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- EMDB-18192: X. laevis CMG dimer bound to dimeric DONSON - MCM ATPase -

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Basic information

Entry
Database: EMDB / ID: EMD-18192
TitleX. laevis CMG dimer bound to dimeric DONSON - MCM ATPase
Map data
Sample
  • 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: Protein downstream neighbor of son homolog
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsDNA replication initiation / Xenopus egg extract / primordial dwarfism / replicative helicase / genome stability / REPLICATION
Function / homology
Function and homology information


premeiotic DNA replication / CMG complex / MCM complex / replisome / mitotic DNA replication checkpoint signaling / double-strand break repair via break-induced replication / mitotic DNA replication initiation / single-stranded DNA helicase activity / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication ...premeiotic DNA replication / CMG complex / MCM complex / replisome / mitotic DNA replication checkpoint signaling / double-strand break repair via break-induced replication / mitotic DNA replication initiation / single-stranded DNA helicase activity / 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 / replication fork / helicase activity / single-stranded DNA binding / DNA helicase / DNA replication / cell division / chromatin binding / chromatin / ATP hydrolysis activity / DNA binding / ATP binding / nucleus / metal ion binding
Similarity search - Function
Donson / : / 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 ...Donson / : / 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 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 licensing factor mcm7-B
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.53 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

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Structure visualization

Supplemental images

emd_18192.png

Downloads & links

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Map

FileDownload / File: emd_18192.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.3077148 - 1.8445758
Average (Standard dev.)0.00021190722 (±0.027067706)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #2

Fileemd_18192_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_18192_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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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: Protein downstream neighbor of son homolog
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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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-#7
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 1.54 MDa

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Macromolecule #1: DNA replication licensing factor mcm2

MacromoleculeName: DNA replication licensing factor mcm2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: 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

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Macromolecule #2: Maternal DNA replication licensing factor mcm3

MacromoleculeName: Maternal DNA replication licensing factor mcm3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / 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

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Macromolecule #3: DNA replication licensing factor mcm4-B

MacromoleculeName: DNA replication licensing factor mcm4-B / type: protein_or_peptide / ID: 3 / Number of copies: 1 / 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

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Macromolecule #4: DNA replication licensing factor mcm5-A

MacromoleculeName: DNA replication licensing factor mcm5-A / type: protein_or_peptide / ID: 4 / Number of copies: 1 / 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

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Macromolecule #5: Maternal DNA replication licensing factor mcm6

MacromoleculeName: Maternal DNA replication licensing factor mcm6 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / 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

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Macromolecule #6: DNA replication licensing factor mcm7-B

MacromoleculeName: DNA replication licensing factor mcm7-B / type: protein_or_peptide / ID: 6 / Number of copies: 1 / 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

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Macromolecule #7: Protein downstream neighbor of son homolog

MacromoleculeName: Protein downstream neighbor of son homolog / type: protein_or_peptide / ID: 7 / Number of copies: 1 / 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

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Macromolecule #8: ADENOSINE-5'-TRIPHOSPHATE

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

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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

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

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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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 144989
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
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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