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- PDB-8s09: H. sapiens MCM2-7 double hexamer bound to double stranded DNA -

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Basic information

Entry
Database: PDB / ID: 8s09
TitleH. sapiens MCM2-7 double hexamer bound to double stranded DNA
Components
  • (DNA (45-mer)) x 2
  • (DNA replication licensing factor ...) x 6
KeywordsREPLICATION / AAA+ ATPase / DNA helicase
Function / homology
Function and homology information


Switching of origins to a post-replicative state / Unwinding of DNA / nuclear origin of replication recognition complex / alpha DNA polymerase:primase complex / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / mitotic DNA replication / regulation of phosphorylation / CMG complex / MCM complex / double-strand break repair via break-induced replication ...Switching of origins to a post-replicative state / Unwinding of DNA / nuclear origin of replication recognition complex / alpha DNA polymerase:primase complex / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / mitotic DNA replication / regulation of phosphorylation / CMG complex / MCM complex / double-strand break repair via break-induced replication / mitotic DNA replication initiation / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / DNA replication origin binding / cochlea development / DNA replication initiation / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / cellular response to interleukin-4 / DNA helicase activity / cellular response to epidermal growth factor stimulus / Assembly of the pre-replicative complex / helicase activity / cellular response to xenobiotic stimulus / Orc1 removal from chromatin / nucleosome assembly / single-stranded DNA binding / histone binding / DNA helicase / chromosome, telomeric region / DNA replication / cell population proliferation / cilium / intracellular membrane-bounded organelle / apoptotic process / DNA damage response / chromatin / perinuclear region of cytoplasm / enzyme binding / ATP hydrolysis activity / DNA binding / zinc ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
DNA replication licensing factor MCM2-like, winged-helix domain / : / MCM5, C-terminal domain / DNA replication licensing factor MCM7, winged helix / DNA replication licensing factor Mcm5 / MCM4, winged helix domain / DNA replication licensing factor Mcm3 / Mini-chromosome maintenance complex protein 4 / : / MCM3-like, winged helix domain ...DNA replication licensing factor MCM2-like, winged-helix domain / : / MCM5, C-terminal domain / DNA replication licensing factor MCM7, winged helix / DNA replication licensing factor Mcm5 / MCM4, winged helix domain / DNA replication licensing factor Mcm3 / Mini-chromosome maintenance complex protein 4 / : / MCM3-like, winged helix domain / 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. / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / 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 / DNA replication licensing factor MCM6
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 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 visualized with human proteins.
Authors: Florian Weissmann / Julia F Greiwe / Thomas Pühringer / Evelyn L Eastwood / Emma C Couves / Thomas C R Miller / John F X Diffley / Alessandro Costa /
Abstract: Eukaryotic DNA replication begins with the loading of the MCM replicative DNA helicase as a head-to-head double hexamer at origins of DNA replication. Our current understanding of how the double ...Eukaryotic DNA replication begins with the loading of the MCM replicative DNA helicase as a head-to-head double hexamer at origins of DNA replication. Our current understanding of how the double hexamer is assembled by the origin recognition complex (ORC), CDC6 and CDT1 comes mostly from budding yeast. Here we characterize human double hexamer (hDH) loading using biochemical reconstitution and cryo-electron microscopy with purified proteins. We show that the human double hexamer engages DNA differently from the yeast double hexamer (yDH), and generates approximately five base pairs of underwound DNA at the interface between hexamers, as seen in hDH isolated from cells. We identify several differences from the yeast double hexamer in the order of factor recruitment and dependencies during hDH assembly. Unlike in yeast, the ORC6 subunit of the ORC is not essential for initial MCM recruitment or hDH loading, but contributes to an alternative hDH assembly pathway that requires an intrinsically disordered region in ORC1, which may work through a MCM-ORC intermediate. Our work presents a detailed view of how double hexamers are assembled in an organism that uses sequence-independent replication origins, provides further evidence for diversity in eukaryotic double hexamer assembly mechanisms, and represents a first step towards reconstitution of DNA replication initiation with purified human proteins.
#1: Journal: Biorxiv / Year: 2024
Title: MCM Double Hexamer Loading Visualised with Human Proteins
Authors: Weissmann, F. / Greiwe, J.F. / Puhringer, T. / Miller, T.C.R. / Diffley, J.F.X. / Costa, A.
#2: 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
Revision 1.1Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: citation / em_admin / pdbx_entry_details
Item: _citation.pdbx_database_id_DOI / _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2Dec 11, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin / Item: _em_admin.last_update
Revision 1.3Dec 25, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: DNA (45-mer)
Y: DNA (45-mer)
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
A: DNA replication licensing factor MCM2
B: DNA replication licensing factor MCM3
C: DNA replication licensing factor MCM4
D: DNA replication licensing factor MCM5
E: DNA replication licensing factor MCM6
F: DNA replication licensing factor MCM7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,126,72342
Polymers1,121,44214
Non-polymers5,28128
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "2"
d_2ens_1chain "A"
d_1ens_2chain "3"
d_2ens_2chain "B"
d_1ens_3chain "C"
d_2ens_3chain "4"
d_1ens_4chain "5"
d_2ens_4chain "D"
d_1ens_5chain "E"
d_2ens_5chain "6"
d_1ens_6chain "F"
d_2ens_6chain "7"
d_1ens_7(chain "X" and (resid 1 through 22 or resid 24 through 45))
d_2ens_7(chain "Y" and (resid -45 through -24 or resid -22 through -1))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1HISHISGLNGLN2C180 - 902180 - 902
d_12ens_1ATPATPATPATP2O1001
d_13ens_1MGMGMGMG2P1002
d_21ens_1HISHISGLNGLNAI180 - 902180 - 902
d_22ens_1ATPATPATPATPACA1001
d_23ens_1MGMGMGMGADA1002
d_11ens_2ALAALALYSLYS3D2 - 6564 - 658
d_12ens_2ADPADPADPADP3R901
d_21ens_2ALAALALYSLYSBJ2 - 6564 - 658
d_22ens_2ADPADPADPADPBFA901
d_11ens_3LYSLYSILEILECK149 - 783149 - 783
d_21ens_3LYSLYSILEILE4E149 - 783149 - 783
d_11ens_4SERSERLYSLYS5F2 - 7342 - 734
d_12ens_4ADPADPADPADP5V801
d_21ens_4SERSERLYSLYSDL2 - 7342 - 734
d_22ens_4ADPADPADPADPDJA801
d_11ens_5GLUGLUGLNGLNEM17 - 79217 - 792
d_12ens_5ADPADPADPADPCIA902
d_13ens_5MGMGMGMGELA901
d_21ens_5GLUGLUGLNGLN6G17 - 79217 - 792
d_22ens_5ADPADPADPADP4U902
d_23ens_5MGMGMGMG6X901
d_11ens_6LEULEUASPASPFN3 - 6423 - 642
d_12ens_6ADPADPADPADPFNA801
d_13ens_6MGMGMGMGFOA802
d_21ens_6LEULEUASPASP7H3 - 6423 - 642
d_22ens_6ADPADPADPADP7Z801
d_23ens_6MGMGMGMG7AA802
d_11ens_7DGDGDCDCXA1 - 21 - 2
d_21ens_7DGDGDCDCYB-45 - -441 - 2

