[English] 日本語
Yorodumi
- EMDB-18191: X. laevis CMG dimer bound to dimeric DONSON - without ATPase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-18191
TitleX. laevis CMG dimer bound to dimeric DONSON - without ATPase
Map data
Sample
  • Complex: X. laevis CMG dimer bound to dimeric DONSON
    • Protein or peptide: x 12 types
  • Ligand: x 1 types
KeywordsDNA replication initiation / Xenopus egg extract / primordial dwarfism / replicative helicase / genome stability / REPLICATION
Function / homology
Function and homology information


GINS complex / premeiotic DNA replication / CMG complex / MCM complex / mitotic DNA replication checkpoint signaling / double-strand break repair via break-induced replication / mitotic DNA replication initiation / single-stranded DNA helicase activity / replisome / regulation of DNA-templated DNA replication initiation ...GINS complex / premeiotic DNA replication / CMG complex / MCM complex / mitotic DNA replication checkpoint signaling / double-strand break repair via break-induced replication / mitotic DNA replication initiation / single-stranded DNA helicase activity / replisome / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / DNA unwinding involved in DNA replication / replication fork processing / mitotic G2 DNA damage checkpoint signaling / DNA replication origin binding / DNA replication initiation / DNA helicase activity / DNA damage checkpoint signaling / regulation of DNA-templated transcription elongation / replication fork / helicase activity / DNA-templated DNA replication / single-stranded DNA binding / DNA helicase / DNA replication / cell division / chromatin binding / chromatin / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Donson / GINS/PriA/YqbF domain / CDC45 family / DNA replication complex GINS protein Psf2 / CDC45-like protein / GINS complex, subunit Psf1 / GINS complex, subunit Psf3 / GINS complex, subunit Psf3 superfamily / DNA replication complex GINS protein SLD5, C-terminal / GINS, helical bundle-like domain superfamily ...Donson / GINS/PriA/YqbF domain / CDC45 family / DNA replication complex GINS protein Psf2 / CDC45-like protein / GINS complex, subunit Psf1 / GINS complex, subunit Psf3 / GINS complex, subunit Psf3 superfamily / DNA replication complex GINS protein SLD5, C-terminal / GINS, helical bundle-like domain superfamily / GINS complex protein Sld5, alpha-helical domain / DNA replication complex GINS protein SLD5 C-terminus / GINS complex subunit Sld5 / GINS subunit, domain A / GINS complex protein helical bundle domain / : / 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 / 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 mcm4-B / Maternal DNA replication licensing factor mcm3 / DNA replication licensing factor mcm2 / DNA replication licensing factor mcm5-A / Maternal DNA replication licensing factor mcm6 / Protein downstream neighbor of son homolog / DNA replication complex GINS protein PSF3 / DNA replication complex GINS protein PSF2 / DNA replication complex GINS protein PSF1 / DNA replication complex GINS protein SLD5 ...DNA replication licensing factor mcm4-B / Maternal DNA replication licensing factor mcm3 / DNA replication licensing factor mcm2 / DNA replication licensing factor mcm5-A / Maternal DNA replication licensing factor mcm6 / Protein downstream neighbor of son homolog / DNA replication complex GINS protein PSF3 / DNA replication complex GINS protein PSF2 / DNA replication complex GINS protein PSF1 / DNA replication complex GINS protein SLD5 / DNA replication licensing factor mcm7-B / Cell division control protein 45 homolog
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.14 Å
AuthorsCvetkovic MA / Costa A
Funding support United Kingdom, European Union, 5 items
OrganizationGrant numberCountry
The Francis Crick InstituteFC001065 United Kingdom
European Research Council (ERC)820102European Union
Marie Sklodowska-Curie Actions, FragNET ITN845939European Union
Wellcome Trust215510/Z/19/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/T001860/1 United Kingdom
CitationJournal: Mol Cell / Year: 2023
Title: The structural mechanism of dimeric DONSON in replicative helicase activation.
Authors: Milos A Cvetkovic / Paolo Passaretti / Agata Butryn / Alicja Reynolds-Winczura / Georgia Kingsley / Aggeliki Skagia / Cyntia Fernandez-Cuesta / Divyasree Poovathumkadavil / Roger George / ...Authors: Milos A Cvetkovic / Paolo Passaretti / Agata Butryn / Alicja Reynolds-Winczura / Georgia Kingsley / Aggeliki Skagia / Cyntia Fernandez-Cuesta / Divyasree Poovathumkadavil / Roger George / Anoop S Chauhan / Satpal S Jhujh / Grant S Stewart / Agnieszka Gambus / Alessandro Costa /
Abstract: The MCM motor of the replicative helicase is loaded onto origin DNA as an inactive double hexamer before replication initiation. Recruitment of activators GINS and Cdc45 upon S-phase transition ...The MCM motor of the replicative helicase is loaded onto origin DNA as an inactive double hexamer before replication initiation. Recruitment of activators GINS and Cdc45 upon S-phase transition promotes the assembly of two active CMG helicases. Although work with yeast established the mechanism for origin activation, how CMG is formed in higher eukaryotes is poorly understood. Metazoan Downstream neighbor of Son (DONSON) has recently been shown to deliver GINS to MCM during CMG assembly. What impact this has on the MCM double hexamer is unknown. Here, we used cryoelectron microscopy (cryo-EM) on proteins isolated from replicating Xenopus egg extracts to identify a double CMG complex bridged by a DONSON dimer. We find that tethering elements mediating complex formation are essential for replication. DONSON reconfigures the MCM motors in the double CMG, and primordial dwarfism patients' mutations disrupting DONSON dimerization affect GINS and MCM engagement in human cells and DNA synthesis in Xenopus egg extracts.
History
DepositionAug 14, 2023-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_18191.png

