[English] 日本語
Yorodumi
- EMDB-19619: H. sapiens MCM2-7 hexamer bound to double stranded DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-19619
TitleH. sapiens MCM2-7 hexamer bound to double stranded DNA
Map dataMap of the human MCM2-7 hexamer bound to double stranded DNA. The map is the output of a local refinement in cryoSPARC.
Sample
  • Complex: H. sapiens MCM2-7 hexamer bound to double stranded DNA
    • Complex: Double stranded DNA
      • DNA: x 2 types
    • Complex: H. sapiens MCM2-7
      • Protein or peptide: x 6 types
  • Ligand: x 4 types
KeywordsAAA+ ATPase / DNA helicase / REPLICATION
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
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 speciessynthetic construct (others) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGreiwe JF / Weissmann F / Diffley JFX / Costa A
Funding support United Kingdom, European Union, 4 items
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: 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.
#1: Journal: Biorxiv / Year: 2024
Title: MCM Double Hexamer Loading Visualised with Human Proteins
Authors: Weissmann F / Greiwe JF / Puhringer T / Miller TCR / Diffley JFX / Costa A
History
DepositionFeb 13, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateDec 25, 2024-
Current statusDec 25, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_19619.png

Downloads & links

-
Map

FileDownload / File: emd_19619.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of the human MCM2-7 hexamer bound to double stranded DNA. The map is the output of a local refinement in cryoSPARC.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å		1.08 Å/pix.
x 400 pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.33
Minimum - Maximum-0.7256253 - 1.7720125
Average (Standard dev.)0.0029155666 (±0.049469337)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 432.00003 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Map of the human MCM2-7 hexamer bound to...

Fileemd_19619_half_map_1.map
AnnotationMap of the human MCM2-7 hexamer bound to double stranded DNA. The map is the output of a local refinement in cryoSPARC.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half map 1 of the main map.

Fileemd_19619_half_map_2.map
AnnotationHalf map 1 of the main map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : H. sapiens MCM2-7 hexamer bound to double stranded DNA

EntireName: H. sapiens MCM2-7 hexamer bound to double stranded DNA
Components
  • Complex: H. sapiens MCM2-7 hexamer bound to double stranded DNA
    • Complex: Double stranded DNA
      • DNA: DNA (22-mer)
      • DNA: DNA (22-mer)
    • Complex: H. sapiens MCM2-7
      • 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: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

+
Supramolecule #1: H. sapiens MCM2-7 hexamer bound to double stranded DNA

SupramoleculeName: H. sapiens MCM2-7 hexamer bound to double stranded DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Molecular weightTheoretical: 600 KDa

+
Supramolecule #2: Double stranded DNA

SupramoleculeName: Double stranded DNA / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: synthetic construct (others)

+
Supramolecule #3: H. sapiens MCM2-7

SupramoleculeName: H. sapiens MCM2-7 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#8
Source (natural)Organism: Homo sapiens (human)

+
Macromolecule #1: DNA (22-mer)

MacromoleculeName: DNA (22-mer) / type: dna / ID: 1 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.752366 KDa
SequenceString:
(DA)(DT)(DG)(DC)(DA)(DT)(DG)(DC)(DA)(DT) (DG)(DC)(DG)(DC)(DA)(DT)(DG)(DC)(DA)(DT) (DG)(DC)

+
Macromolecule #2: DNA (22-mer)

MacromoleculeName: DNA (22-mer) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 6.752366 KDa
SequenceString:
(DG)(DC)(DA)(DT)(DG)(DC)(DA)(DT)(DG)(DC) (DG)(DC)(DA)(DT)(DG)(DC)(DA)(DT)(DG)(DC) (DA)(DT)

+
Macromolecule #3: DNA replication licensing factor MCM2

MacromoleculeName: DNA replication licensing factor MCM2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 102.034102 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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