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4
ens_5
ens_6
ens_7

NCS oper:
IDCodeMatrixVector
1given(-0.999999814964, 0.000575269678117, -0.000197830413718), (-0.000575256568493, -0.999999832341, -6.63175000109E-5), (-0.000197868530997, -6.62036844948E-5, 0.999999978233)431.881371423, 432.106261169, 0.0634953624242
2given(-0.999999817902, 0.000556978905473, -0.00023231477709), (-0.000556962886706, -0.999999842515, -6.90118515156E-5), (-0.000232353178649, -6.88824482398E-5, 0.999999970634)431.895937208, 432.105369094, 0.0691159215867
3given(-0.999999801798, -0.000586489522028, -0.000228983596045), (0.000586487039662, -0.999999827957, 1.09078029996E-5), (-0.000228989953962, 1.07735049262E-5, 0.999999973724)432.140604474, 431.838946499, 0.0408288919818
4given(-0.999999827896, 0.000558689389954, -0.000179091389259), (-0.000558687034161, -0.999999843847, -1.32038949043E-5), (-0.00017909873817, -1.31038365948E-5, 0.999999983876)431.882903389, 432.091631251, 0.0446893185058
5given(-0.999999821578, -0.000566069046469, -0.000190816124806), (0.000566080859654, -0.999999837863, -6.18604126212E-5), (-0.000190781076603, -6.19684189399E-5, 0.999999979881)432.127372144, 431.859938305, 0.0478488492866
6given(-0.999999821041, -0.000567797711516, -0.000188476440008), (0.000567809113418, -0.999999836969, -6.04471085042E-5), (-0.000188442087551, -6.0554116327E-5, 0.999999980411)432.12736784, 431.859109171, 0.0468955124324
7given(-0.999999400817, 0.000358231972157, -0.00103442496852), (-0.000357314156306, -0.999999542495, -0.000887320088813), (-0.00103474236169, -0.000886949942461, 0.999999071314)432.132052767, 432.190756282, 0.428640240165

