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- EMDB-43710: Cryo-EM structure of the human MCM2-7 heterohexamer -

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Basic information

Entry
Database: EMDB / ID: EMD-43710
TitleCryo-EM structure of the human MCM2-7 heterohexamer
Map dataunsharpened map
Sample
  • Complex: human MCM2-7 heterohexamer
    • Protein or peptide: DNA replication licensing factor MCM2
    • Protein or peptide: DNA replication licensing factor MCM3
    • Protein or peptide: DNA replication licensing factor MCM4
    • Protein or peptide: DNA replication licensing factor MCM5
    • Protein or peptide: DNA replication licensing factor MCM6
    • Protein or peptide: DNA replication licensing factor MCM7
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordscomplex / helicase / replication / AAA+ ATPase / DNA BINDING PROTEIN
Function / homology
Function and homology information


Switching of origins to a post-replicative state / Unwinding of DNA / nuclear origin of replication recognition complex / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / alpha DNA polymerase:primase complex / mitotic DNA replication / CMG complex / regulation of phosphorylation / 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 / Regulation of MITF-M-dependent genes involved in DNA replication, damage repair and senescence / alpha DNA polymerase:primase complex / mitotic DNA replication / CMG complex / regulation of phosphorylation / 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 / cochlea development / DNA replication origin binding / Activation of the pre-replicative complex / DNA replication initiation / Activation of ATR in response to replication stress / cellular response to epidermal growth factor stimulus / cellular response to interleukin-4 / Assembly of the pre-replicative complex / Orc1 removal from chromatin / cellular response to xenobiotic stimulus / nucleosome assembly / single-stranded DNA binding / DNA helicase / histone binding / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / chromosome, telomeric region / cell population proliferation / DNA replication / 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 / cytosol / cytoplasm
Similarity search - Function
DNA replication licensing factor MCM2-like, winged-helix domain / : / MCM5, C-terminal domain / DNA replication licensing factor Mcm5 / MCM3-like, winged helix domain / 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 ...DNA replication licensing factor MCM2-like, winged-helix domain / : / MCM5, C-terminal domain / DNA replication licensing factor Mcm5 / MCM3-like, winged helix domain / 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. / 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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYang R / Hunker O / Bleichert F
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM141313 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32-GM008283 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)1F31-CA278331-01 United States
CitationJournal: Nature / Year: 2024
Title: Multiple mechanisms for licensing human replication origins.
Authors: Ran Yang / Olivia Hunker / Marleigh Wise / Franziska Bleichert /
Abstract: Loading of replicative helicases is obligatory for the assembly of DNA replication machineries. The eukaryotic MCM2-7 replicative helicase motor is deposited onto DNA by the origin recognition ...Loading of replicative helicases is obligatory for the assembly of DNA replication machineries. The eukaryotic MCM2-7 replicative helicase motor is deposited onto DNA by the origin recognition complex (ORC) and co-loader proteins as a head-to-head double hexamer to license replication origins. Although extensively studied in budding yeast, the mechanisms of origin licensing in multicellular eukaryotes remain poorly defined. Here we use biochemical reconstitution and electron microscopy to reconstruct the human MCM loading pathway. We find that unlike in yeast, the ORC6 subunit of the ORC is not essential for-but enhances-human MCM loading. Electron microscopy analyses identify several intermediates en route to MCM double hexamer formation in the presence and absence of ORC6, including a DNA-loaded, closed-ring MCM single hexamer intermediate that can mature into a head-to-head double hexamer through multiple mechanisms. ORC6 and ORC3 facilitate the recruitment of the ORC to the dimerization interface of the first hexamer into MCM-ORC (MO) complexes that are distinct from the yeast MO complex and may orient the ORC for second MCM hexamer loading. Additionally, MCM double hexamer formation can proceed through dimerization of independently loaded MCM single hexamers, promoted by a propensity of human MCM2-7 hexamers to self-dimerize. This flexibility in human MCM loading may provide resilience against cellular replication stress, and the reconstitution system will enable studies addressing outstanding questions regarding DNA replication initiation and replication-coupled events in the future.
History
DepositionFeb 13, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43710.png

