 7jps
TitleORC-DNA: Human Origin Recognition Complex (ORC) with DNA bound in the core
Components
  • (Origin recognition complex subunit ...) x 5
  • DNA (5'-D(*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*AP*T)-3')
  • DNA (5'-D(*AP*TP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)-3')
Keywordsreplication/DNA / replication / AAA+ / ORC / DNA-binding / cryoEM / replication-DNA complex
Function / homology
Function and homology information


polar body extrusion after meiotic divisions / CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / nuclear origin of replication recognition complex / nuclear pre-replicative complex / inner kinetochore / DNA replication preinitiation complex / mitotic DNA replication checkpoint signaling / neural precursor cell proliferation ...polar body extrusion after meiotic divisions / CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / nuclear origin of replication recognition complex / nuclear pre-replicative complex / inner kinetochore / DNA replication preinitiation complex / mitotic DNA replication checkpoint signaling / neural precursor cell proliferation / G1/S-Specific Transcription / regulation of DNA replication / DNA replication origin binding / protein polymerization / DNA replication initiation / Activation of the pre-replicative complex / glial cell proliferation / heterochromatin / Activation of ATR in response to replication stress / Assembly of the ORC complex at the origin of replication / Assembly of the pre-replicative complex / Orc1 removal from chromatin / DNA replication / chromosome, telomeric region / nuclear body / nucleotide binding / centrosome / chromatin binding / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / membrane / nucleus / metal ion binding / cytosol
Similarity search - Function
Origin recognition complex subunit 3, insertion domain / Origin recognition complex subunit 3 insertion domain / CDC6, C terminal / Origin recognition complex subunit 4 / Origin recognition complex, subunit 3 / Origin recognition complex, subunit 5 / Origin recognition complex subunit 4, C-terminal / Origin recognition complex subunit 3, winged helix C-terminal / Origin recognition complex subunit 3, N-terminal / : ...Origin recognition complex subunit 3, insertion domain / Origin recognition complex subunit 3 insertion domain / CDC6, C terminal / Origin recognition complex subunit 4 / Origin recognition complex, subunit 3 / Origin recognition complex, subunit 5 / Origin recognition complex subunit 4, C-terminal / Origin recognition complex subunit 3, winged helix C-terminal / Origin recognition complex subunit 3, N-terminal / : / : / Origin recognition complex (ORC) subunit 3 N-terminus / Origin recognition complex (ORC) subunit 4 C-terminus / Origin recognition complex (ORC) subunit 5 C-terminus / Origin recognition complex winged helix C-terminal / ORC5, lid domain / Cdc6, C-terminal / CDC6, C terminal winged helix domain / Orc1-like, AAA ATPase domain / Origin recognition complex subunit 2 / AAA ATPase domain / Origin recognition complex, subunit 2 / 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. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / Origin recognition complex subunit 5 / Origin recognition complex subunit 4 / Origin recognition complex subunit 1 / Origin recognition complex subunit 2 / Origin recognition complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Spodoptera frugiperda (fall armyworm)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsJaremko, M.J. / Joshua-Tor, L.
Funding support United States, 3items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM129923 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM45436 United States
CitationJournal: Elife / Year: 2020
Title: The dynamic nature of the human origin recognition complex revealed through five cryoEM structures.
Authors: Matt J Jaremko / Kin Fan On / Dennis R Thomas / Bruce Stillman / Leemor Joshua-Tor /
Abstract: Genome replication is initiated from specific origin sites established by dynamic events. The Origin Recognition Complex (ORC) is necessary for orchestrating the initiation process by binding to ...Genome replication is initiated from specific origin sites established by dynamic events. The Origin Recognition Complex (ORC) is necessary for orchestrating the initiation process by binding to origin DNA, recruiting CDC6, and assembling the MCM replicative helicase on DNA. Here we report five cryoEM structures of the human ORC (HsORC) that illustrate the native flexibility of the complex. The absence of ORC1 revealed a compact, stable complex of ORC2-5. Introduction of ORC1 opens the complex into several dynamic conformations. Two structures revealed dynamic movements of the ORC1 AAA+ and ORC2 winged-helix domains that likely impact DNA incorporation into the ORC core. Additional twist and pinch motions were observed in an open ORC conformation revealing a hinge at the ORC5·ORC3 interface that may facilitate ORC binding to DNA. Finally, a structure of ORC was determined with endogenous DNA bound in the core revealing important differences between human and yeast origin recognition.
History
DepositionAug 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 2.0Oct 26, 2022Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Polymer sequence / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_poly / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity_poly.type
Revision 2.1May 15, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
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

