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- EMDB-20607: Structure of the S. cerevisiae replicative helicase CMG in comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-20607
TitleStructure of the S. cerevisiae replicative helicase CMG in complex with a forked DNA
Map dataeukaryotic replicative CMG helicase
Sample
  • Complex: CMG-forkDNA
    • Protein or peptide: x 11 types
    • DNA: x 2 types
  • Ligand: x 1 types
KeywordsDNA replication / CMG-Mcm10 / REPLICATION-DNA complex
Function / homology
Function and homology information


Unwinding of DNA / MCM core complex / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / DNA strand elongation involved in mitotic DNA replication / GINS complex / MCM complex binding / mitotic DNA replication preinitiation complex assembly / nuclear DNA replication / premeiotic DNA replication ...Unwinding of DNA / MCM core complex / Assembly of the pre-replicative complex / Switching of origins to a post-replicative state / DNA strand elongation involved in mitotic DNA replication / GINS complex / MCM complex binding / mitotic DNA replication preinitiation complex assembly / nuclear DNA replication / premeiotic DNA replication / replication fork protection complex / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / Activation of the pre-replicative complex / mitotic DNA replication / CMG complex / nuclear pre-replicative complex / DNA replication preinitiation complex / Activation of ATR in response to replication stress / MCM complex / double-strand break repair via break-induced replication / mitotic DNA replication initiation / single-stranded DNA helicase activity / silent mating-type cassette heterochromatin formation / regulation of DNA-templated DNA replication initiation / DNA strand elongation involved in DNA replication / nuclear replication fork / DNA replication origin binding / DNA replication initiation / subtelomeric heterochromatin formation / DNA helicase activity / transcription elongation by RNA polymerase II / helicase activity / DNA-templated DNA replication / heterochromatin formation / single-stranded DNA binding / DNA helicase / chromosome, telomeric region / DNA replication / DNA damage response / chromatin binding / ATP hydrolysis activity / zinc ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
: / PSF2 N-terminal domain / : / : / PSF3 N-terminal domain / PSF1 C-terminal domain / CDC45 family / DNA replication complex GINS protein Psf2 / CDC45 / GINS complex, subunit Psf3 ...: / PSF2 N-terminal domain / : / : / PSF3 N-terminal domain / PSF1 C-terminal domain / CDC45 family / DNA replication complex GINS protein Psf2 / CDC45 / GINS complex, subunit Psf3 / DNA replication complex GINS protein SLD5, C-terminal / GINS complex, subunit Psf3 superfamily / GINS complex protein Sld5, alpha-helical domain / DNA replication complex GINS protein SLD5 C-terminus / GINS complex subunit Sld5 / : / MCM3 winged helix domain / GINS subunit, domain A / GINS complex protein helical bundle domain / GINS complex, subunit Psf1 / GINS, helical bundle-like domain superfamily / : / MCM5, C-terminal domain / DNA replication licensing factor MCM7, winged helix / DNA replication licensing factor Mcm5 / MCM4, winged helix domain / DNA replication licensing factor Mcm3 / Mini-chromosome maintenance complex protein 4 / : / MCM3-like, winged helix domain / DNA replication licensing factor Mcm6 / DNA replication licensing factor Mcm7 / Mcm6, C-terminal winged-helix domain / MCM6 C-terminal winged-helix domain / DNA replication licensing factor Mcm2 / Mini-chromosome maintenance protein 2 / Mini-chromosome maintenance, conserved site / MCM family signature. / MCM N-terminal domain / MCM N-terminal domain / MCM OB domain / MCM OB domain / Mini-chromosome maintenance protein / MCM, AAA-lid domain / MCM P-loop domain / MCM AAA-lid domain / MCM family domain profile. / minichromosome maintenance proteins / MCM domain / Winged helix-like DNA-binding domain superfamily / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA replication licensing factor MCM3 / DNA replication licensing factor MCM2 / Minichromosome maintenance protein 5 / DNA replication licensing factor MCM4 / DNA replication licensing factor MCM7 / DNA replication complex GINS protein PSF2 / DNA replication licensing factor MCM6 / DNA replication complex GINS protein SLD5 / Cell division control protein 45 / DNA replication complex GINS protein PSF3 / DNA replication complex GINS protein PSF1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsYuan Z / Georgescu R
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM111472 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)OD12272 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM45436 United States
CitationJournal: Nat Commun / Year: 2020
Title: DNA unwinding mechanism of a eukaryotic replicative CMG helicase.
Authors: Zuanning Yuan / Roxana Georgescu / Lin Bai / Dan Zhang / Huilin Li / Michael E O'Donnell /
Abstract: High-resolution structures have not been reported for replicative helicases at a replication fork at atomic resolution, a prerequisite to understanding the unwinding mechanism. The eukaryotic ...High-resolution structures have not been reported for replicative helicases at a replication fork at atomic resolution, a prerequisite to understanding the unwinding mechanism. The eukaryotic replicative CMG (Cdc45, Mcm2-7, GINS) helicase contains a Mcm2-7 motor ring, with the N-tier ring in front and the C-tier motor ring behind. The N-tier ring is structurally divided into a zinc finger (ZF) sub-ring followed by the oligosaccharide/oligonucleotide-binding (OB) fold ring. Here we report the cryo-EM structure of CMG on forked DNA at 3.9 Å, revealing that parental DNA enters the ZF sub-ring and strand separation occurs at the bottom of the ZF sub-ring, where the lagging strand is blocked and diverted sideways by OB hairpin-loops of Mcm3, Mcm4, Mcm6, and Mcm7. Thus, instead of employing a specific steric exclusion process, or even a separation pin, unwinding is achieved via a "dam-and-diversion tunnel" mechanism that does not require specific protein-DNA interaction. The C-tier motor ring contains spirally configured PS1 and H2I loops of Mcms 2, 3, 5, 6 that translocate on the spirally-configured leading strand, and thereby pull the preceding DNA segment through the diversion tunnel for strand separation.
History
DepositionAug 14, 2019-
Header (metadata) releaseOct 2, 2019-
Map releaseMar 25, 2020-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6u0m
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20607.png