Downloads & links

-
Map

FileDownload / File: emd_18191.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 540 pix.
= 513. Å		0.95 Å/pix.
x 540 pix.
= 513. Å		0.95 Å/pix.
x 540 pix.
= 513. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.4901651 - 2.7502327
Average (Standard dev.)0.0020799853 (±0.057802036)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions540540540
Spacing540540540
CellA=B=C: 513.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_18191_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_18191_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : X. laevis CMG dimer bound to dimeric DONSON

EntireName: X. laevis CMG dimer bound to dimeric DONSON
Components
  • Complex: X. laevis CMG dimer bound to dimeric DONSON
    • Protein or peptide: DNA replication licensing factor mcm2
    • Protein or peptide: Maternal DNA replication licensing factor mcm3
    • Protein or peptide: DNA replication licensing factor mcm4-B
    • Protein or peptide: DNA replication licensing factor mcm5-A
    • Protein or peptide: Maternal DNA replication licensing factor mcm6
    • Protein or peptide: DNA replication licensing factor mcm7-B
    • Protein or peptide: DNA replication complex GINS protein PSF1
    • Protein or peptide: DNA replication complex GINS protein PSF2
    • Protein or peptide: DNA replication complex GINS protein PSF3
    • Protein or peptide: Cell division control protein 45 homolog
    • Protein or peptide: DNA replication complex GINS protein SLD5
    • Protein or peptide: Protein downstream neighbor of son homolog
  • Ligand: ZINC ION

+
Supramolecule #1: X. laevis CMG dimer bound to dimeric DONSON

SupramoleculeName: X. laevis CMG dimer bound to dimeric DONSON / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#12
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 1.54 MDa