+
Macromolecule #4: DNA replication licensing factor MCM3

MacromoleculeName: DNA replication licensing factor MCM3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.297023 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GEMAGTVVLD DVELREAQRD YLDFLDDEED QGIYQSKVRE LISDNQYRLI VNVNDLRRKN EKRANRLLNN AFEELVAFQR ALKDFVASI DATYAKQYEE FYVGLEGSFG SKHVSPRTLT SCFLSCVVCV EGIVTKCSLV RPKVVRSVHY CPATKKTIER R YSDLTTLV ...String:
GEMAGTVVLD 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

+
Macromolecule #5: DNA replication licensing factor MCM4

MacromoleculeName: DNA replication licensing factor MCM4 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 96.702891 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MSSPASTPSR RGSRRGRATP AQTPRSEDAR SSPSQRRRGE DSTSTGELQP MPTSPGVDLQ SPAAQDVLFS SPPQMHSSAI PLDFDVSSP LTYGTPSSRV EGTPRSGVRG TPVRQRPDLG SAQKGLQVDL QSDGAAAEDI VASEQSLGQK LVIWGTDVNV A ACKENFQR ...String:
MSSPASTPSR RGSRRGRATP AQTPRSEDAR SSPSQRRRGE DSTSTGELQP MPTSPGVDLQ SPAAQDVLFS SPPQMHSSAI PLDFDVSSP LTYGTPSSRV EGTPRSGVRG TPVRQRPDLG SAQKGLQVDL QSDGAAAEDI VASEQSLGQK LVIWGTDVNV A ACKENFQR FLQRFIDPLA KEEENVGIDI TEPLYMQRLG EINVIGEPFL NVNCEHIKSF DKNLYRQLIS YPQEVIPTFD MA VNEIFFD RYPDSILEHQ IQVRPFNALK TKNMRNLNPE DIDQLITISG MVIRTSQLIP EMQEAFFQCQ VCAHTTRVEM DRG RIAEPS VCGRCHTTHS MALIHNRSLF SDKQMIKLQE SPEDMPAGQT PHTVILFAHN DLVDKVQPGD RVNVTGIYRA VPIR VNPRV SNVKSVYKTH IDVIHYRKTD AKRLHGLDEE AEQKLFSEKR VELLKELSRK PDIYERLASA LAPSIYEHED IKKGI LLQL FGGTRKDFSH TGRGKFRAEI NILLCGDPGT SKSQLLQYVY NLVPRGQYTS GKGSSAVGLT AYVMKDPETR QLVLQT GAL VLSDNGICCI DEFDKMNEST RSVLHEVMEQ QTLSIAKAGI ICQLNARTSV LAAANPIESQ WNPKKTTIEN IQLPHTL LS RFDLIFLMLD PQDEAYDRRL AHHLVALYYQ SEEQAEEELL DMAVLKDYIA YAHSTIMPRL SEEASQALIE AYVDMRKI G SSRGMVSAYP RQLESLIRLA EAHAKVRLSN KVEAIDVEEA KRLHREALKQ SATDPRTGIV DISILTTGMS ATSRKRKEE LAEALKKLIL SKGKTPALKY QQLFEDIRGQ SDIAITKDMF EEALRALADD DFLTVTGKTV RLL

UniProtKB: DNA replication licensing factor MCM4

+
Macromolecule #6: DNA replication licensing factor MCM5

MacromoleculeName: DNA replication licensing factor MCM5 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.406633 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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

+
Macromolecule #7: DNA replication licensing factor MCM6

MacromoleculeName: DNA replication licensing factor MCM6 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.010273 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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

+
Macromolecule #8: DNA replication licensing factor MCM7

MacromoleculeName: DNA replication licensing factor MCM7 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 81.411875 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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

+
Macromolecule #9: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

+
Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #11: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 11 / Number of copies: 5 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #12: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 12 / Number of copies: 4 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
DetailsThe 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.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3589 / Average exposure time: 9.4 sec. / Average electron dose: 49.19 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 25069
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: AlphaFold multimer
Output model

PDB-8s0a:
H. sapiens MCM2-7 hexamer bound to double stranded DNA

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more