Downloads & links

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Map

FileDownload / File: emd_20607.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationeukaryotic replicative CMG helicase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 274.944 Å		1.07 Å/pix.
x 256 pix.
= 274.944 Å		1.07 Å/pix.
x 256 pix.
= 274.944 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.074 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.052924566 - 0.14437133
Average (Standard dev.)0.0017881448 (±0.0078117005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 274.944 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0741.0741.074
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z274.944274.944274.944
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0530.1440.002

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Supplemental data

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Sample components

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Entire : CMG-forkDNA

EntireName: CMG-forkDNA
Components
  • Complex: CMG-forkDNA
    • 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: DNA replication complex GINS protein SLD5
    • Protein or peptide: Cell division control protein 45
    • 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: Minichromosome maintenance protein 5
    • Protein or peptide: DNA replication licensing factor MCM6
    • Protein or peptide: DNA replication licensing factor MCM7
    • DNA: DNA (26-MER)
    • DNA: DNA (15-MER)
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: CMG-forkDNA

SupramoleculeName: CMG-forkDNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: DNA replication complex GINS protein PSF1

MacromoleculeName: DNA replication complex GINS protein PSF1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 24.230576 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MYGDLGNKLV LEAKRTKQLY ARSNQDVNLP MYHEDIIRNI LKEVSNLRKN TEYLKEQQQL GMLDDKVAKC QYFVTLLCME RNKRCLLAY QRLRTDILDS MAWNNNGLDL MSSITFSQQD TNNLSHQEQE YLKEYCDLIT DLKSGDLVDI DLSGSLVPPS D VFIDVRVL ...String:
MYGDLGNKLV LEAKRTKQLY ARSNQDVNLP MYHEDIIRNI LKEVSNLRKN TEYLKEQQQL GMLDDKVAKC QYFVTLLCME RNKRCLLAY QRLRTDILDS MAWNNNGLDL MSSITFSQQD TNNLSHQEQE YLKEYCDLIT DLKSGDLVDI DLSGSLVPPS D VFIDVRVL KDAGEIQTEY GVFNLIKDSQ FFVRQSDVER LIQQGYLQKI