Downloads & links

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Map

FileDownload / File: emd_43710.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 600 pix.
= 499.2 Å		0.83 Å/pix.
x 600 pix.
= 499.2 Å		0.83 Å/pix.
x 600 pix.
= 499.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.29969415 - 0.9900078
Average (Standard dev.)0.0004003934 (±0.025884194)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 499.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: deepEMhancer map

Fileemd_43710_additional_1.map
AnnotationdeepEMhancer map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map

Fileemd_43710_half_map_1.map
Annotationhalf-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-map

Fileemd_43710_half_map_2.map
Annotationhalf-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : human MCM2-7 heterohexamer

EntireName: human MCM2-7 heterohexamer
Components
  • Complex: human MCM2-7 heterohexamer
    • Protein or peptide: DNA replication licensing factor MCM2
    • Protein or peptide: DNA replication licensing factor MCM3
    • Protein or peptide: DNA replication licensing factor MCM4
    • Protein or peptide: DNA replication licensing factor MCM5
    • Protein or peptide: DNA replication licensing factor MCM6
    • Protein or peptide: DNA replication licensing factor MCM7
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: human MCM2-7 heterohexamer

SupramoleculeName: human MCM2-7 heterohexamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA replication licensing factor MCM2

MacromoleculeName: DNA replication licensing factor MCM2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 102.034102 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAESSESFTM ASSPAQRRRG NDPLTSSPGR SSRRTDALTS SPGRDLPPFE DESEGLLGTE GPLEEEEDGE ELIGDGMERD YRAIPELDA YEAEGLALDD EDVEELTASQ REAAERAMRQ RDREAGRGLG RMRRGLLYDS DEEDEERPAR KRRQVERATE D GEEDEEMI ...String:
MAESSESFTM ASSPAQRRRG NDPLTSSPGR SSRRTDALTS SPGRDLPPFE DESEGLLGTE GPLEEEEDGE ELIGDGMERD YRAIPELDA YEAEGLALDD EDVEELTASQ REAAERAMRQ RDREAGRGLG RMRRGLLYDS DEEDEERPAR KRRQVERATE D GEEDEEMI ESIENLEDLK GHSVREWVSM AGPRLEIHHR FKNFLRTHVD SHGHNVFKER ISDMCKENRE SLVVNYEDLA AR EHVLAYF LPEAPAELLQ IFDEAALEVV LAMYPKYDRI TNHIHVRISH LPLVEELRSL RQLHLNQLIR TSGVVTSCTG VLP QLSMVK YNCNKCNFVL GPFCQSQNQE VKPGSCPECQ SAGPFEVNME ETIYQNYQRI RIQESPGKVA AGRLPRSKDA ILLA DLVDS CKPGDEIELT GIYHNNYDGS LNTANGFPVF ATVILANHVA KKDNKVAVGE LTDEDVKMIT SLSKDQQIGE KIFAS IAPS IYGHEDIKRG LALALFGGEP KNPGGKHKVR GDINVLLCGD PGTAKSQFLK YIEKVSSRAI FTTGQGASAV GLTAYV QRH PVSREWTLEA GALVLADRGV CLIDEFDKMN DQDRTSIHEA MEQQSISISK AGIVTSLQAR CTVIAAANPI GGRYDPS LT FSENVDLTEP IISRFDILCV VRDTVDPVQD EMLARFVVGS HVRHHPSNKE EEGLANGSAA EPAMPNTYGV EPLPQEVL K KYIIYAKERV HPKLNQMDQD KVAKMYSDLR KESMATGSIP ITVRHIESMI RMAEAHARIH LRDYVIEDDV NMAIRVMLE SFIDTQKFSV MRSMRKTFAR YLSFRRDNNE LLLFILKQLV AEQVTYQRNR FGAQQDTIEV PEKDLVDKAR QINIHNLSAF YDSELFRMN KFSHDLKRKM ILQQF

UniProtKB: DNA replication licensing factor MCM2

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Macromolecule #2: DNA replication licensing factor MCM3