+
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: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 100.397648 KDa
SequenceString: MADSSESFNI ATSPRAGSRR DALTSSPGRD LPPFEDESEG MFGDGVVPEE EEDGEELIGD AMERDYRPIS ELDRYEVEGL DDEEDVEDL TASQREAAEQ SMRMRDREMG RELGRMRRGL LYDSDEEEED RPARKRRMAE RAAEGAPEED EEMIESIENL E DMKGHTVR ...String:
MADSSESFNI ATSPRAGSRR DALTSSPGRD LPPFEDESEG MFGDGVVPEE EEDGEELIGD AMERDYRPIS ELDRYEVEGL DDEEDVEDL TASQREAAEQ SMRMRDREMG RELGRMRRGL LYDSDEEEED RPARKRRMAE RAAEGAPEED EEMIESIENL E DMKGHTVR EWVSMAATRL EIYHRFKNFL RTHVDEHGHN VFKEKISDMC KENKESLPVN YEDLAAREHV LAYFLPEAPA EM LKIFDEA AKEVVLVMYP KYDRIAREIH VRISHLPLVE ELRSLRQLHL NQLIRTSGVV TCCTGVLPQL SMVKYNCNKC NFI LGPFFQ SQNQEVRPGS CPECQSFGPF EINMEETVYQ NYQRITIQES PGKVAAGRLP RSKDAILLAD LVDSCKPGDE IELT GIYHN NYDGSLNTAN GFPVFATVIL ANHITKKDDK VAVGELTDED VKAIVALSKD ERIGERIFAS IAPSIYGHED IKRGL ALAL FGGEAKNPGG KHKVRGDINV LLCGDPGTAK SQFLKYVEKV ASRAVFTTGQ GASAVGLTAY VQRHPVTKEW TLEAGA LVL ADRGVCLIDE FDKMNDQDRT SIHEAMEQQS ISISKAGIVT SLQARCTVIA ASNPIGGRYD PSLTFSENVD LTEPIVS RF DILCVVRDTV DPVQDEMLAR FVVSSHIKHH PSSKDIANGD AAEFALPNTF GVEALPQEVL KKYIMYAKEK IRPKLNQM D QDKVAKMYSD LRKESMATGS IPITVRHIES MIRMAEAHAR MHLRDYVVED DVNMAIRVML ESFIDTQKFS VMRSMRKTF ARYLAFRRDN NELLLFVLKQ LIAEQVTYQR NRYGAQQDTI EVPEKDLVDK ARQINIHNLS AFYDSDLFKM NKFTHDVKKK LIIQQF

UniProtKB: DNA replication licensing factor mcm2

+
Macromolecule #2: Maternal DNA replication licensing factor mcm3

MacromoleculeName: Maternal DNA replication licensing factor mcm3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 90.5365 KDa
SequenceString: MDYGGGFEDH ELREAQREYL DFLDDDQDQG LYHGKVRDMI GSNEHRLIVN LNDVRRKNDK RANLMLNDAF AETIAFQRAL KDLVASIDA TYAKQFEEFS VGFEGSFGSK HVSPRTLTAS LLGSLVCVEG IVTKCSLVRP KVMRSVHYCP ATKKTLERKY S DLTSLEAF ...String:
MDYGGGFEDH ELREAQREYL DFLDDDQDQG LYHGKVRDMI GSNEHRLIVN LNDVRRKNDK RANLMLNDAF AETIAFQRAL KDLVASIDA TYAKQFEEFS VGFEGSFGSK HVSPRTLTAS LLGSLVCVEG IVTKCSLVRP KVMRSVHYCP ATKKTLERKY S DLTSLEAF PSSSIYPTKD EENNPLETEY GLSTYKDHQT LSIQEMPEKA PAGQLPRSVD IIADDDLVDK CKPGDRVQIV GI YRCLPSK QGGFTSGTFR TILLANNIKL MSKEIAPTFS ADDVAKIKKF CKAHSKDIFE HLSKSLAPSI HGHEYIKKAI LCM LLGGNE KVLENGTRIR GDINVLLIGD PSVAKSQLLR YVLHTAPRAI PTTGRGSSGV GLTAAVTTDQ ETGERRLEAG AMVL ADRGV VCIDEFDKMS DMDRTAIHEV MEQGRVTIAK AGIQARLNAR CSVLAAANPV YGRYDQYRTP MENIGLQDSL LSRFD LLFI VLDKMDADND QEIADHVLRM HRYRTPGEQD GYALPLGCSV EIFATDDPNA SDVTDQELQI YEKHDNLLHG PRKNKS KIV SMQFIRKYIH VAKLIKPVLT SEAADYISQE YAKIRNHDQI NNDSARTMPV TARALETMIR LSTAHAKVRM SKTIERQ DA ETALELVQFA YFKKVLAKEK KKTDKDLHDE NLSQDTLSQE SVRKSSRRAG KIADSQDDSM DPYSFSEQDS SLNENLSQ S LRPQRKKAES QDGKRSLSQN RTKEFKAALL KAFKSSRSQS VAVSQLLELI NKGNPEPFER SEVKEALDNM QNDNQVMVS EDVVFLI