UniProtKB: DNA replication complex GINS protein PSF1

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Macromolecule #2: DNA replication complex GINS protein PSF2

MacromoleculeName: DNA replication complex GINS protein PSF2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 23.428115 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: LPAHLQQTFS PEEIQFIVEN EPIKIFPRIT TRQKIRGDDR GTGNHTRWQL ITTDDKALNN MVAMRSTEVV LWIALLLKQQ SKCSIVAPQ WLTTKELDRK IQYEKTHPDR FSELPWNWLV LARILFNKAK DDFHDPIHEL RGKIQDLREI RQIKVLKGLK Y LNESHLQL ...String:
LPAHLQQTFS PEEIQFIVEN EPIKIFPRIT TRQKIRGDDR GTGNHTRWQL ITTDDKALNN MVAMRSTEVV LWIALLLKQQ SKCSIVAPQ WLTTKELDRK IQYEKTHPDR FSELPWNWLV LARILFNKAK DDFHDPIHEL RGKIQDLREI RQIKVLKGLK Y LNESHLQL DNLSLLEINE LRPFITEIMD KLREIHTASL

UniProtKB: DNA replication complex GINS protein PSF2

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Macromolecule #3: DNA replication complex GINS protein PSF3

MacromoleculeName: DNA replication complex GINS protein PSF3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 21.659705 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString:
YYDIDDVLAD GTEFPCKFQY DIPGLGYLEN NPGRPITKNT KLSLPLWLAR ILAIVGGDEA LVDEEPVPFV ELLPPDMFST KVMNAIKTD PVALDLHSIN SHFFSLAIKW IMLFSEKELA NVVSELLLQR AQELNHHASS LSIDLNADST GKNSANTNIA T STFLLKLE EMEKEIYKKS HESYKDTKRW MFK

UniProtKB: DNA replication complex GINS protein PSF3

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Macromolecule #4: DNA replication complex GINS protein SLD5

MacromoleculeName: DNA replication complex GINS protein SLD5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 33.62418 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: INIDDILAEL DKETTAVDST KITQGSSSTT HRDANTIVGS SLDLNDKTQI YVSPQQDFSD LMKSWKNERC SPELLPYPHQ LMKRLLNRI SMQSQLIENI SMGFLDMQNA SNANPPMPNE SKLPLLCMET ELERLKFVIR SYIRCRLSKI DKFSLYLRQL N EDENSLIS ...String:
INIDDILAEL DKETTAVDST KITQGSSSTT HRDANTIVGS SLDLNDKTQI YVSPQQDFSD LMKSWKNERC SPELLPYPHQ LMKRLLNRI SMQSQLIENI SMGFLDMQNA SNANPPMPNE SKLPLLCMET ELERLKFVIR SYIRCRLSKI DKFSLYLRQL N EDENSLIS LTDLLSKDEI KYHDTHSLIW LKLVNDSILK YMPEELQAIN DTEGSVNMID EPDWNKFVFI HVNGPPDGKW NE DPLLQEN EFGKPCYTVT IPDLKEEVEL TIGSIYVMRY EVIRDLLRDD KVAL

UniProtKB: DNA replication complex GINS protein SLD5

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Macromolecule #5: Cell division control protein 45