MacromoleculeName: DNA replication licensing factor MCM3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.251914 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAAGTVVLD DVELREAQRD YLDFLDDEED QGIYQSKVRE LISDNQYRLI VNVNDLRRKN EKRANRLLNN AFEELVAFQR ALKDFVASI DATYAKQYEE FYVGLEGSFG SKHVSPRTLT SCFLSCVVCV EGIVTKCSLV RPKVVRSVHY CPATKKTIER R YSDLTTLV ...String:
SNAAGTVVLD DVELREAQRD YLDFLDDEED QGIYQSKVRE LISDNQYRLI VNVNDLRRKN EKRANRLLNN AFEELVAFQR ALKDFVASI DATYAKQYEE FYVGLEGSFG SKHVSPRTLT SCFLSCVVCV EGIVTKCSLV RPKVVRSVHY CPATKKTIER R YSDLTTLV AFPSSSVYPT KDEENNPLET EYGLSVYKDH QTITIQEMPE KAPAGQLPRS VDVILDDDLV DKAKPGDRVQ VV GTYRCLP GKKGGYTSGT FRTVLIACNV KQMSKDAQPS FSAEDIAKIK KFSKTRSKDI FDQLAKSLAP SIHGHDYVKK AIL CLLLGG VERDLENGSH IRGDINILLI GDPSVAKSQL LRYVLCTAPR AIPTTGRGSS GVGLTAAVTT DQETGERRLE AGAM VLADR GVVCIDEFDK MSDMDRTAIH EVMEQGRVTI AKAGIHARLN ARCSVLAAAN PVYGRYDQYK TPMENIGLQD SLLSR FDLL FIMLDQMDPE QDREISDHVL RMHRYRAPGE QDGDAMPLGS AVDILATDDP NFSQEDQQDT QIYEKHDNLL HGTKKK KEK MVSAAFMKKY IHVAKIIKPV LTQESATYIA EEYSRLRSQD SMSSDTARTS PVTARTLETL IRLATAHAKA RMSKTVD LQ DAEEAVELVQ YAYFKKVLEK EKKRKKRSED ESETEDEEEK SQEDQEQKRK RRKTRQPDAK DGDSYDPYDF SDTEEEMP Q VHTPKTADSQ ETKESQKVEL SESRLKAFKV ALLDVFREAH AQSIGMNRLT ESINRDSEEP FSSVEIQAAL SKMQDDNQV MVSEGIIFLI

UniProtKB: DNA replication licensing factor MCM3

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Macromolecule #3: DNA replication licensing factor MCM4

MacromoleculeName: DNA replication licensing factor MCM4 / type: protein_or_peptide / ID: 3 / Details: Natural variant L650M / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 96.975141 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAMSSPAST PSRRGSRRGR ATPAQTPRSE DARSSPSQRR RGEDSTSTGE LQPMPTSPGV DLQSPAAQDV LFSSPPQMHS SAIPLDFDV SSPLTYGTPS SRVEGTPRSG VRGTPVRQRP DLGSAQKGLQ VDLQSDGAAA EDIVASEQSL GQKLVIWGTD V NVAACKEN ...String:
SNAMSSPAST PSRRGSRRGR ATPAQTPRSE DARSSPSQRR RGEDSTSTGE LQPMPTSPGV DLQSPAAQDV LFSSPPQMHS SAIPLDFDV SSPLTYGTPS SRVEGTPRSG VRGTPVRQRP DLGSAQKGLQ VDLQSDGAAA EDIVASEQSL GQKLVIWGTD V NVAACKEN FQRFLQRFID PLAKEEENVG IDITEPLYMQ RLGEINVIGE PFLNVNCEHI KSFDKNLYRQ LISYPQEVIP TF DMAVNEI FFDRYPDSIL EHQIQVRPFN ALKTKNMRNL NPEDIDQLIT ISGMVIRTSQ LIPEMQEAFF QCQVCAHTTR VEM DRGRIA EPSVCGRCHT THSMALIHNR SLFSDKQMIK LQESPEDMPA GQTPHTVILF AHNDLVDKVQ PGDRVNVTGI YRAV PIRVN PRVSNVKSVY KTHIDVIHYR KTDAKRLHGL DEEAEQKLFS EKRVELLKEL SRKPDIYERL ASALAPSIYE HEDIK KGIL LQLFGGTRKD FSHTGRGKFR AEINILLCGD PGTSKSQLLQ YVYNLVPRGQ YTSGKGSSAV GLTAYVMKDP ETRQLV LQT GALVLSDNGI CCIDEFDKMN ESTRSVLHEV MEQQTLSIAK AGIICQLNAR TSVLAAANPI ESQWNPKKTT IENIQLP HT LLSRFDLIFL MLDPQDEAYD RRLAHHLVAL YYQSEEQAEE ELLDMAVLKD YIAYAHSTIM PRLSEEASQA LIEAYVDM R KIGSSRGMVS AYPRQLESLI RLAEAHAKVR LSNKVEAIDV EEAKRLHREA LKQSATDPRT GIVDISILTT GMSATSRKR KEELAEALKK LILSKGKTPA LKYQQLFEDI RGQSDIAITK DMFEEALRAL ADDDFLTVTG KTVRLL