UniProtKB: Maternal DNA replication licensing factor mcm3

+
Macromolecule #3: DNA replication licensing factor mcm4-B

MacromoleculeName: DNA replication licensing factor mcm4-B / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 97.256305 KDa
SequenceString: MSSPTSTPSR RRNKRGRGSN PPTPHGEEVQ SPPSQRRRTE DSTSIGELLP MPTSPSGDVQ SPSGQELLFS SPAPSRHSAH QSELDLSSP LTYGTPSSRV EGTPRSGIRG TPARQRPDLG SARKVKQVDL HSDQPAAEEL VTSEQSLGQK LVIWGTDVNV A TCKEKFQR ...String:
MSSPTSTPSR RRNKRGRGSN PPTPHGEEVQ SPPSQRRRTE DSTSIGELLP MPTSPSGDVQ SPSGQELLFS SPAPSRHSAH QSELDLSSP LTYGTPSSRV EGTPRSGIRG TPARQRPDLG SARKVKQVDL HSDQPAAEEL VTSEQSLGQK LVIWGTDVNV A TCKEKFQR FVQRFIDPSA KEEDNVGLDL NEPIYMQRLE EINVVGDPFL NIDCDHLRNF DQDLYRQLVC YPQEVIPTFD MA ANEIFFE RYPDSILEHQ IQVRPYNALK TRNMRSLNPE DIDQLITISG MVIRTSQIIP EMQEAFFKCQ VCAFTTRVEI DRG RIAEPS VCKHCNTTHS MALIHNRSMF SDKQMIKLQE SPEDMPAGQT PHTTILYGHN DLVDKVQPGD RVNVTGIYRA VPIR VNPRV RNVKSVYKTH IDVIHYRKTD SKRLHGIDED TEQKLFTEER VAMLKELAAK PDIYERLAAA LAPSIYEHED IKKGI LLQL FGGTRKDFSH TGRGKFRAEV NILLCGDPGT SKSQLLQYVF NLVPRGQYTS GKGSSAVGLT AYVMKDPETR QLVLQT GAL VLSDNGICCI DEFDKMNEST RSVLHEVMEQ QTLSIAKAGI ICQLNARTSV LAAANPVESQ WNPKKTTIEN IQLPHTL LS RFDLIFLMLD PQDEAYDRRL AHHLVALYYQ SEEQMKEEHL DMAVLKDYIA YARTYVNPRL SEEASQALIE AYVSMRKI G SGRGMVSAYP RQLESLIRLS EAHAKVRFSN KVETIDVEEA KRLHREALKQ SATDPRTGIV DISILTTGMS ATARKRKEE LAQVLKKLIQ SKGKTPALKY QQLFEDLRGQ SDAAITKDMF DEALHALADD DYLTVTGKTV RLL