MacromoleculeName: Cell division control protein 45 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 73.81025 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: ISQFSEAYNK ILRNSSSHSS CQLVIFVSCL NIDALCATKM LSLLFKKQLV QSQIVPIFGY SELRRHYSQL DDNINSLLLV GFGGVIDLE AFLEIDPQEY VIDTDEKSGE QSFRRDIYVL DAHRPWNLDN IFGSQIIQCF DDGTVDDTLG EQKEAYYKLL E LDEESGDD ...String:
ISQFSEAYNK ILRNSSSHSS CQLVIFVSCL NIDALCATKM LSLLFKKQLV QSQIVPIFGY SELRRHYSQL DDNINSLLLV GFGGVIDLE AFLEIDPQEY VIDTDEKSGE QSFRRDIYVL DAHRPWNLDN IFGSQIIQCF DDGTVDDTLG EQKEAYYKLL E LDEESGDD ELSGDENDNN GGDDEATDAD EVTDEDEEDE DETISNKRGN SSIGPNDLSK RKQRKKQIHE YEGVLEEYYS QG TTVVNSI SAQIYSLLSA IGETNLSNLW LNILGTTSLD IAYAQVYNRL YPLLQDEVKR LTPSSRNSVK TPDTLTLNIQ PDY YLFLLR HSSLYDSFYY SNYVNAKLSL WNENGKKRLH KMFARMGIPL STAQETWLYM DHSIKRELGI IFDKNLDRYG LQDI IRDGF VRTLGYRGSI SASEFVEALT ALLEVGNSTD KDSVKINNDN NDDTDGEEEE DNSAQKLTNL RKRWVSNFWL SWDAL DDRK VELLNRGIQL AQDLQRAIFN TGVAILEKKL IKHLRIYRLC VLQDGPDLDL YRNPLTLLRL GNWLIECCAE SEDKQL LPM VLASIDENTD TYLVAGLTPR YPRGLDTIHT KKPILNNFSM AFQQITAETD AKVRIDNFES SIIEIRREDL SPFLEKL TL SGLL

UniProtKB: Cell division control protein 45

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Macromolecule #6: DNA replication licensing factor MCM2

MacromoleculeName: DNA replication licensing factor MCM2 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 74.98707 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: PNVSRTIARE LKSFLLEYTD ETGRSVYGAR IRTLGEMNSE SLEVNYRHLA ESKAILALFL AKCPEEMLKI FDLVAMEATE LHYPDYARI HSEIHVRISD FPTIYSLREL RESNLSSLVR VTGVVTRRTG VFPQLKYVKF NCLKCGSILG PFFQDSNEEI R ISFCTNCK ...String:
PNVSRTIARE LKSFLLEYTD ETGRSVYGAR IRTLGEMNSE SLEVNYRHLA ESKAILALFL AKCPEEMLKI FDLVAMEATE LHYPDYARI HSEIHVRISD FPTIYSLREL RESNLSSLVR VTGVVTRRTG VFPQLKYVKF NCLKCGSILG PFFQDSNEEI R ISFCTNCK SKGPFRVNGE KTVYRNYQRV TLQEAPGTVP PGRLPRHREV ILLADLVDVS KPGEEVEVTG IYKNNYDGNL NA KNGFPVF ATIIEANSIK RREGNTANEG EEGLDVFSWT EEEEREFRKI SRDRGIIDKI ISSMAPSIYG HRDIKTAVAC SLF GGVPKN VNGKHSIRGD INVLLLGDPG TAKSQILKYV EKTAHRAVFA TGQGASAVGL TASVRKDPIT KEWTLEGGAL VLAD KGVCL IDEFDKMNDQ DRTSIHEAME QQSISISKAG IVTTLQARCS IIAAANPNGG RYNSTLPLAQ NVSLTEPILS RFDIL CVVR DLVDEEADER LATFVVDSHV RSHPENDEDR EGEELKNNGE SAIEQGEDEI NEQLNARQRR LQRQRKKEEE ISPIPQ ELL MKYIHYARTK IYPKLHQMDM DKVSRVYADL RRESISTGSF PITVRHLESI LRIAESFAKM RLSEFVSSYD LDRAIKV VV DSFVDAQKVS VRRQLRRSFA IY

UniProtKB: DNA replication licensing factor MCM2

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Macromolecule #7: DNA replication licensing factor MCM3