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Components

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DNA chain , 2 types, 2 molecules XY

#1: DNA chain DNA (45-mer)


Mass: 13853.882 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (45-mer)


Mass: 13862.896 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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DNA replication licensing factor ... , 6 types, 12 molecules 2A3B4C5D6E7F

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


Mass: 102034.102 Da / Num. of mol.: 2
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
#4: 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.: 2
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
#5: Protein DNA replication licensing factor MCM4 / CDC21 homolog / P1-CDC21


Mass: 96702.891 Da / Num. of mol.: 2
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
#6: Protein DNA replication licensing factor MCM5 / CDC46 homolog / P1-CDC46


Mass: 82406.633 Da / Num. of mol.: 2
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
#7: Protein DNA replication licensing factor MCM6 / p105MCM


Mass: 93010.273 Da / Num. of mol.: 2
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
#8: Protein DNA replication licensing factor MCM7 / CDC47 homolog / P1.1-MCM3


Mass: 81411.875 Da / Num. of mol.: 2
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

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Non-polymers , 4 types, 28 molecules

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


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#10: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationN

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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

Component
IDNameTypeEntity IDParent-IDSource
1H. sapiens MCM2-7 double hexamer bound to double stranded DNACOMPLEX#1-#80MULTIPLE SOURCES
2Double stranded DNACOMPLEX#1-#21RECOMBINANT
3H. sapiens MCM2-7COMPLEX#3-#81RECOMBINANT
Molecular weightValue: 1.2 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22synthetic construct (others)32630
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22synthetic construct (others)32630
33Spodoptera frugiperda (fall armyworm)7108
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The origin licensing reaction was reconstituted in vitro using purified H. sapiens proteins, a short DNA template and ATP. Four microlitres of the entire reaction was applied on a grid and ...Details: The origin licensing reaction was reconstituted in vitro using purified H. sapiens proteins, a short DNA template and ATP. 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

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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 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: 49.19 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3589
EM imaging opticsEnergyfilter name: GIF Bioquantum

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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
11PHENIX1.21_5207model refinement
12ISOLDEmodel refinement
13cryoSPARC3.3.2initial Euler assignment
14cryoSPARC3.3.2final Euler assignment
16cryoSPARC3.3.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15874 / Symmetry type: POINT
Atomic model buildingDetails: AlphaFold multimer / Source name: Other / Type: in silico model
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 48.13 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00465396
ELECTRON MICROSCOPYf_angle_d0.570388693
ELECTRON MICROSCOPYf_chiral_restr0.042310026
ELECTRON MICROSCOPYf_plane_restr0.004411174
ELECTRON MICROSCOPYf_dihedral_angle_d12.57939762
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2C2ELECTRON MICROSCOPYNCS constraints2.4653283481E-10
ens_2d_2G6ELECTRON MICROSCOPYNCS constraints2.77453637873E-11
ens_3d_2Z7ELECTRON MICROSCOPYNCS constraints1.40042415549E-11
ens_4d_2X6ELECTRON MICROSCOPYNCS constraints2.78792316129E-11
ens_5d_2AA7ELECTRON MICROSCOPYNCS constraints1.99785212708E-11
ens_6d_2BA7ELECTRON MICROSCOPYNCS constraints2.14658678471E-10
ens_7d_2AXELECTRON MICROSCOPYNCS constraints4.40950501142E-13

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