UniProtKB: DNA replication licensing factor mcm4-B

+
Macromolecule #4: DNA replication licensing factor mcm5-A

MacromoleculeName: DNA replication licensing factor mcm5-A / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 82.556414 KDa
SequenceString: MSGFDDLGVY YSDSFGGEQQ VGDDGQAKKS QLKKRFREFL RQYRIGTDRT GFTFKYRDEL KRHYNLGEYW IEVEMEDLAS FDEDLADYL YKQPTEHLQL LEEAAQEVAD EVTRPRPAGE ETIQEIQVML RSDANPANIR SLKSEQMSHL VKIPGIIIAA T AVRAKATK ...String:
MSGFDDLGVY YSDSFGGEQQ VGDDGQAKKS QLKKRFREFL RQYRIGTDRT GFTFKYRDEL KRHYNLGEYW IEVEMEDLAS FDEDLADYL YKQPTEHLQL LEEAAQEVAD EVTRPRPAGE ETIQEIQVML RSDANPANIR SLKSEQMSHL VKIPGIIIAA T AVRAKATK ISIQCRSCRN TIGNIAVRPG LEGYAMPRKC NTEQAGRPNC PLDPYFIIPD KCKCVDFQTL KLQESPDAVP HG ELPRHMQ LYCDRYLCDK VVPGNRVTIM GIYSIRKSGK TSTKGRDRVG VGIRSSYIRV VGIQVDTEGT GRSAAGAITP QEE EEFRRL AAKPDIYETV AKSIAPSIYG SSDIKKAIAC LLFGGSRKRL PDGLTRRGDV NLLMLGDPGT AKSQLLKFVE RCSP IGVYT SGKGSSAAGL TASVMRDPVS RNFIMEGGAM VLADGGVVCI DEFDKMREDD RVAIHEAMEQ QTISIAKAGI TTTLN SRCS VLAAANSVYG RWDDTKGEEN IDFMPTILSR FDMIFIVKDE HNEQRDMTLA KHVMNVHLSA RTQSSSVEGE VDLNTL KKY IAYCRAKCGP RLSAEAAEKL KNRYILMRSG AREHERETEK RSSIPITVRQ LEAIVRISES LGKMKLQPFA TETDVEE AL RLFQVSTLDA AMSGSLSGVE GFTTQEDQEM LSRIEKQMKK RFAIGSQVSE HSIIQDFLKQ KYPEHAIHKV LSLMMRRG E IQHRLQRKVL YRIK

UniProtKB: DNA replication licensing factor mcm5-A

+
Macromolecule #5: Maternal DNA replication licensing factor mcm6

MacromoleculeName: Maternal DNA replication licensing factor mcm6 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 92.752969 KDa
SequenceString: MELGGPAAAG DTDIAGQQLF KDELSDKCQK LFLEFLEECK GKDGSNLYVS AAEELIRPER NTLAVNFTDI EYYNQQLATT IQEEYYRVY PHLCRAVRSF ARQMGNIPAN KEFYIAFSDF PARQKIRELS SAKIGTLLRI SGQVVRTHPV HPELVSGTFL C MDCQSIVK ...String:
MELGGPAAAG DTDIAGQQLF KDELSDKCQK LFLEFLEECK GKDGSNLYVS AAEELIRPER NTLAVNFTDI EYYNQQLATT IQEEYYRVY PHLCRAVRSF ARQMGNIPAN KEFYIAFSDF PARQKIRELS SAKIGTLLRI SGQVVRTHPV HPELVSGTFL C MDCQSIVK DVEQQFRYTQ PTICKNPVCA NRRRFTLDTN KSRFVDFQKV RIQETQAELP RGAIPRSVEI ILRAEAVESA MA GDRCDFT GTLIVVPDVS ALAAGDARME TGAKVTGGEG FNSEGVQGLK ALGVRDLSYR LAFLACYVGA TNPRFGGKDL REE DQTAES IKNQMTVQEW EKVFEMSQDK NLYHNLCTSL FPTIHGNDEI KRGVLLMLFG GVPKTTMEGT SLRGDINVCI VGDP STSKS QFLKHVEEFS PRAVYTSGKA SSAAGLTAAV VKDEESHEFV IEAGALMLAD NGVCCIDEFD KMDLKDQVAI HEAME QQTI SITKAGVKAT LNARTSILAA ANPVGGRYER SKSLKHNVNL SAPIMSRFDL FFILVDECNE VTDYAIARRI VDLHAR NEE SIERVYSIED IQRYLLFARQ FQPKITKEAE EFIVEQYRRL RQRDGSGVAK SSWRITVRQL ESLIRLSESM ARMHCSD EV QPKHVKEAFR LLSKSIIRVD TPDVSFDQGE DEKNIEGENN GNLNNGEEAM ETNQDEPINE KPSSNAGLKM SFAEYKQI S NLLVLYMQKM EETEEECHLT TTDLVNWYLK EMEAEIETET ELILKKRLIE KVIHRLIYYD HILIELNKSE LKTMDDTKE TGEDAAEDRI LVVNPNYMLE D