MacromoleculeName: DNA replication licensing factor MCM3 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 79.986094 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: PDAVFGDRVR RFQEFLDTFT SYRDSVRSIQ VYNSNNAANY NDDQDDADER DLLGDDDGDD LEKEKKAASS TSLNILPHRI IISLDDLRE FDRSFWSGIL VEPAYFIPPA EKALTDLADS MDDVPHPNAS AVSSRHPWKL SFKGSFGAHA LSPRTLTAQH L NKLVSVEG ...String:
PDAVFGDRVR RFQEFLDTFT SYRDSVRSIQ VYNSNNAANY NDDQDDADER DLLGDDDGDD LEKEKKAASS TSLNILPHRI IISLDDLRE FDRSFWSGIL VEPAYFIPPA EKALTDLADS MDDVPHPNAS AVSSRHPWKL SFKGSFGAHA LSPRTLTAQH L NKLVSVEG IVTKTSLVRP KLIRSVHYAA KTGRFHYRDY TDATTTLTTR IPTPAIYPTE DTEGNKLTTE YGYSTFIDHQ RI TVQEMPE MAPAGQLPRS IDVILDDDLV DKTKPGDRVN VVGVFKSLGA GGMNQSNSNT LIGFKTLILG NTVYPLHARS TGV AARQML TDFDIRNINK LSKKKDIFDI LSQSLAPSIY GHDHIKKAIL LMLMGGVEKN LENGSHLRGD INILMVGDPS TAKS QLLRF VLNTASLAIA TTGRGSSGVG LTAAVTTDRE TGERRLEAGA MVLADRGVVC IDEFDKMTDV DRVAIHEVME QQTVT IAKA GIHTTLNARC SVIAAANPVF GQYDVNRDPH QNIALPDSLL SRFDLLFVVT DDINEIRDRS ISEHVLRTHR YLPPGY LEG EPVRERLNLS LAVGEDADIN PEEHSNSGAG VENEGEDDED HVFEKFNPLL QAGAKLAKNK GNYNGTEIPK LVTIPFL RK YVQYAKERVI PQLTQEAINV IVKNYTDLRN DDNTKKSPIT ARTLETLIRL ATAHAKVRLS KTVNKVDAKV AANLLRFA L L

UniProtKB: DNA replication licensing factor MCM3

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Macromolecule #8: DNA replication licensing factor MCM4

MacromoleculeName: DNA replication licensing factor MCM4 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 85.821812 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: LRIIWGTNVS IQECTTNFRN FLMSFKYKFR KILDEREEFI NNTTDEELYY IKQLNEMREL GTSNLNLDAR NLLAYKQTED LYHQLLNYP QEVISIMDQT IKDCMVSLIV DNNLDYDLDE IETKFYKVRP YNVGSCKGMR ELNPNDIDKL INLKGLVLRS T PVIPDMKV ...String:
LRIIWGTNVS IQECTTNFRN FLMSFKYKFR KILDEREEFI NNTTDEELYY IKQLNEMREL GTSNLNLDAR NLLAYKQTED LYHQLLNYP QEVISIMDQT IKDCMVSLIV DNNLDYDLDE IETKFYKVRP YNVGSCKGMR ELNPNDIDKL INLKGLVLRS T PVIPDMKV AFFKCNVCDH TMAVEIDRGV IQEPARCERI DCNEPNSMSL IHNRCSFADK QVIKLQETPD FVPDGQTPHS IS LCVYDEL VDSCRAGDRI EVTGTFRSIP IRANSRQRVL KSLYKTYVDV VHVKKVSDKR LDVDTSTIEQ ELMQNKVDHN EVE EVRQIT DQDLAKIREV AAREDLYSLL ARSIAPSIYE LEDVKKGILL QLFGGTNKTF TKGGRYRGDI NILLCGDPST SKSQ ILQYV HKITPRGVYT SGKGSSAVGL TAYITRDVDT KQLVLESGAL VLSDGGVCCI DEFDKMSDST RSVLHEVMEQ QTISI AKAG IITTLNARSS ILASANPIGS RYNPNLPVTE NIDLPPPLLS RFDLVYLVLD KVDEKNDREL AKHLTNLYLE DKPEHI SQD DVLPVEFLTM YISYAKEHIH PIITEAAKTE LVRAYVGMRK MGDDSRSDEK RITATTRQLE SMIRLAEAHA KMKLKNV VE LEDVQEAVRL IRSAIKDYAT DPKTGKIDMN LVQTGKSVIQ RKLQEDLSRE IMNVLKDQAS DSMSFNELIK QINEHSQD R VESSDIQEAL SRLQQEDKVI VLGEGVRRSV RL

