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- EMDB-8541: Structure of the active form of human Origin Recognition Complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-8541
TitleStructure of the active form of human Origin Recognition Complex and its ATPase motor module
Map datahuman Origin Recognition Complex and its ATPase motor module
Sample
  • Complex: Human ORC
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 / inner kinetochore / nuclear pre-replicative complex / 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 / inner kinetochore / nuclear pre-replicative complex / 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 / Activation of ATR in response to replication stress / heterochromatin / Assembly of the ORC complex at the origin of replication / Assembly of the pre-replicative complex / Orc1 removal from chromatin / chromosome, telomeric region / DNA replication / 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 / metal ion binding / nucleus / membrane / cytosol
Similarity search - Function
Origin recognition complex subunit 3, insertion domain / Origin recognition complex subunit 3 insertion domain / CDC6, C terminal / Cdc6, C-terminal / CDC6, C terminal winged helix domain / 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, insertion domain / Origin recognition complex subunit 3 insertion domain / CDC6, C terminal / Cdc6, C-terminal / CDC6, C terminal winged helix domain / 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 / Orc1-like, AAA ATPase domain / : / : / Origin recognition complex subunit 2 RecA-like domain / ORC2 WHD / 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 18.0 Å
AuthorsTocilj A / On K / Yuan Z / Sun J / Elkayam E / Li H / Stillman B / Joshua-Tor L
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM111742 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA13016 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM45436 United States
Robertson Research Fund of Cold Spring Harbor Laboratory United States
CitationJournal: Elife / Year: 2017
Title: Structure of the active form of human origin recognition complex and its ATPase motor module.
Authors: Ante Tocilj / Kin Fan On / Zuanning Yuan / Jingchuan Sun / Elad Elkayam / Huilin Li / Bruce Stillman / Leemor Joshua-Tor /
Abstract: Binding of the Origin Recognition Complex (ORC) to origins of replication marks the first step in the initiation of replication of the genome in all eukaryotic cells. Here, we report the structure of ...Binding of the Origin Recognition Complex (ORC) to origins of replication marks the first step in the initiation of replication of the genome in all eukaryotic cells. Here, we report the structure of the active form of human ORC determined by X-ray crystallography and cryo-electron microscopy. The complex is composed of an ORC1/4/5 motor module lobe in an organization reminiscent of the DNA polymerase clamp loader complexes. A second lobe contains the ORC2/3 subunits. The complex is organized as a double-layered shallow corkscrew, with the AAA+ and AAA+-like domains forming one layer, and the winged-helix domains (WHDs) forming a top layer. CDC6 fits easily between ORC1 and ORC2, completing the ring and the DNA-binding channel, forming an additional ATP hydrolysis site. Analysis of the ATPase activity of the complex provides a basis for understanding ORC activity as well as molecular defects observed in Meier-Gorlin Syndrome mutations.
History
DepositionDec 26, 2016-
Header (metadata) releaseFeb 8, 2017-
Map releaseFeb 8, 2017-
UpdateJan 29, 2020-
Current statusJan 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5ujm
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8541.png

Downloads & links

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Map

FileDownload / File: emd_8541.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman Origin Recognition Complex and its ATPase motor module
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.04 Å/pix.
x 64 pix.
= 258.56 Å		4.04 Å/pix.
x 64 pix.
= 258.56 Å		4.04 Å/pix.
x 64 pix.
= 258.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.009 / Movie #1: 0.007
Minimum - Maximum-0.0054991385 - 0.020294882
Average (Standard dev.)0.00023368909 (±0.0014564645)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 258.56 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.044.044.04
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z258.560258.560258.560
α/β/γ90.00090.00090.000
start NX/NY/NZ-38-19-20
NX/NY/NZ858082
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-0.0050.0200.000

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Supplemental data

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Sample components

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Entire : Human ORC

EntireName: Human ORC
Components
  • Complex: Human ORC

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Supramolecule #1: Human ORC

SupramoleculeName: Human ORC / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others) / Recombinant plasmid: pSPL, pFL

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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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 18.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 10980
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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