UniProtKB: Maternal DNA replication licensing factor mcm6

+
Macromolecule #6: DNA replication licensing factor mcm7-B

MacromoleculeName: DNA replication licensing factor mcm7-B / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 81.841539 KDa
SequenceString: MPRDYQAEKE KCKTFLQEFY KDDEFGKKNF KYGVQLANIA HREQVALCID LDDLAEEDPE LVDAICENTR RYTNLFADAV QELLPQYKE REVVHKDALD VYIEHRLMME QRGRDPNEMR DPHNQYPPEL MRRFELYFKA PSSSKARVVR DVKADSIGKL V TVRGIVTR ...String:
MPRDYQAEKE KCKTFLQEFY KDDEFGKKNF KYGVQLANIA HREQVALCID LDDLAEEDPE LVDAICENTR RYTNLFADAV QELLPQYKE REVVHKDALD VYIEHRLMME QRGRDPNEMR DPHNQYPPEL MRRFELYFKA PSSSKARVVR DVKADSIGKL V TVRGIVTR VTEVKPMMVV ATYTCDQCGA ETYQPIQSPT FMPLIMCPSR ECQTNRSGGR LYLQTRGSKF IKFQELKIQE HS DQVPVGN IPRCMSVYVR GENTRLAQPG DHVGITGVFL PMLRTGFRQV VQGLLSETYL ESHRLVKMNK TEDDELGTEE LSE EELRQI TEEDFYEKLA ASIAPEIYGH EDVKKALLLL LVGGVDHSPR GMKIRGNINV CLMGDPGVAK SQLLSYIDRL APRS QYTTG RGSSGVGLTA AVMKDPVTGE MTLEGGALVL ADQGVCCIDE FDKMMDSDRT AIHEVMEQQT ISIAKAGIMT TLNAR CSIL AAANPAYGRY NPKKTVEQNI QLPAALLSRF DLLWLIQDKP DRDNDLRLAQ HITYVHQHSK QPPSQFQPMD MKLMRR YIT MCKSKQPAIP ESLADYLTAA YVEMRKEART NKDMTFTSAR TLLSILRLST ALARLRLEDV VEKEDVNEAM RLTEMSK DS LQGDKGHASR TQRPADVIFS TIREMVPEKG ARSVKYSEAE QRCVSKGFTP AQFEAALEEY EELNVWLVNQ ARTKITFV

