[English] 日本語
Yorodumi
- PDB-8s0d: H. sapiens MCM bound to double stranded DNA and ORC1-6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8s0d
TitleH. sapiens MCM bound to double stranded DNA and ORC1-6
Components
  • (DNA (58-mer)) x 2
  • (DNA replication licensing factor ...) x 6
  • (Origin recognition complex subunit ...) x 5
  • Isoform 2 of Origin recognition complex subunit 3
KeywordsREPLICATION / AAA+ ATPase / DNA helicase
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 / Switching of origins to a post-replicative state / Unwinding of DNA / nuclear origin of replication recognition complex / alpha DNA polymerase:primase complex / mitotic DNA replication / CMG complex ...polar body extrusion after meiotic divisions / CDC6 association with the ORC:origin complex / origin recognition complex / E2F-enabled inhibition of pre-replication complex formation / Switching of origins to a post-replicative state / Unwinding of DNA / nuclear origin of replication recognition complex / alpha DNA polymerase:primase complex / mitotic DNA replication / CMG complex / nuclear pre-replicative complex / inner kinetochore / DNA replication preinitiation complex / regulation of phosphorylation / MCM complex / mitotic DNA replication checkpoint signaling / double-strand break repair via break-induced replication / mitotic DNA replication initiation / neural precursor cell proliferation / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / cochlea development / G1/S-Specific Transcription / DNA unwinding involved in DNA replication / regulation of DNA replication / DNA replication origin binding / protein polymerization / Activation of the pre-replicative complex / DNA replication initiation / glial cell proliferation / cellular response to interleukin-4 / heterochromatin / Activation of ATR in response to replication stress / DNA helicase activity / Assembly of the ORC complex at the origin of replication / helicase activity / Assembly of the pre-replicative complex / fibrillar center / Orc1 removal from chromatin / cellular response to xenobiotic stimulus / nucleosome assembly / single-stranded DNA binding / histone binding / DNA helicase / DNA replication / cell population proliferation / chromosome, telomeric region / nuclear body / nucleotide binding / centrosome / DNA damage response / chromatin binding / chromatin / nucleolus / apoptotic process / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Origin recognition complex, subunit 6, metazoa/plant / : / ORC6 second cyclin-like domain / Origin recognition complex subunit 3, insertion domain / Origin recognition complex subunit 3 insertion domain / Origin recognition complex, subunit 6 / Origin recognition complex subunit 6 (ORC6) / Cdc6, C-terminal / CDC6, C terminal / CDC6, C terminal winged helix domain ...Origin recognition complex, subunit 6, metazoa/plant / : / ORC6 second cyclin-like domain / Origin recognition complex subunit 3, insertion domain / Origin recognition complex subunit 3 insertion domain / Origin recognition complex, subunit 6 / Origin recognition complex subunit 6 (ORC6) / 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 / Origin recognition complex subunit 2 / Orc1-like, AAA ATPase domain / AAA ATPase domain / Origin recognition complex, subunit 2 / AAA lid domain / AAA lid domain / : / MCM4, winged helix domain / DNA replication licensing factor Mcm5 / DNA replication licensing factor Mcm3 / Mini-chromosome maintenance complex protein 4 / DNA replication licensing factor Mcm6 / DNA replication licensing factor Mcm7 / Mcm6, C-terminal winged-helix domain / MCM6 C-terminal winged-helix domain / DNA replication licensing factor Mcm2 / Mini-chromosome maintenance protein 2 / Mini-chromosome maintenance, conserved site / MCM family signature. / Bromo adjacent homology domain / BAH domain / Bromo adjacent homology (BAH) domain superfamily / Bromo adjacent homology (BAH) domain / BAH domain profile. / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM OB domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / Origin recognition complex subunit 5 / Origin recognition complex subunit 4 / DNA replication licensing factor MCM3 / DNA replication licensing factor MCM4 / DNA replication licensing factor MCM5 / DNA replication licensing factor MCM7 ...ADENOSINE-5'-DIPHOSPHATE / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / DNA / DNA (> 10) / Origin recognition complex subunit 5 / Origin recognition complex subunit 4 / DNA replication licensing factor MCM3 / DNA replication licensing factor MCM4 / DNA replication licensing factor MCM5 / DNA replication licensing factor MCM7 / DNA replication licensing factor MCM2 / Origin recognition complex subunit 1 / Origin recognition complex subunit 2 / DNA replication licensing factor MCM6 / Origin recognition complex subunit 3 / Origin recognition complex subunit 6
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsGreiwe, J.F. / Weissmann, F. / Diffley, J.F.X. / Costa, A.
Funding support United Kingdom, European Union, 4items
OrganizationGrant numberCountry
The Francis Crick InstituteCC2002, CC2009 United Kingdom
European Research Council (ERC)820102European Union
Wellcome Trust219527/Z/19/Z United Kingdom
European Research Council (ERC)101020432-MeChroRepEuropean Union
Citation
Journal: Nature / Year: 2024
Title: MCM Double Hexamer Loading Visualised with Human Proteins
Authors: Weissmann, F. / Greiwe, J.F. / Puehringer, T. / Eastwood, E.L. / Couves, E.C. / Miller, T.C.R. / Diffley, J.F.X. / Costa, A.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionFeb 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
F: Origin recognition complex subunit 6
2: DNA replication licensing factor MCM2
3: DNA replication licensing factor MCM3
4: DNA replication licensing factor MCM4
5: DNA replication licensing factor MCM5
6: DNA replication licensing factor MCM6
7: DNA replication licensing factor MCM7
X: DNA (58-mer)
Y: DNA (58-mer)
A: Origin recognition complex subunit 1
B: Origin recognition complex subunit 2
C: Isoform 2 of Origin recognition complex subunit 3
D: Origin recognition complex subunit 4
E: Origin recognition complex subunit 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)961,56335
Polymers957,14414
Non-polymers4,41921
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area83980 Å2
ΔGint-479 kcal/mol
Surface area273590 Å2
MethodPISA