UniProtKB: DNA replication licensing factor MCM4

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Macromolecule #9: Minichromosome maintenance protein 5

MacromoleculeName: Minichromosome maintenance protein 5 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 74.401297 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: NTEIIKSFKN FILEFRLDSQ FIYRDQLRNN ILVKNYSLTV NMEHLIGYNE DIYKKLSDEP SDIIPLFETA ITQVAKRISI LSRAQSANN NDKDPENTSM DTDSLLLNSL PTFQLILNSN ANQIPLRDLD SEHVSKIVRL SGIIISTSVL SSRATYLSIM C RNCRHTTS ...String:
NTEIIKSFKN FILEFRLDSQ FIYRDQLRNN ILVKNYSLTV NMEHLIGYNE DIYKKLSDEP SDIIPLFETA ITQVAKRISI LSRAQSANN NDKDPENTSM DTDSLLLNSL PTFQLILNSN ANQIPLRDLD SEHVSKIVRL SGIIISTSVL SSRATYLSIM C RNCRHTTS ITINNFNSIT GNTVSLPRSC LSTIESESSM ANESNIGDES TKKNCGPDPY IIIHESSKFI DQQFLKLQEI PE LVPVGEM PRNLTMTCDR YLTNKVIPGT RVTIVGIYSI YNSKNGAGSG RSGGGNGGSG VAIRTPYIKI LGIQSDVETS SIW NSVTMF TEEEEEEFLQ LSRNPKLYEI LTNSIAPSIF GNEDIKKAIV CLLMGGSKKI LPDGMRLRGD INVLLLGDPG TAKS QLLKF VEKVSPIAVY TSGKGSSAAG LTASVQRDPM TREFYLEGGA MVLADGGVVC IDEFDKMRDE DRVAIHEAME QQTIS IAKA GITTVLNSRT SVLAAANPIY GRYDDLKSPG DNIDFQTTIL SRFDMIFIVK DDHNEERDIS IANHVINIHT GNANAM QNQ QEENGSEISI EKMKRYITYC RLKCAPRLSP QAAEKLSSNF VTIRKQLLIN ELESTERSSI PITIRQLEAI IRITESL AK LELSPIAQER HVDEAIRLFQ ASTMDAAS

UniProtKB: Minichromosome maintenance protein 5

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Macromolecule #10: DNA replication licensing factor MCM6

MacromoleculeName: DNA replication licensing factor MCM6 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 73.927719 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: VDDVTGEKVR EAFEQFLEDF SVQSTDTGEV EKVYRAQIEF MKIYDLNTIY IDYQHLSMRE NGALAMAISE QYYRFLPFLQ KGLRRVVRK YAP(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)ER VFQISFFNLP ...String:
VDDVTGEKVR EAFEQFLEDF SVQSTDTGEV EKVYRAQIEF MKIYDLNTIY IDYQHLSMRE NGALAMAISE QYYRFLPFLQ KGLRRVVRK YAP(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)ER VFQISFFNLP TVHRIRDIRS EKIGSLLSIS GTVTRTSEVR PELYKASFTC DMCRAIVDNV EQSFKYTEPT FCP NPSCEN RAFWTLNVTR SRFLDWQKVR IQENANEIPT GSMPRTLDVI LRGDSVERAK PGDRCKFTGV EIVVPDVTQL GLPG VKPSS TLDTRGISKT TEGLNSGVTG LRSLGVRDLT YKISFLACHV ISIG(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)SDEINELK EMVKDEHIYD KLVRSIAPAV FGHEAVKKGI LLQMLGGVHK STVEGIKLRG DI NICVVGD PSTSKSQFLK YVVGFAPRSV YTSGKASSAA GLTAAVVRDE EGGDYTIEAG ALMLADNGIC CIDEFDKMDI SDQ VAIHEA MEQQTISIAK AGIHATLNAR TSILAAANPV GGRYNRKLSL RGNLNMTAPI MSRFDLFFVI LDDCNEKIDT ELAS HIVDL HMKRDEAIEP PFSAEQLRRY IKYARTFKPI LTKEARSYLV EKYKELRKDD AQGFSRSSYR ITVRQLESMI RLSEA IARA NCVDEITPSF IAEAYDLLRQ SIIRVDV

