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- EMDB-40234: Structure of Walker B mutated MCM8/9 heterohexamer complex with ADP -

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Basic information

Entry
Database: EMDB / ID: EMD-40234
TitleStructure of Walker B mutated MCM8/9 heterohexamer complex with ADP
Map data
Sample
  • Complex: Structure of Walker B mutated MCM8/9 heterohexamer complex with ADP
    • Protein or peptide: DNA helicase MCM8
    • Protein or peptide: DNA helicase MCM9
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsHelicase DNA Replication DNA repair / DNA BINDING PROTEIN
Function / homology
Function and homology information


MutLbeta complex binding / MutSbeta complex binding / recombinational interstrand cross-link repair / MCM8-MCM9 complex / male gamete generation / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / CDC6 association with the ORC:origin complex / female gamete generation / MutSalpha complex binding / E2F-enabled inhibition of pre-replication complex formation ...MutLbeta complex binding / MutSbeta complex binding / recombinational interstrand cross-link repair / MCM8-MCM9 complex / male gamete generation / mismatch repair involved in maintenance of fidelity involved in DNA-dependent DNA replication / CDC6 association with the ORC:origin complex / female gamete generation / MutSalpha complex binding / E2F-enabled inhibition of pre-replication complex formation / Unwinding of DNA / MCM complex / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / protein localization to chromatin / DNA helicase activity / helicase activity / double-strand break repair via homologous recombination / Orc1 removal from chromatin / single-stranded DNA binding / chromosome / DNA helicase / protein stabilization / DNA damage response / chromatin binding / protein-containing complex binding / enzyme binding / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus
Similarity search - Function
: / MCM8 winged helix 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 ...: / MCM8 winged helix 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
DNA helicase MCM9 / DNA helicase MCM8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsLi C / Gao Y
Funding support United States, 1 items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RR190046 United States
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Activity, substrate preference and structure of the HsMCM8/9 helicase.
Authors: David R McKinzey / Chuxuan Li / Yang Gao / Michael A Trakselis /
Abstract: The minichromosomal maintenance proteins, MCM8 and MCM9, are more recent evolutionary additions to the MCM family, only cooccurring in selected higher eukaryotes. Mutations in these genes are ...The minichromosomal maintenance proteins, MCM8 and MCM9, are more recent evolutionary additions to the MCM family, only cooccurring in selected higher eukaryotes. Mutations in these genes are directly linked to ovarian insufficiency, infertility, and several cancers. MCM8/9 appears to have ancillary roles in fork progression and recombination of broken replication forks. However, the biochemical activity, specificities and structures have not been adequately illustrated, making mechanistic determination difficult. Here, we show that human MCM8/9 (HsMCM8/9) is an ATP dependent DNA helicase that unwinds fork DNA substrates with a 3'-5' polarity. High affinity ssDNA binding occurs in the presence of nucleoside triphosphates, while ATP hydrolysis weakens the interaction with DNA. The cryo-EM structure of the HsMCM8/9 heterohexamer was solved at 4.3 Å revealing a trimer of heterodimer configuration with two types of interfacial AAA+ nucleotide binding sites that become more organized upon binding ADP. Local refinements of the N or C-terminal domains (NTD or CTD) improved the resolution to 3.9 or 4.1 Å, respectively, and shows a large displacement in the CTD. Changes in AAA+ CTD upon nucleotide binding and a large swing between the NTD and CTD likely implies that MCM8/9 utilizes a sequential subunit translocation mechanism for DNA unwinding.
History
DepositionMar 27, 2023-
Header (metadata) releaseJun 7, 2023-
Map releaseJun 7, 2023-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40234.png

Downloads & links

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Map

FileDownload / File: emd_40234.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 320 pix.
= 355.2 Å		1.11 Å/pix.
x 320 pix.
= 355.2 Å		1.11 Å/pix.
x 320 pix.
= 355.2 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.83326423 - 1.189463
Average (Standard dev.)-0.0009964515 (±0.027669989)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 355.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_40234_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_40234_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Structure of Walker B mutated MCM8/9 heterohexamer complex with ADP

EntireName: Structure of Walker B mutated MCM8/9 heterohexamer complex with ADP
Components
  • Complex: Structure of Walker B mutated MCM8/9 heterohexamer complex with ADP
    • Protein or peptide: DNA helicase MCM8
    • Protein or peptide: DNA helicase MCM9
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Structure of Walker B mutated MCM8/9 heterohexamer complex with ADP

SupramoleculeName: Structure of Walker B mutated MCM8/9 heterohexamer complex with ADP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 500 KDa

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Macromolecule #1: DNA helicase MCM8