UniProtKB: DNA replication licensing factor mcm7-B

+
Macromolecule #7: DNA replication complex GINS protein PSF1

MacromoleculeName: DNA replication complex GINS protein PSF1 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 23.171678 KDa
SequenceString: MFCEKAIELI RELQRASDGQ LPAFNEDGIR QILEEMKALY EQNQADVNEA KTEGRSDLIP TIKFRHCCLL RNRRCIVAYL YDRLLRIRA LRWEYGSVLP SALRFHMSTE EMDWFNQYKR SLATYMRSLG GEEGLDITQD MKPPKSLYIE VRCLRDYGEF E IDDGTTIL ...String:
MFCEKAIELI RELQRASDGQ LPAFNEDGIR QILEEMKALY EQNQADVNEA KTEGRSDLIP TIKFRHCCLL RNRRCIVAYL YDRLLRIRA LRWEYGSVLP SALRFHMSTE EMDWFNQYKR SLATYMRSLG GEEGLDITQD MKPPKSLYIE VRCLRDYGEF E IDDGTTIL LKKNSQHFLP RWKCEQLIRQ GVLEHVLS

UniProtKB: DNA replication complex GINS protein PSF1

+
Macromolecule #8: DNA replication complex GINS protein PSF2

MacromoleculeName: DNA replication complex GINS protein PSF2 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 21.348309 KDa
SequenceString:
MDASEVEFLA EKEQVTVIPN FSLDKVYLIG GDLGPFNPSL PVEVPLWLAI NLKQRQKCRI VPPEWMDVEK LEAIRDQERR EETFTPMPS PYYMELTKLL LNHAADNIPK ADEIRTLVKD TWDTRIAKLR LSADSFVKGQ EAHAKLDNLT LMEINTIGTF F TESLNHMY KLRTSLQNPE EGQSQDY

UniProtKB: DNA replication complex GINS protein PSF2

+
Macromolecule #9: DNA replication complex GINS protein PSF3

MacromoleculeName: DNA replication complex GINS protein PSF3 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 23.948078 KDa
SequenceString: MWEPYMPVEP GLGREENFLS LEDLLMSQEK LPCCIESGFP RLGFLDKGGD SDSIPEGSKM ELPLWLAKGL YDNKRRVLSV ELPKIYREG WRTVFSADAN VVDLHKMGPH YYGFGSQLLN FDSPENPEIA KTILQTFVGR FRRIMDSSQN AYNEDTSGLV A RLDELERS ...String:
MWEPYMPVEP GLGREENFLS LEDLLMSQEK LPCCIESGFP RLGFLDKGGD SDSIPEGSKM ELPLWLAKGL YDNKRRVLSV ELPKIYREG WRTVFSADAN VVDLHKMGPH YYGFGSQLLN FDSPENPEIA KTILQTFVGR FRRIMDSSQN AYNEDTSGLV A RLDELERS LFRAGQRGLN AFQSWERGKA AQITASNLVQ NYKKRKFNEA DA

UniProtKB: DNA replication complex GINS protein PSF3

+
Macromolecule #10: Cell division control protein 45 homolog

MacromoleculeName: Cell division control protein 45 homolog / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 65.695906 KDa
SequenceString: MFVSDLRKEF FDVIVTERVL LLVAPDVDAL CACKILQALF QCDHVQYTLV PVSGWQELET LFLEHKEQFR YFVLINCGAN IDLLETLQP QEEAIFYICD THRPIDVVNI YNDSQVKLLI RQDDDLEIPA YDDIFNDDEE DGEDSGNESD GAEPSGKRRR F DEAAVERR ...String:
MFVSDLRKEF FDVIVTERVL LLVAPDVDAL CACKILQALF QCDHVQYTLV PVSGWQELET LFLEHKEQFR YFVLINCGAN IDLLETLQP QEEAIFYICD THRPIDVVNI YNDSQVKLLI RQDDDLEIPA YDDIFNDDEE DGEDSGNESD GAEPSGKRRR F DEAAVERR IERRRQRREW EARRREIIFD YEQYEYHGTS SAMMMFELAW IMSKDSNDML WWAIVGLTDQ WVQDRITQMK YV TDVGTLQ RHVSRHNHRN EDEENSLSID CMRIAFEYDL RLSLYQHWSL YESICNSCYT SATLKLWSLQ GQKKLQEFLA DMG MPLKQV KQKFNSMDIS LKENLREMLE ESANKFGMKD VRVQTFSVQF GFKNKFLASD IVFAVLSLLE NTERDEKGTD NFIK ALDSL SRSNLDKLHT GLEMGKKLLC AIQQTVASCI CTNLILSQGP FLYCYLMEGT PDVKMFSNPI SLCLLCKYLL KSFVC STKN KRCKLLPLVL AAPLDAEKGT VIMVGIPPEA ESSDKKNFFG RAFEKAAEST SSRTLHNHFD MSIIELRTED RSKFLD ALI SLLS