UniProtKB: DNA replication licensing factor MCM4

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Macromolecule #4: DNA replication licensing factor MCM5

MacromoleculeName: DNA replication licensing factor MCM5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.406633 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MSGFDDPGIF YSDSFGGDAQ ADEGQARKSQ LQRRFKEFLR QYRVGTDRTG FTFKYRDELK RHYNLGEYWI EVEMEDLASF DEDLADYLY KQPAEHLQLL EEAAKEVADE VTRPRPSGEE VLQDIQVMLK SDASPSSIRS LKSDMMSHLV KIPGIIIAAS A VRAKATRI ...String:
MSGFDDPGIF YSDSFGGDAQ ADEGQARKSQ LQRRFKEFLR QYRVGTDRTG FTFKYRDELK RHYNLGEYWI EVEMEDLASF DEDLADYLY KQPAEHLQLL EEAAKEVADE VTRPRPSGEE VLQDIQVMLK SDASPSSIRS LKSDMMSHLV KIPGIIIAAS A VRAKATRI SIQCRSCRNT LTNIAMRPGL EGYALPRKCN TDQAGRPKCP LDPYFIMPDK CKCVDFQTLK LQELPDAVPH GE MPRHMQL YCDRYLCDKV VPGNRVTIMG IYSIKKFGLT TSRGRDRVGV GIRSSYIRVL GIQVDTDGSG RSFAGAVSPQ EEE EFRRLA ALPNVYEVIS KSIAPSIFGG TDMKKAIACL LFGGSRKRLP DGLTRRGDIN LLMLGDPGTA KSQLLKFVEK CSPI GVYTS GKGSSAAGLT ASVMRDPSSR NFIMEGGAMV LADGGVVCID EFDKMREDDR VAIHEAMEQQ TISIAKAGIT TTLNS RCSV LAAANSVFGR WDETKGEDNI DFMPTILSRF DMIFIVKDEH NEERDVMLAK HVITLHVSAL TQTQAVEGEI DLAKLK KFI AYCRVKCGPR LSAEAAEKLK NRYIIMRSGA RQHERDSDRR SSIPITVRQL EAIVRIAEAL SKMKLQPFAT EADVEEA LR LFQVSTLDAA LSGTLSGVEG FTSQEDQEML SRIEKQLKRR FAIGSQVSEH SIIKDFTKQK YPEHAIHKVL QLMLRRGE I QHRMQRKVLY RLK

UniProtKB: DNA replication licensing factor MCM5

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Macromolecule #5: DNA replication licensing factor MCM6