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Macromolecule #11: DNA replication licensing factor MCM7

MacromoleculeName: DNA replication licensing factor MCM7 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA helicase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 82.034445 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MSAALPSIQL PVDYNNLFNE ITDFLVTFKQ DTLSSDATRN ENEDENLDAE NIEQHLLEKG PKYMAMLQKV ANRELNSVII DLDDILQYQ NEKFLQGTQA DDLVSAIQQN ANHFTELFCR AIDNNMPLPT KEIDYKDDVL DVILNQRRLR NERMLSDRTN E IRSENLMD ...String:
MSAALPSIQL PVDYNNLFNE ITDFLVTFKQ DTLSSDATRN ENEDENLDAE NIEQHLLEKG PKYMAMLQKV ANRELNSVII DLDDILQYQ NEKFLQGTQA DDLVSAIQQN ANHFTELFCR AIDNNMPLPT KEIDYKDDVL DVILNQRRLR NERMLSDRTN E IRSENLMD TTMDPPSSMN DALREVVEDE TELFPPNLTR RYFLYFKPLS QNCARRYRKK AISSKPLSVR QIKGDFLGQL IT VRGIITR VSDVKPAVEV IAYTCDQCGY EVFQEVNSRT FTPLSECTSE ECSQNQTKGQ LFMSTRASKF SAFQECKIQE LSQ QVPVGH IPRSLNIHVN GTLVRSLSPG DIVDVTGIFL PAPYTGFKAL KAGLLTETYL EAQFVRQHKK KFASFSLTSD VEER VMELI TSGDVYNRLA KSIAPEIYGN LDVKKALLLL LVGGVDKRVG DGMKIRGDIN VCLMGDPGVA KSQLLKAICK ISPRG VYTT GKGSSGVGLT AAVMKDPVTD EMILEGGALV LADNGICCID EFDKMDESDR TAIHEVMEQQ TISISKAGIN TTLNAR TSI LAAANPLYGR YNPRLSPLDN INLPAALLSR FDILFLMLDI PSRDDDEKLA EHVTYVHMHN KQPDLDFTPV EPSKMRE YI AYAKTKRPVM SEAVNDYVVQ AYIRLRQDSK REMDSKFSFG QATPRTLLGI IRLSQALAKL RLADMVDIDD VEEALRLV R VSKESLYQ

UniProtKB: DNA replication licensing factor MCM7

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Macromolecule #12: DNA (26-MER)

MacromoleculeName: DNA (26-MER) / type: dna / ID: 12 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 7.075591 KDa
SequenceString:
(DG)(DA)(DT)(DC)(DG)(DA)(DT)(DC)(DG)(DA) (DT)(DA)(DA)(DA)(DG)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)

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Macromolecule #13: DNA (15-MER)

MacromoleculeName: DNA (15-MER) / type: dna / ID: 13 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 4.593011 KDa
SequenceString:
(DA)(DA)(DT)(DC)(DG)(DA)(DT)(DC)(DG)(DA) (DT)(DC)(DG)(DA)(DT)

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Macromolecule #14: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 14 / Number of copies: 3 / 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
GridDetails: unspecified
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 162550
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6u0m:
Structure of the S. cerevisiae replicative helicase CMG in complex with a forked DNA

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