UniProtKB: Cell division control protein 45 homolog

+
Macromolecule #11: DNA replication complex GINS protein SLD5

MacromoleculeName: DNA replication complex GINS protein SLD5 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 25.577172 KDa
SequenceString: MEDELALSDQ GSDEDEEVLT PAELINKLEE AWLNEKFAPE LLESKSEVVE CVMEQLNHME QNLHRAKPGD LKISFHHMEI ERIRYMLSS YLRSRMLKIE KFFPHILEKE KSRGEGEPPH LSPEEFAFAK EYMTNTETLL KSVALRHMPP NLQTVDLLKS V PKPNLDSF ...String:
MEDELALSDQ GSDEDEEVLT PAELINKLEE AWLNEKFAPE LLESKSEVVE CVMEQLNHME QNLHRAKPGD LKISFHHMEI ERIRYMLSS YLRSRMLKIE KFFPHILEKE KSRGEGEPPH LSPEEFAFAK EYMTNTETLL KSVALRHMPP NLQTVDLLKS V PKPNLDSF VFLRVKEEQN NILVEPETDE QSEYAIDMEV GSQHLIRYRT IAPLVASGAV KLI

UniProtKB: DNA replication complex GINS protein SLD5

+
Macromolecule #12: Protein downstream neighbor of son homolog

MacromoleculeName: Protein downstream neighbor of son homolog / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 63.864559 KDa
SequenceString: MAELLPGYSP SFKKPSEILR LSRRRSRSEA SKTGLSPFSP GDVIKRVPGL RPFSPGPNKG AGVKRRNPFA SLENTVCSPV KRRAETVAE YGAASLEPRA LSAVRPSCLG QDSPEPPQFN SVEDVIWGDP LAADADPLVK TESPEKPAPA CEIPKGSVTF P ADWSLKTR ...String:
MAELLPGYSP SFKKPSEILR LSRRRSRSEA SKTGLSPFSP GDVIKRVPGL RPFSPGPNKG AGVKRRNPFA SLENTVCSPV KRRAETVAE YGAASLEPRA LSAVRPSCLG QDSPEPPQFN SVEDVIWGDP LAADADPLVK TESPEKPAPA CEIPKGSVTF P ADWSLKTR LLFTSSHSFS WADHLKAQEE AQGLVMQCRA TAVNLPHSIQ EPKLSTDLRC AFQQSLVHWI HPSLPWVQLF PR IGVDRKM AGKNTPWSQD ESLQQVLMSE WALSFTSLYN LLKAKLCPYF YVCTYQFTVL FRAAGLAGSD VITAVMSPTT RGL REAMKN EGITFSQPLV EDDTGKKQKK PEAASQGDIN PEKENGTAEA DEASDESDED ESFSWLEEMG VEDKIKKPDS ISIK LRKEK NEVKLDHKPE SVVLVKGTNT FTLLNFLINC KSIVAAAGLQ AGLPPTLLSP VAFRGATMHA LKARSVNVKT RVNSG YKDQ FSLEITGPIM PHSLHSLTML LQSAQRGSFS AGLYTHEPTA VFNTPIHSQA VKEISADLQN CGLHPCTVEQ LTQVNE LGK LSLRHLEMTD YRYTWK

UniProtKB: Protein downstream neighbor of son homolog

+
Macromolecule #13: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 13 / Number of copies: 10 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 33.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.4 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.14 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 100667
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

+
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