[English] 日本語
Yorodumi
- EMDB-32258: Human MCM double hexamer bound to natural DNA duplex (polyAT/polyTA) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-32258
TitleHuman MCM double hexamer bound to natural DNA duplex (polyAT/polyTA)
Map data
Sample
  • Complex: human Mini-chromosome maintenance complexMinichromosome maintenance
    • Complex: DNA replication licensing factor MCM 2/3/4/5/6/7
      • Protein or peptide: x 6 types
    • Complex: DNA
      • DNA: x 2 types
  • Ligand: x 4 types
Function / homology
Function and homology information


Switching of origins to a post-replicative state / Unwinding of DNA / nuclear origin of replication recognition complex / mitotic DNA replication / alpha DNA polymerase:primase complex / CMG complex / MCM complex / regulation of phosphorylation / double-strand break repair via break-induced replication / mitotic DNA replication initiation ...Switching of origins to a post-replicative state / Unwinding of DNA / nuclear origin of replication recognition complex / mitotic DNA replication / alpha DNA polymerase:primase complex / CMG complex / MCM complex / regulation of phosphorylation / 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 unwinding involved in DNA replication / DNA replication origin binding / DNA replication initiation / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / DNA helicase activity / cellular response to interleukin-4 / helicase activity / Assembly of the pre-replicative complex / nucleosome assembly / Orc1 removal from chromatin / cellular response to xenobiotic stimulus / single-stranded DNA binding / histone binding / DNA helicase / cell population proliferation / DNA replication / chromosome, telomeric region / cell cycle / centrosome / apoptotic process / DNA damage response / chromatin / perinuclear region of cytoplasm / enzyme binding / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / membrane / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
MCM4, winged helix domain / DNA replication licensing factor Mcm5 / 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 ...MCM4, winged helix domain / DNA replication licensing factor Mcm5 / 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 / 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
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) / Human (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsLi J / Dong J / Dang S / Zhai Y
Funding support Hong Kong, 1 items
OrganizationGrant numberCountry
The University Grants Committee, Research Grants Council (RGC) Hong Kong
CitationJournal: Cell / Year: 2023
Title: The human pre-replication complex is an open complex.
Authors: Jian Li / Jiangqing Dong / Weitao Wang / Daqi Yu / Xinyu Fan / Yan Chit Hui / Clare S K Lee / Wai Hei Lam / Nathan Alary / Yang Yang / Yingyi Zhang / Qian Zhao / Chun-Long Chen / Bik-Kwoon ...Authors: Jian Li / Jiangqing Dong / Weitao Wang / Daqi Yu / Xinyu Fan / Yan Chit Hui / Clare S K Lee / Wai Hei Lam / Nathan Alary / Yang Yang / Yingyi Zhang / Qian Zhao / Chun-Long Chen / Bik-Kwoon Tye / Shangyu Dang / Yuanliang Zhai /
Abstract: In eukaryotes, DNA replication initiation requires assembly and activation of the minichromosome maintenance (MCM) 2-7 double hexamer (DH) to melt origin DNA strands. However, the mechanism for this ...In eukaryotes, DNA replication initiation requires assembly and activation of the minichromosome maintenance (MCM) 2-7 double hexamer (DH) to melt origin DNA strands. However, the mechanism for this initial melting is unknown. Here, we report a 2.59-Å cryo-electron microscopy structure of the human MCM-DH (hMCM-DH), also known as the pre-replication complex. In this structure, the hMCM-DH with a constricted central channel untwists and stretches the DNA strands such that almost a half turn of the bound duplex DNA is distorted with 1 base pair completely separated, generating an initial open structure (IOS) at the hexamer junction. Disturbing the IOS inhibits DH formation and replication initiation. Mapping of hMCM-DH footprints indicates that IOSs are distributed across the genome in large clusters aligning well with initiation zones designed for stochastic origin firing. This work unravels an intrinsic mechanism that couples DH formation with initial DNA melting to license replication initiation in human cells.
History
DepositionNov 21, 2021-
Header (metadata) releaseFeb 8, 2023-
Map releaseFeb 8, 2023-
UpdateFeb 8, 2023-
Current statusFeb 8, 2023Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_32258.png

Downloads & links

-
Map

FileDownload / File: emd_32258.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.1412559 - 4.637665
Average (Standard dev.)-0.00016733941 (±0.11543764)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

+
Entire : human Mini-chromosome maintenance complex

EntireName: human Mini-chromosome maintenance complexMinichromosome maintenance
Components
  • Complex: human Mini-chromosome maintenance complexMinichromosome maintenance
    • Complex: DNA replication licensing factor MCM 2/3/4/5/6/7
      • Protein or peptide: DNA replication licensing factor MCM2
      • Protein or peptide: Isoform 2 of 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
    • Complex: DNA
      • DNA: DNA (49-MER)
      • DNA: DNA (49-MER)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

+
Supramolecule #1: human Mini-chromosome maintenance complex

SupramoleculeName: human Mini-chromosome maintenance complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.09 MDa

+
Supramolecule #2: DNA replication licensing factor MCM 2/3/4/5/6/7

SupramoleculeName: DNA replication licensing factor MCM 2/3/4/5/6/7 / type: complex / ID: 2 / Chimera: Yes / Parent: 1 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

+
Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Chimera: Yes / Parent: 1 / Macromolecule list: #7-#8

+
Macromolecule #1: DNA replication licensing factor MCM2

MacromoleculeName: DNA replication licensing factor MCM2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 102.034102 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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

+
Macromolecule #2: Isoform 2 of DNA replication licensing factor MCM3

MacromoleculeName: Isoform 2 of DNA replication licensing factor MCM3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 96.04332 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MLPRSPPLPR GNLWWREEFG SFRAGVESSW EPPRDFGGGS SLAAGMAGTV VLDDVELREA QRDYLDFLDD EEDQGIYQSK VRELISDNQ YRLIVNVNDL RRKNEKRANR LLNNAFEELV AFQRALKDFV ASIDATYAKQ YEEFYVGLEG SFGSKHVSPR T LTSCFLSC ...String:
MLPRSPPLPR GNLWWREEFG SFRAGVESSW EPPRDFGGGS SLAAGMAGTV VLDDVELREA QRDYLDFLDD EEDQGIYQSK VRELISDNQ YRLIVNVNDL RRKNEKRANR LLNNAFEELV AFQRALKDFV ASIDATYAKQ YEEFYVGLEG SFGSKHVSPR T LTSCFLSC VVCVEGIVTK CSLVRPKVVR SVHYCPATKK TIERRYSDLT TLVAFPSSSV YPTKDEENNP LETEYGLSVY KD HQTITIQ EMPEKAPAGQ LPRSVDVILD DDLVDKAKPG DRVQVVGTYR CLPGKKGGYT SGTFRTVLIA CNVKQMSKDA QPS FSAEDI AKIKKFSKTR SKDIFDQLAK SLAPSIHGHD YVKKAILCLL LGGVERDLEN GSHIRGDINI LLIGDPSVAK SQLL RYVLC TAPRAIPTTG RGSSGVGLTA AVTTDQETGE RRLEAGAMVL ADRGVVCIDE FDKMSDMDRT AIHEVMEQGR VTIAK AGIH ARLNARCSVL AAANPVYGRY DQYKTPMENI GLQDSLLSRF DLLFIMLDQM DPEQDREISD HVLRMHRYRA PGEQDG DAM PLGSAVDILA TDDPNFSQED QQDTQIYEKH DNLLHGTKKK KEKMVSAAFM KKYIHVAKII KPVLTQESAT YIAEEYS RL RSQDSMSSDT ARTSPVTART LETLIRLATA HAKARMSKTV DLQDAEEAVE LVQYAYFKKV LEKEKKRKKR SEDESETE D EEEKSQEDQE QKRKRRKTRQ PDAKDGDSYD PYDFSDTEEE MPQVHTPKTA DSQETKESQK VELSESRLKA FKVALLDVF REAHAQSIGM NRLTESINRD SEEPFSSVEI QAALSKMQDD NQVMVSEGII FLI

+
Macromolecule #3: DNA replication licensing factor MCM4

MacromoleculeName: DNA replication licensing factor MCM4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 96.684852 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 RFDLIFLLLD PQDEAYDRRL AHHLVALYYQ SEEQAEEELL DMAVLKDYIA YAHSTIMPRL SEEASQALIE AYVDMRKI G SSRGMVSAYP RQLESLIRLA EAHAKVRLSN KVEAIDVEEA KRLHREALKQ SATDPRTGIV DISILTTGMS ATSRKRKEE LAEALKKLIL SKGKTPALKY QQLFEDIRGQ SDIAITKDMF EEALRALADD DFLTVTGKTV RLL

+
Macromolecule #4: DNA replication licensing factor MCM5

MacromoleculeName: DNA replication licensing factor MCM5 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.406633 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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

+
Macromolecule #5: DNA replication licensing factor MCM6

MacromoleculeName: DNA replication licensing factor MCM6 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 93.010273 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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

+
Macromolecule #6: DNA replication licensing factor MCM7

MacromoleculeName: DNA replication licensing factor MCM7 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 81.411875 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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

+
Macromolecule #7: DNA (49-MER)

MacromoleculeName: DNA (49-MER) / type: dna / ID: 7
Details: Since the register of origin DNA engaged with endogenous hMCM-DHs is heterogenous, it is likely that there is a mix of purines and pyrimidines at each nucleotide position. For this reason we ...Details: Since the register of origin DNA engaged with endogenous hMCM-DHs is heterogenous, it is likely that there is a mix of purines and pyrimidines at each nucleotide position. For this reason we could not build the origin DNA sequence with certainty. Instead, two superposed polyA:polyT and polyT:polyA duplexes, in which all atoms is set at 50 % occupancy, were modelled to surrogate for the heterogenous sequences.
Number of copies: 1 / Classification: DNA
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 15.30217 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)

+
Macromolecule #8: DNA (49-MER)

MacromoleculeName: DNA (49-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Human (human)
Molecular weightTheoretical: 14.86049 KDa
SequenceString:
(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)

+
Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 10 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 12 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #11: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 11 / Number of copies: 8 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

+
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 / Adenosine diphosphate

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
100.0 mML-GluL-GlutamateGlutamic acid
50.0 mMHEPES/KOHHEPES
8.0 mMMgCl2Magnesium chloride
1.0 mMEDTAEthylenediaminetetraacetic acidEthylene Diamine Tetraacetic Acid
0.02 %NP-40NP-40
3.0 mMATPAdenosine triphosphateAdenosine Triphosphate
2.0 mMNaFSodium fluoride
1.0 mMNa3VO4Sodium vanadate
1.0 mMPMSFPhenylmethanesulfonyl fluoride
1.0 *PICProtein inhibitor cocktail

Details: Solutions were made fresh from concentrated to avoid microbial contamination
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 3710 / Average electron dose: 51.78 e/Å2
Details: Movies are collected in movie-mode containing 40 frames.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 808142
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.0.1)
Final 3D classificationNumber classes: 1
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.0.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: EXACT BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.0.1) / Number images used: 329847

-
Atomic model buiding 1

Initial modelPDB ID:

3ja8

RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-7w1y:
Human MCM double hexamer bound to natural DNA duplex (polyAT/polyTA)

+
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