MacromoleculeName: DNA helicase MCM8 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.817703 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MNGEYRGRGF GRGRFQSWKR GRGGGNFSGK WREREHRPDL SKTTGKRTSE QTPQFLLSTK TPQSMQSTLD RFIPYKGWKL YFSEVYSDS SPLIEKIQAF EKFFTRHIDL YDKDEIERKG SILVDFKELT EGGEVTNLIP DIATELRDAP EKTLACMGLA I HQVLTKDL ...String:
MNGEYRGRGF GRGRFQSWKR GRGGGNFSGK WREREHRPDL SKTTGKRTSE QTPQFLLSTK TPQSMQSTLD RFIPYKGWKL YFSEVYSDS SPLIEKIQAF EKFFTRHIDL YDKDEIERKG SILVDFKELT EGGEVTNLIP DIATELRDAP EKTLACMGLA I HQVLTKDL ERHAAELQAQ EGLSNDGETM VNVPHIHARV YNYEPLTQLK NVRANYYGKY IALRGTVVRV SNIKPLCTKM AF LCAACGE IQSFPLPDGK YSLPTKCPVP VCRGRSFTAL RSSPLTVTMD WQSIKIQELM SDDQREAGRI PRTIECELVH DLV DSCVPG DTVTITGIVK VSNAEEGSRN KNDKCMFLLY IEANSISNSK GQKTKSSEDG CKHGMLMEFS LKDLYAIQEI QAEE NLFKL IVNSLCPVIF GHELVKAGLA LALFGGSQKY ADDKNRIPIR GDPHILVVGD PGLGKSQMLQ AACNVAPRGV YVCGN TTTT SGLTVTLSKD SSSGDFALEA GALVLGDQGI CGIDQFDKMG NQHQALLEAM EQQSISLAKA GVVCSLPART SIIAAA NPV GGHYNKAKTV SENLKMGSAL LSRFDLVFIL LDTPNEHHDH LLSEHVIAIR AGKQRTISSA TVARMNSQDS NTSVLEV VS EKPLSERLKV VPGETIDPIP HQLLRKYIGY ARQYVYPRLS TEAARVLQDF YLELRKQSQR LNSSPITTRQ LESLIRLT E ARARLELREE ATKEDAEDIV EIMKYSMLGT YSDEFGNLDF ERSQHGSGMS NRSTAKRFIS ALNNVAERTY NNIFQFHQL RQIAKELNIQ VADFENFIGS LNDQGYLLKK GPKVYQLQTM

UniProtKB: DNA helicase MCM8

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Macromolecule #2: DNA helicase MCM9

MacromoleculeName: DNA helicase MCM9 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 127.485594 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MNSDQVTLVG QVFESYVSEY HKNDILLILK ERDEDAHYPV VVNAMTLFET NMEIGEYFNM FPSEVLTIFD SALRRSALTI LQSLSQPEA VSMKQNLHAR ISGLPVCPEL VREHIPKTKD VGHFLSVTGT VIRTSLVKVL EFERDYMCNK CKHVFVIKAD F EQYYTFCR ...String:
MNSDQVTLVG QVFESYVSEY HKNDILLILK ERDEDAHYPV VVNAMTLFET NMEIGEYFNM FPSEVLTIFD SALRRSALTI LQSLSQPEA VSMKQNLHAR ISGLPVCPEL VREHIPKTKD VGHFLSVTGT VIRTSLVKVL EFERDYMCNK CKHVFVIKAD F EQYYTFCR PSSCPSLESC DSSKFTCLSG LSSSPTRCRD YQEIKIQEQV QRLSVGSIPR SMKVILEDDL VDSCKSGDDL TI YGIVMQR WKPFQQDVRC EVEIVLKANY IQVNNEQSSG IIMDEEVQKE FEDFWEYYKS DPFAGRNVIL ASLCPQVFGM YLV KLAVAM VLAGGIQRTD ATGTRVRGES HLLLVGDPGT GKSQFLKYAA KITPRSVLTT GIGSTSAGLT VTAVKDSGEW NLEA GALVL ADAGLCCIDQ FNSLKEHDRT SIHEAMEQQT ISVAKAGLVC KLNTRTTILA ATNPKGQYDP QESVSVNIAL GSPLL SRFD LILVLLDTKN EDWDRIISSF ILENKGYPSK SEKLWSMEKM KTYFCLIRNL QPTLSDVGNQ VLLRYYQMQR QSDCRN AAR TTIRLLESLI RLAEAHARLM FRDTVTLEDA ITVVSVMESS MQGGALLGGV NALHTSFPEN PGEQYQRQCE LILEKLE LQ SLLSEELRRL ERLQNQSVHQ SQPRVLEVET TPGSLRNGPG EESNFRTSSQ QEINYSTHIF SPGGSPEGSP VLDPPPHL E PNRSTSRKHS AQHKNNRDDS LDWFDFMATH QSEPKNTVVV SPHPKTSGEN MASKISNSTS QGKEKSEPGQ RSKVDIGLL PSPGETGVPW RADNVESNKK KRLALDSEAA VSADKPDSVL THHVPRNLQK LCKERAQKLC RNSTRVPAQC TVPSHPQSTP VHSPDRMLD SPKRKRPKSL AQVEEPAIEN VKPPGSPVAK LAKFTFKQKS KLIHSFEDHS HVSPGATKIA VHSPKISQRR T RRDAALPV KRPGKLTSTP GNQISSQPQG ETKEVSQQPP EKHGPREKVM CAPEKRIIQP ELELGNETGC AHLTCEGDKK EE VSGSNKS GKVHACTLAR LANFCFTPPS ESKSKSPPPE RKNRGERGPS SPPTTTAPMR VSKRKSFQLR GSTEKLIVSK ESL FTLPEL GDEAFDCDWD EEMRKKS

UniProtKB: DNA helicase MCM9

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration0.5 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 49.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 227818
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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