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Yorodumi- EMDB-40237: Structure of wild-type MCM8/9 heterohexamer complex with ATP-gamma-S -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-40237 | |||||||||
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Title | Structure of wild-type MCM8/9 heterohexamer complex with ATP-gamma-S | |||||||||
Map data | ||||||||||
Sample |
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Keywords | 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 / 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 | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.5 Å | |||||||||
Authors | Li C / Gao Y | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_40237.map.gz | 117.3 MB | EMDB map data format | |
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Header (meta data) | emd-40237-v30.xml emd-40237.xml | 16.2 KB 16.2 KB | Display Display | EMDB header |
Images | emd_40237.png | 179.2 KB | ||
Others | emd_40237_half_map_1.map.gz emd_40237_half_map_2.map.gz | 115.8 MB 115.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-40237 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40237 | HTTPS FTP |
-Validation report
Summary document | emd_40237_validation.pdf.gz | 825.3 KB | Display | EMDB validaton report |
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Full document | emd_40237_full_validation.pdf.gz | 824.9 KB | Display | |
Data in XML | emd_40237_validation.xml.gz | 14 KB | Display | |
Data in CIF | emd_40237_validation.cif.gz | 16.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40237 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-40237 | HTTPS FTP |
-Related structure data
Related structure data | 8s91C 8s92C 8s94C C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_40237.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.11 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_40237_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_40237_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Structure of wild-type MCM8/9 heterohexamer complex with ATP-gamma-S
Entire | Name: Structure of wild-type MCM8/9 heterohexamer complex with ATP-gamma-S |
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Components |
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-Supramolecule #1: Structure of wild-type MCM8/9 heterohexamer complex with ATP-gamma-S
Supramolecule | Name: Structure of wild-type MCM8/9 heterohexamer complex with ATP-gamma-S type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 500 KDa |
-Macromolecule #1: MCM8_HUMAN
Macromolecule | Name: MCM8_HUMAN / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MNGEYRGRGF GRGRFQSWKR GRGGGNFSGK WREREHRPDL SKTTGKRTSE QTPQFLLSTK TPQSMQSTLD RFIPYKGWKL YFSEVYSDSS PLIEKIQAFE KFFTRHIDLY DKDEIERKGS ILVDFKELTE GGEVTNLIPD IATELRDAPE KTLACMGLAI HQVLTKDLER ...String: MNGEYRGRGF GRGRFQSWKR GRGGGNFSGK WREREHRPDL SKTTGKRTSE QTPQFLLSTK TPQSMQSTLD RFIPYKGWKL YFSEVYSDSS PLIEKIQAFE KFFTRHIDLY DKDEIERKGS ILVDFKELTE GGEVTNLIPD IATELRDAPE KTLACMGLAI HQVLTKDLER HAAELQAQEG LSNDGETMVN VPHIHARVYN YEPLTQLKNV RANYYGKYIA LRGTVVRVSN IKPLCTKMAF LCAACGEIQS FPLPDGKYSL PTKCPVPVCR GRSFTALRSS PLTVTMDWQS IKIQELMSDD QREAGRIPRT IECELVHDLV DSCVPGDTVT ITGIVKVSNA EEGSRNKNDK CMFLLYIEAN SISNSKGQKT KSSEDGCKHG MLMEFSLKDL YAIQEIQAEE NLFKLIVNSL CPVIFGHELV KAGLALALFG GSQKYADDKN RIPIRGDPHI LVVGDPGLGK SQMLQAACNV APRGVYVCGN TTTTSGLTVT LSKDSSSGDF ALEAGALVLG DQGICGIDEF DKMGNQHQAL LEAMEQQSIS LAKAGVVCSL PARTSIIAAA NPVGGHYNKA KTVSENLKMG SALLSRFDLV FILLDTPNEH HDHLLSEHVI AIRAGKQRTI SSATVARMNS QDSNTSVLEV VSEKPLSERL KVVPGETIDP IPHQLLRKYI GYARQYVYPR LSTEAARVLQ DFYLELRKQS QRLNSSPITT RQLESLIRLT EARARLELRE EATKEDAEDI VEIMKYSMLG TYSDEFGNLD FERSQHGSGM SNRSTAKRFI SALNNVAERT YNNIFQFHQL RQIAKELNIQ VADFENFIGS LNDQGYLLKK GPKVYQLQTM UniProtKB: DNA helicase MCM8 |
-Macromolecule #2: MCM9_HUMAN
Macromolecule | Name: MCM9_HUMAN / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MNSDQVTLVG QVFESYVSEY HKNDILLILK ERDEDAHYPV VVNAMTLFET NMEIGEYFNM FPSEVLTIFD SALRRSALTI LQSLSQPEAV SMKQNLHARI SGLPVCPELV REHIPKTKDV GHFLSVTGTV IRTSLVKVLE FERDYMCNKC KHVFVIKADF EQYYTFCRPS ...String: MNSDQVTLVG QVFESYVSEY HKNDILLILK ERDEDAHYPV VVNAMTLFET NMEIGEYFNM FPSEVLTIFD SALRRSALTI LQSLSQPEAV SMKQNLHARI SGLPVCPELV REHIPKTKDV GHFLSVTGTV IRTSLVKVLE FERDYMCNKC KHVFVIKADF EQYYTFCRPS SCPSLESCDS SKFTCLSGLS SSPTRCRDYQ EIKIQEQVQR LSVGSIPRSM KVILEDDLVD SCKSGDDLTI YGIVMQRWKP FQQDVRCEVE IVLKANYIQV NNEQSSGIIM DEEVQKEFED FWEYYKSDPF AGRNVILASL CPQVFGMYLV KLAVAMVLAG GIQRTDATGT RVRGESHLLL VGDPGTGKSQ FLKYAAKITP RSVLTTGIGS TSAGLTVTAV KDSGEWNLEA GALVLADAGL CCIDEFNSLK EHDRTSIHEA MEQQTISVAK AGLVCKLNTR TTILAATNPK GQYDPQESVS VNIALGSPLL SRFDLILVLL DTKNEDWDRI ISSFILENKG YPSKSEKLWS MEKMKTYFCL IRNLQPTLSD VGNQVLLRYY QMQRQSDCRN AARTTIRLLE SLIRLAEAHA RLMFRDTVTL EDAITVVSVM ESSMQGGALL GGVNALHTSF PENPGEQYQR QCELILEKLE LQSLLSEELR RLERLQNQSV HQSQPRVLEV ETTPGSLRNG PGEESNFRTS SQQEINYSTH IFSPGGSPEG SPVLDPPPHL EPNRSTSRKH SAQHKNNRDD SLDWFDFMAT HQSEPKNTVV VSPHPKTSGE NMASKISNST SQGKEKSEPG QRSKVDIGLL PSPGETGVPW RADNVESNKK KRLALDSEAA VSADKPDSVL THHVPRNLQK LCKERAQKLC RNSTRVPAQC TVPSHPQSTP VHSPDRMLDS PKRKRPKSLA QVEEPAIENV KPPGSPVAKL AKFTFKQKSK LIHSFEDHSH VSPGATKIAV HSPKISQRRT RRDAALPVKR PGKLTSTPGN QISSQPQGET KEVSQQPPEK HGPREKVMCA PEKRIIQPEL ELGNETGCAH LTCEGDKKEE VSGSNKSGKV HACTLARLAN FCFTPPSESK SKSPPPERKN RGERGPSSPP TTTAPMRVSK RKSFQLRGST EKLIVSKESL FTLPELGDEA FDCDWDEEMR KKS UniProtKB: Large ribosomal subunit protein uL22 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.5 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK I |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 49.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57384 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |