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- EMDB-45400: Cryo-EM structure of a human MCM2-7 double hexamer formed from in... -

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Basic information

Entry
Database: EMDB / ID: EMD-45400
TitleCryo-EM structure of a human MCM2-7 double hexamer formed from independently loaded MCM2-7 single hexamers
Map dataDeepEMhancer sharpened EM map
Sample
  • Complex: In vitro loaded, human MCM2-7 double hexamer on dsDNA (formed by dimerization of independently loaded MCM2-7 single hexamers)
    • Protein or peptide: x 6 types
    • DNA: x 2 types
  • Ligand: x 4 types
Keywordscomplex / helicase / replication / AAA+ ATPase
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 / cellular response to interleukin-4 / Activation of ATR in response to replication stress / DNA helicase activity / Assembly of the pre-replicative complex / helicase activity / Orc1 removal from chromatin / cellular response to xenobiotic stimulus / nucleosome assembly / single-stranded DNA binding / histone binding / DNA helicase / DNA replication / cell population proliferation / chromosome, telomeric region / centrosome / DNA damage response / chromatin / apoptotic process / perinuclear region of cytoplasm / enzyme binding / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
: / MCM5, C-terminal 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 ...: / MCM5, C-terminal 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 / 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 / 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) / Saccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYang R / Hunker O / Bleichert F
Funding support United States, 4 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
National Institutes of Health/National Cancer Institute (NIH/NCI)S10OD023603 United States
CitationJournal: To Be Published
Title: Multiple pathways for licensing human replication origins
Authors: Yang R / Hunker O / Wise M / Bleichert F
History
DepositionJun 17, 2024-
Header (metadata) releaseOct 2, 2024-
Map releaseOct 2, 2024-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45400.png

Downloads & links

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Map

FileDownload / File: emd_45400.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhancer sharpened EM map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 500 pix.
= 434. Å		0.87 Å/pix.
x 500 pix.
= 434. Å		0.87 Å/pix.
x 500 pix.
= 434. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.868 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.019387186 - 2.5334327
Average (Standard dev.)0.0019645465 (±0.031437505)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 434.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened EM map

Fileemd_45400_additional_1.map
AnnotationSharpened EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened EM map

Fileemd_45400_additional_2.map
AnnotationUnsharpened EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half EM map

Fileemd_45400_half_map_1.map
AnnotationHalf EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half EM map

Fileemd_45400_half_map_2.map
AnnotationHalf EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : In vitro loaded, human MCM2-7 double hexamer on dsDNA (formed by ...

EntireName: In vitro loaded, human MCM2-7 double hexamer on dsDNA (formed by dimerization of independently loaded MCM2-7 single hexamers)
Components
  • Complex: In vitro loaded, human MCM2-7 double hexamer on dsDNA (formed by dimerization of independently loaded MCM2-7 single hexamers)
    • 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
    • DNA: DNA (44-MER)
    • DNA: DNA (44-MER)
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: In vitro loaded, human MCM2-7 double hexamer on dsDNA (formed by ...

SupramoleculeName: In vitro loaded, human MCM2-7 double hexamer on dsDNA (formed by dimerization of independently loaded MCM2-7 single hexamers)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
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: 2 / 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: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.110852 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MAGTVVLDDV ELREAQRDYL DFLDDEEDQG IYQSKVRELI SDNQYRLIVN VNDLRRKNEK RANRLLNNAF EELVAFQRAL KDFVASIDA TYAKQYEEFY VGLEGSFGSK HVSPRTLTSC FLSCVVCVEG IVTKCSLVRP KVVRSVHYCP ATKKTIERRY S DLTTLVAF ...String:
MAGTVVLDDV ELREAQRDYL DFLDDEEDQG IYQSKVRELI SDNQYRLIVN VNDLRRKNEK RANRLLNNAF EELVAFQRAL KDFVASIDA TYAKQYEEFY VGLEGSFGSK HVSPRTLTSC FLSCVVCVEG IVTKCSLVRP KVVRSVHYCP ATKKTIERRY S DLTTLVAF PSSSVYPTKD EENNPLETEY GLSVYKDHQT ITIQEMPEKA PAGQLPRSVD VILDDDLVDK AKPGDRVQVV GT YRCLPGK KGGYTSGTFR TVLIACNVKQ MSKDAQPSFS AEDIAKIKKF SKTRSKDIFD QLAKSLAPSI HGHDYVKKAI LCL LLGGVE RDLENGSHIR GDINILLIGD PSVAKSQLLR YVLCTAPRAI PTTGRGSSGV GLTAAVTTDQ ETGERRLEAG AMVL ADRGV VCIDEFDKMS DMDRTAIHEV MEQGRVTIAK AGIHARLNAR CSVLAAANPV YGRYDQYKTP MENIGLQDSL LSRFD LLFI MLDQMDPEQD REISDHVLRM HRYRAPGEQD GDAMPLGSAV DILATDDPNF SQEDQQDTQI YEKHDNLLHG TKKKKE KMV SAAFMKKYIH VAKIIKPVLT QESATYIAEE YSRLRSQDSM SSDTARTSPV TARTLETLIR LATAHAKARM SKTVDLQ DA EEAVELVQYA YFKKVLEKEK KRKKRSEDES ETEDEEEKSQ EDQEQKRKRR KTRQPDAKDG DSYDPYDFSD TEEEMPQV H TPKTADSQET KESQKVELSE SRLKAFKVAL LDVFREAHAQ SIGMNRLTES INRDSEEPFS SVEIQAALSK MQDDNQVMV SEGIIFLI

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: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 96.702891 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
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

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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: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 82.678898 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAMSGFDDP GIFYSDSFGG DAQADEGQAR KSQLQRRFKE FLRQYRVGTD RTGFTFKYRD ELKRHYNLGE YWIEVEMEDL ASFDEDLAD YLYKQPAEHL QLLEEAAKEV ADEVTRPRPS GEEVLQDIQV MLKSDASPSS IRSLKSDMMS HLVKIPGIII A ASAVRAKA ...String:
SNAMSGFDDP GIFYSDSFGG DAQADEGQAR KSQLQRRFKE FLRQYRVGTD RTGFTFKYRD ELKRHYNLGE YWIEVEMEDL ASFDEDLAD YLYKQPAEHL QLLEEAAKEV ADEVTRPRPS GEEVLQDIQV MLKSDASPSS IRSLKSDMMS HLVKIPGIII A ASAVRAKA TRISIQCRSC RNTLTNIAMR PGLEGYALPR KCNTDQAGRP KCPLDPYFIM PDKCKCVDFQ TLKLQELPDA VP HGEMPRH MQLYCDRYLC DKVVPGNRVT IMGIYSIKKF GLTTSRGRDR VGVGIRSSYI RVLGIQVDTD GSGRSFAGAV SPQ EEEEFR RLAALPNVYE VISKSIAPSI FGGTDMKKAI ACLLFGGSRK RLPDGLTRRG DINLLMLGDP GTAKSQLLKF VEKC SPIGV YTSGKGSSAA GLTASVMRDP SSRNFIMEGG AMVLADGGVV CIDEFDKMRE DDRVAIHEAM EQQTISIAKA GITTT LNSR CSVLAAANSV FGRWDETKGE DNIDFMPTIL SRFDMIFIVK DEHNEERDVM LAKHVITLHV SALTQTQAVE GEIDLA KLK KFIAYCRVKC GPRLSAEAAE KLKNRYIIMR SGARQHERDS DRRSSIPITV RQLEAIVRIA EALSKMKLQP FATEADV EE ALRLFQVSTL DAALSGTLSG VEGFTSQEDQ EMLSRIEKQL KRRFAIGSQV SEHSIIKDFT KQKYPEHAIH KVLQLMLR R GEIQHRMQRK VLYRLK

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: 2 / 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: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 81.684133 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: SNAMALKDYA LEKEKVKKFL QEFYQDDELG KKQFKYGNQL VRLAHREQVA LYVDLDDVAE DDPELVDSIC ENARRYAKLF ADAVQELLP QYKEREVVNK DVLDVYIEHR LMMEQRSRDP GMVRSPQNQY PAELMRRFEL YFQGPSSNKP RVIREVRADS V GKLVTVRG ...String:
SNAMALKDYA LEKEKVKKFL QEFYQDDELG KKQFKYGNQL VRLAHREQVA LYVDLDDVAE DDPELVDSIC ENARRYAKLF ADAVQELLP QYKEREVVNK DVLDVYIEHR LMMEQRSRDP GMVRSPQNQY PAELMRRFEL YFQGPSSNKP RVIREVRADS V GKLVTVRG IVTRVSEVKP KMVVATYTCD QCGAETYQPI QSPTFMPLIM CPSQECQTNR SGGRLYLQTR GSRFIKFQEM KM QEHSDQV PVGNIPRSIT VLVEGENTRI AQPGDHVSVT GIFLPILRTG FRQVVQGLLS ETYLEAHRIV KMNKSEDDES GAG ELTREE LRQIAEEDFY EKLAASIAPE IYGHEDVKKA LLLLLVGGVD QSPRGMKIRG NINICLMGDP GVAKSQLLSY IDRL APRSQ YTTGRGSSGV GLTAAVLRDS VSGELTLEGG ALVLADQGVC CIDEFDKMAE ADRTAIHEVM EQQTISIAKA GILTT LNAR CSILAAANPA YGRYNPRRSL EQNIQLPAAL LSRFDLLWLI QDRPDRDNDL RLAQHITYVH QHSRQPPSQF EPLDMK LMR RYIAMCREKQ PMVPESLADY ITAAYVEMRR EAWASKDATY TSARTLLAIL RLSTALARLR MVDVVEKEDV NEAIRLM EM SKDSLLGDKG QTARTQRPAD VIFATVRELV SGGRSVRFSE AEQRCVSRGF TPAQFQAALD EYEELNVWQV NASRTRIT F V

UniProtKB: DNA replication licensing factor MCM7

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Macromolecule #7: DNA (44-MER)

MacromoleculeName: DNA (44-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 13.54685 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)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT)

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Macromolecule #8: DNA (44-MER)

MacromoleculeName: DNA (44-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 13.528821 KDa
SequenceString:
(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DA)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT) (DT)(DT)(DT)(DT)

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Macromolecule #9: ZINC ION

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

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Macromolecule #10: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 10 / Number of copies: 9 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #11: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 11 / Number of copies: 2 / 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 #12: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 12 / Number of copies: 8 / 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: 7.6
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.54 e/Å2
Electron beamAcceleration voltage: 200 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

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 46418
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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