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Structure visualization

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  • Deposited structure unit
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-22421
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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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: DNA (5'-D(*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*AP*T)-3')
G: DNA (5'-D(*AP*TP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,17314
Polymers301,5407
Non-polymers1,6347
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, mass spectrometry, analysis after streptactin affinity purification, microscopy, cryoEM, initial 2D classification revealed the quaternary structure
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Origin recognition complex subunit ... , 5 types, 5 molecules ABCDE

#1: Protein Origin recognition complex subunit 1 / Replication control protein 1


Mass: 44310.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ORC1, ORC1L, PARC1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13415
#2: Protein Origin recognition complex subunit 2


Mass: 66063.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ORC2, ORC2L / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13416
#3: Protein Origin recognition complex subunit 3 / Origin recognition complex subunit Latheo


Mass: 82436.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ORC3, LATHEO, ORC3L / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UBD5
#4: Protein Origin recognition complex subunit 4


Mass: 50443.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ORC4, ORC4L / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43929
#5: Protein Origin recognition complex subunit 5


Mass: 50349.934 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ORC5, ORC5L / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O43913

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DNA chain , 2 types, 2 molecules FG

#6: DNA chain DNA (5'-D(*AP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*AP*T)-3')


Mass: 3972.647 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spodoptera frugiperda (fall armyworm) / Production host: Spodoptera frugiperda (fall armyworm)
#7: DNA chain DNA (5'-D(*AP*TP*TP*AP*TP*AP*TP*AP*TP*AP*TP*AP*T)-3')


Mass: 3963.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Spodoptera frugiperda (fall armyworm) / Production host: Spodoptera frugiperda (fall armyworm)

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Non-polymers , 3 types, 7 molecules

#8: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#10: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K

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Details

Has ligand of interestY

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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: ORC-DNA / Type: COMPLEX / Details: 5 subunit ORC complex with DNA bound in the core / Entity ID: #1-#7 / Source: RECOMBINANT
Molecular weightValue: .29653 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESC8H18N2O4S1
280 mMsodium chlorideNaCl1
33.3 mMDTTC4H10O2S21
40.8 mMATPC10H16N5O13P31
50.05 % w/vLauryl Maltose Neopentyl GlycolC47H88O221
SpecimenConc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2400 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Image recordingAverage exposure time: 6 sec. / Electron dose: 66 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 9068
Image scansMovie frames/image: 30

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameVersionCategoryFitting-ID
1Warp1.0.7particle selection
2EPUimage acquisition
4RELION3CTF correction
7UCSF Chimeramodel fitting1
9cryoSPARC2initial Euler assignment
10RELION3final Euler assignment
12RELION33D reconstruction
40PHENIX1.18model refinement2
41Coot0.9model refinement2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2097508
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 37734 / Symmetry type: POINT
Atomic model building
IDB valueProtocolSpaceTarget criteria
1231RIGID BODY FITREALCorrelation Coefficient
2BACKBONE TRACEREAL
Atomic model building
IDPDB-IDPdb chain-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
15UJM

5ujm

A15UJM1PDBexperimental model
25UJM

5ujm

B15UJM1PDBexperimental model
35UJM

5ujm

C15UJM1PDBexperimental model
45UJM

5ujm

D15UJM1PDBexperimental model
55UJM

5ujm

E15UJM1PDBexperimental model
62
72
82
92
102
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00616747
ELECTRON MICROSCOPYf_angle_d1.13922772
ELECTRON MICROSCOPYf_dihedral_angle_d17.0332359
ELECTRON MICROSCOPYf_chiral_restr0.062600
ELECTRON MICROSCOPYf_plane_restr0.0082773

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