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- EMDB-33989: Cryo-EM structure of the N-terminal domain of hMCM8/9 and HROB -

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Basic information

Entry
Database: EMDB / ID: EMD-33989
TitleCryo-EM structure of the N-terminal domain of hMCM8/9 and HROB
Map datacomplex of human MCM8/9 NTD and HROB
Sample
  • Complex: Minichromosome maintenance 8 and 9
    • Protein or peptide: DNA helicase MCM8
    • Protein or peptide: DNA helicase MCM9
KeywordsMCM8/9 / HYDROLASE
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 / MutSalpha complex binding / CDC6 association with the ORC:origin complex / female gamete generation / 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 / MutSalpha complex binding / CDC6 association with the ORC:origin complex / female gamete generation / E2F-enabled inhibition of pre-replication complex formation / Unwinding of DNA / MCM complex / DNA duplex unwinding / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / protein localization to chromatin / helicase activity / double-strand break repair via homologous recombination / Orc1 removal from chromatin / large ribosomal subunit / single-stranded DNA binding / chromosome / DNA helicase / protein stabilization / structural constituent of ribosome / translation / DNA damage response / chromatin binding / enzyme binding / ATP hydrolysis activity / nucleoplasm / ATP binding / nucleus
Similarity search - Function
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 / Ribosomal protein L22/L17, eukaryotic/archaeal ...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 / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L22/L17, conserved site / Ribosomal protein L22 signature. / Ribosomal protein L22/L17 / Ribosomal protein L22/L17 superfamily / Ribosomal protein L22p/L17e / 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
Large ribosomal subunit protein uL22 / DNA helicase MCM8
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsZheng JF / Weng ZF / Liu YF
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31530015 China
CitationJournal: Elife / Year: 2023
Title: Structural and mechanistic insights into the MCM8/9 helicase complex.
Authors: Zhuangfeng Weng / Jiefu Zheng / Yiyi Zhou / Zuer Lu / Yixi Wu / Dongyi Xu / Huanhuan Li / Huanhuan Liang / Yingfang Liu /
Abstract: MCM8 and MCM9 form a functional helicase complex (MCM8/9) that plays an essential role in DNA homologous recombination repair for DNA double-strand break. However, the structural characterization of ...MCM8 and MCM9 form a functional helicase complex (MCM8/9) that plays an essential role in DNA homologous recombination repair for DNA double-strand break. However, the structural characterization of MCM8/9 for DNA binding/unwinding remains unclear. Here, we report structures of the MCM8/9 complex using cryo-electron microscopy single particle analysis. The structures reveal that MCM8/9 is arranged into a heterohexamer through a threefold symmetry axis, creating a central channel that accommodates DNA. Multiple characteristic hairpins from the N-terminal oligosaccharide/oligonucleotide (OB) domains of MCM8/9 protrude into the central channel and serve to unwind the duplex DNA. When activated by HROB, the structure of MCM8/9's N-tier ring converts its symmetry from to with a conformational change that expands the MCM8/9's trimer interface. Moreover, our structural dynamic analyses revealed that the flexible C-tier ring exhibited rotary motions relative to the N-tier ring, which is required for the unwinding ability of MCM8/9. In summary, our structural and biochemistry study provides a basis for understanding the DNA unwinding mechanism of MCM8/9 helicase in homologous recombination.
History
DepositionAug 2, 2022-
Header (metadata) releaseAug 9, 2023-
Map releaseAug 9, 2023-
UpdateDec 6, 2023-
Current statusDec 6, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33989.png

Downloads & links

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Map

FileDownload / File: emd_33989.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomplex of human MCM8/9 NTD and HROB
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 211.712 Å		0.83 Å/pix.
x 256 pix.
= 211.712 Å		0.83 Å/pix.
x 256 pix.
= 211.712 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.16640186 - 0.3611392
Average (Standard dev.)0.0009943253 (±0.0135401245)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 211.712 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map A

Fileemd_33989_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_33989_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Minichromosome maintenance 8 and 9

EntireName: Minichromosome maintenance 8 and 9
Components
  • Complex: Minichromosome maintenance 8 and 9
    • Protein or peptide: DNA helicase MCM8
    • Protein or peptide: DNA helicase MCM9

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Supramolecule #1: Minichromosome maintenance 8 and 9

SupramoleculeName: Minichromosome maintenance 8 and 9 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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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: 35.482418 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: TPQSMQSTLD RFIPYKGWKL YFSEVYSDSS PLIEKIQAFE KFFTRHIDLY DKDEIERKGS ILVDFKELTE GGEVTNLIPD IATELRDAP EKTLACMGLA IHQVLTKDLE RHAAELQAQE GLSNDGETMV NVPHIHARVY NYEPLTQLKN VRANYYGKYI A LRGTVVRV ...String:
TPQSMQSTLD RFIPYKGWKL YFSEVYSDSS PLIEKIQAFE KFFTRHIDLY DKDEIERKGS ILVDFKELTE GGEVTNLIPD IATELRDAP EKTLACMGLA IHQVLTKDLE RHAAELQAQE GLSNDGETMV NVPHIHARVY NYEPLTQLKN VRANYYGKYI A LRGTVVRV SNIKPLCTKM AFLCAACGEI QSFPLPDGKY SLPTKCPVPV CRGRSFTALR SSPLTVTMDW QSIKIQELMS DD QREAGRI PRTIECELVH DLVDSCVPGD TVTITGIVKV SNAEEGSRNK NDKCMFLLYI EANSISNSKG QKTKSSEDG

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: 31.572082 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 IQVNNEQSS

UniProtKB: Large ribosomal subunit protein uL22

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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: 8
GridMaterial: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k 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 / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7dp3


Details: 7DP3 and 7DPD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 95257
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7yox:
Cryo-EM structure of the N-terminal domain of hMCM8/9 and HROB

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