MacromoleculeName: DNA replication licensing factor MCM6 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.010273 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MDLAAAAEPG AGSQHLEVRD EVAEKCQKLF LDFLEEFQSS DGEIKYLQLA EELIRPERNT LVVSFVDLEQ FNQQLSTTIQ EEFYRVYPY LCRALKTFVK DRKEIPLAKD FYVAFQDLPT RHKIRELTSS RIGLLTRISG QVVRTHPVHP ELVSGTFLCL D CQTVIRDV ...String:
MDLAAAAEPG AGSQHLEVRD EVAEKCQKLF LDFLEEFQSS DGEIKYLQLA EELIRPERNT LVVSFVDLEQ FNQQLSTTIQ EEFYRVYPY LCRALKTFVK DRKEIPLAKD FYVAFQDLPT RHKIRELTSS RIGLLTRISG QVVRTHPVHP ELVSGTFLCL D CQTVIRDV EQQFKYTQPN ICRNPVCANR RRFLLDTNKS RFVDFQKVRI QETQAELPRG SIPRSLEVIL RAEAVESAQA GD KCDFTGT LIVVPDVSKL STPGARAETN SRVSGVDGYE TEGIRGLRAL GVRDLSYRLV FLACCVAPTN PRFGGKELRD EEQ TAESIK NQMTVKEWEK VFEMSQDKNL YHNLCTSLFP TIHGNDEVKR GVLLMLFGGV PKTTGEGTSL RGDINVCIVG DPST AKSQF LKHVEEFSPR AVYTSGKASS AAGLTAAVVR DEESHEFVIE AGALMLADNG VCCIDEFDKM DVRDQVAIHE AMEQQ TISI TKAGVKATLN ARTSILAAAN PISGHYDRSK SLKQNINLSA PIMSRFDLFF ILVDECNEVT DYAIARRIVD LHSRIE ESI DRVYSLDDIR RYLLFARQFK PKISKESEDF IVEQYKHLRQ RDGSGVTKSS WRITVRQLES MIRLSEAMAR MHCCDEV QP KHVKEAFRLL NKSIIRVETP DVNLDQEEEI QMEVDEGAGG INGHADSPAP VNGINGYNED INQESAPKAS LRLGFSEY C RISNLIVLHL RKVEEEEDES ALKRSELVNW YLKEIESEID SEEELINKKR IIEKVIHRLT HYDHVLIELT QAGLKGSTE GSESYEEDPY LVVNPNYLLE D

UniProtKB: DNA replication licensing factor MCM6

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Macromolecule #6: DNA replication licensing factor MCM7

MacromoleculeName: DNA replication licensing factor MCM7 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 81.411875 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MALKDYALEK EKVKKFLQEF YQDDELGKKQ FKYGNQLVRL AHREQVALYV DLDDVAEDDP ELVDSICENA RRYAKLFADA VQELLPQYK EREVVNKDVL DVYIEHRLMM EQRSRDPGMV RSPQNQYPAE LMRRFELYFQ GPSSNKPRVI REVRADSVGK L VTVRGIVT ...String:
MALKDYALEK EKVKKFLQEF YQDDELGKKQ FKYGNQLVRL AHREQVALYV DLDDVAEDDP ELVDSICENA RRYAKLFADA VQELLPQYK EREVVNKDVL DVYIEHRLMM EQRSRDPGMV RSPQNQYPAE LMRRFELYFQ GPSSNKPRVI REVRADSVGK L VTVRGIVT RVSEVKPKMV VATYTCDQCG AETYQPIQSP TFMPLIMCPS QECQTNRSGG RLYLQTRGSR FIKFQEMKMQ EH SDQVPVG NIPRSITVLV EGENTRIAQP GDHVSVTGIF LPILRTGFRQ VVQGLLSETY LEAHRIVKMN KSEDDESGAG ELT REELRQ IAEEDFYEKL AASIAPEIYG HEDVKKALLL LLVGGVDQSP RGMKIRGNIN ICLMGDPGVA KSQLLSYIDR LAPR SQYTT GRGSSGVGLT AAVLRDSVSG ELTLEGGALV LADQGVCCID EFDKMAEADR TAIHEVMEQQ TISIAKAGIL TTLNA RCSI LAAANPAYGR YNPRRSLEQN IQLPAALLSR FDLLWLIQDR PDRDNDLRLA QHITYVHQHS RQPPSQFEPL DMKLMR RYI AMCREKQPMV PESLADYITA AYVEMRREAW ASKDATYTSA RTLLAILRLS TALARLRMVD VVEKEDVNEA IRLMEMS KD SLLGDKGQTA RTQRPADVIF ATVRELVSGG RSVRFSEAEQ RCVSRGFTPA QFQAALDEYE ELNVWQVNAS RTRITFV

UniProtKB: DNA replication licensing factor MCM7

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #8: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 8 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #9: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #10: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

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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: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE
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: 50.96 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 203444
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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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

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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

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