-
Components

-
Origin recognition complex subunit ... , 5 types, 5 molecules FABDE

#1: Protein Origin recognition complex subunit 6


Mass: 28017.697 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ORC6, ORC6L / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5N6
#10: Protein Origin recognition complex subunit 1 / Replication control protein 1


Mass: 97499.867 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
#11: 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
#13: 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
#14: 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

-
DNA replication licensing factor ... , 6 types, 6 molecules 234567

#2: Protein DNA replication licensing factor MCM2 / Minichromosome maintenance protein 2 homolog / Nuclear protein BM28


Mass: 101758.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM2, BM28, CCNL1, CDCL1, KIAA0030 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P49736, DNA helicase
#3: Protein DNA replication licensing factor MCM3 / DNA polymerase alpha holoenzyme-associated protein P1 / P1-MCM3 / RLF subunit beta / p102


Mass: 91297.023 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25205, DNA helicase
#4: Protein DNA replication licensing factor MCM4 / CDC21 homolog / P1-CDC21


Mass: 96702.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM4, CDC21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P33991, DNA helicase
#5: Protein DNA replication licensing factor MCM5 / CDC46 homolog / P1-CDC46


Mass: 82406.633 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM5, CDC46 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P33992, DNA helicase
#6: Protein DNA replication licensing factor MCM6 / p105MCM


Mass: 93010.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM6 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q14566, DNA helicase
#7: Protein DNA replication licensing factor MCM7 / CDC47 homolog / P1.1-MCM3


Mass: 81411.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MCM7, CDC47, MCM2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P33993, DNA helicase

-
DNA chain , 2 types, 2 molecules XY

#8: DNA chain DNA (58-mer)


Mass: 17790.395 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#9: DNA chain DNA (58-mer)


Mass: 17955.539 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Protein , 1 types, 1 molecules C

#12: Protein Isoform 2 of 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

-
Non-polymers , 4 types, 21 molecules

#15: 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.: 5 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#16: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1H. sapiens MCM bound to double stranded DNA and ORC1-6COMPLEX#1-#140MULTIPLE SOURCES
2Double stranded DNACOMPLEX#8-#91RECOMBINANT
3H. sapiens MCMCOMPLEX#2-#71RECOMBINANT
4H. sapiens ORC1-5COMPLEX#10-#141RECOMBINANT
5H. sapiens ORC6COMPLEX#11RECOMBINANT
Molecular weightValue: 1 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22synthetic construct (others)32630
33Homo sapiens (human)9606
44Homo sapiens (human)9606
55Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22synthetic construct (others)32630
33Spodoptera frugiperda (fall armyworm)7108
44Spodoptera frugiperda (fall armyworm)7108
55Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The MCM recruitment reaction was reconstituted in vitro using purified H. sapiens proteins, a short DNA template and ATPgammaS. Four microlitres of the entire reaction was applied on a grid ...Details: The MCM recruitment reaction was reconstituted in vitro using purified H. sapiens proteins, a short DNA template and ATPgammaS. Four microlitres of the entire reaction was applied on a grid and incubated for 1 min at room temperature before blotting with filter paper for 5 s and plunge-freezing in liquid ethane.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 295 K

-
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 FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN
Image recordingAverage exposure time: 9.4 sec. / Electron dose: 49.28 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 31569
EM imaging opticsEnergyfilter name: GIF Bioquantum

-
Processing

EM software
IDNameVersionCategory
1Topaz0.2.4particle selection
2EPUimage acquisition
4CTFFIND4.1.10CTF correction
5RELION4.0b-GPUCTF correction
6cryoSPARC3.3.2CTF correction
9UCSF ChimeraX1.6.1model fitting
11cryoSPARC3.3.2initial Euler assignment
12cryoSPARC3.3.2final Euler assignment
14cryoSPARC3.3.23D reconstruction
15PHENIX1.21_5207model refinement
16ISOLDEmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 182341
Details: The here represented map is a composite map of the consensus refinement and the locally refined map encompassing the ORC1-5 complex.
Symmetry type: POINT
Atomic model buildingDetails: The models of MCM2-7-ORC6 and ORC1-5 that were refined against the consensus refinement of the MCM-ORC complex and the locally refined ORC1-5, respectively, were fitted into the composite ...Details: The models of MCM2-7-ORC6 and ORC1-5 that were refined against the consensus refinement of the MCM-ORC complex and the locally refined ORC1-5, respectively, were fitted into the composite map using rigid body docking.

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more