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- EMDB-10540: Human polymerase delta-FEN1-PCNA toolbelt -

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Basic information

Entry
Database: EMDB / ID: EMD-10540
TitleHuman polymerase delta-FEN1-PCNA toolbelt
Map data
Sample
  • Complex: Toolbelt
    • Complex: DNA polymerase
      • Protein or peptide: x 4 types
    • Complex: Proliferating cell nuclear antigen, flap endonuclease
      • Protein or peptide: x 2 types
    • Complex: DNA primer, template
      • DNA: x 2 types
  • Ligand: x 3 types
KeywordsProtein / REPLICATION
Function / homology
Function and homology information


delta DNA polymerase complex / DNA synthesis involved in UV-damage excision repair / flap endonuclease activity / positive regulation of sister chromatid cohesion / zeta DNA polymerase complex / nucleotide-excision repair complex / telomere maintenance via semi-conservative replication / double-stranded DNA exodeoxyribonuclease activity / Cytosolic iron-sulfur cluster assembly / positive regulation of deoxyribonuclease activity ...delta DNA polymerase complex / DNA synthesis involved in UV-damage excision repair / flap endonuclease activity / positive regulation of sister chromatid cohesion / zeta DNA polymerase complex / nucleotide-excision repair complex / telomere maintenance via semi-conservative replication / double-stranded DNA exodeoxyribonuclease activity / Cytosolic iron-sulfur cluster assembly / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / 5'-flap endonuclease activity / purine-specific mismatch base pair DNA N-glycosylase activity / 3'-5'-DNA exonuclease activity / nucleotide-excision repair, DNA gap filling / nuclear lamina / UV protection / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / MutLalpha complex binding / Processive synthesis on the lagging strand / DNA replication proofreading / PCNA complex / DNA replication, removal of RNA primer / Removal of the Flap Intermediate / HDR through MMEJ (alt-NHEJ) / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / replisome / 5'-3' exonuclease activity / aggresome / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / exonuclease activity / error-free translesion synthesis / response to L-glutamate / DNA biosynthetic process / DNA synthesis involved in DNA repair / DNA strand elongation involved in DNA replication / histone acetyltransferase binding / DNA polymerase processivity factor activity / leading strand elongation / Early Phase of HIV Life Cycle / G1/S-Specific Transcription / response to dexamethasone / replication fork processing / nuclear replication fork / SUMOylation of DNA replication proteins / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / fatty acid homeostasis / error-prone translesion synthesis / translesion synthesis / mismatch repair / response to cadmium ion / response to UV / estrous cycle / cyclin-dependent protein kinase holoenzyme complex / base-excision repair, gap-filling / DNA polymerase binding / positive regulation of endothelial cell proliferation / epithelial cell differentiation / male germ cell nucleus / positive regulation of DNA repair / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / Translesion synthesis by REV1 / Translesion synthesis by POLK / liver regeneration / Translesion synthesis by POLI / replication fork / Gap-filling DNA repair synthesis and ligation in GG-NER / positive regulation of DNA replication / nuclear estrogen receptor binding / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / double-strand break repair via homologous recombination / Translesion Synthesis by POLH / receptor tyrosine kinase binding / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / memory / cellular response to hydrogen peroxide / DNA-templated DNA replication / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA-DNA hybrid ribonuclease activity / cellular response to UV / cellular response to xenobiotic stimulus / double-strand break repair / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / manganese ion binding / heart development / 4 iron, 4 sulfur cluster binding
Similarity search - Function
DNA polymerase delta, subunit 4 / DNA polymerase delta, subunit 4 / DNA polymerase delta subunit 3 / DNA polymerase delta subunit 3 superfamily / DNA polymerase subunit Cdc27 / DNA polymerase delta subunit, OB-fold domain / DNA polymerase delta subunit 2, C-terminal domain / DNA polymerase delta subunit OB-fold domain / Flap endonuclease 1 / DNA polymerase delta/II small subunit family ...DNA polymerase delta, subunit 4 / DNA polymerase delta, subunit 4 / DNA polymerase delta subunit 3 / DNA polymerase delta subunit 3 superfamily / DNA polymerase subunit Cdc27 / DNA polymerase delta subunit, OB-fold domain / DNA polymerase delta subunit 2, C-terminal domain / DNA polymerase delta subunit OB-fold domain / Flap endonuclease 1 / DNA polymerase delta/II small subunit family / C4-type zinc-finger of DNA polymerase delta / : / C4-type zinc-finger of DNA polymerase delta / DNA polymerase delta catalytic subunit-like, N-terminal domain / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / Proliferating cell nuclear antigen signature 2. / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / : / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / DNA polymerase family B, thumb domain / DNA polymerase family B signature. / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B / PIN-like domain superfamily / : / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain / DNA polymerase, palm domain superfamily / DNA polymerase type-B family / DNA-directed DNA polymerase, family B / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Proliferating cell nuclear antigen / DNA polymerase delta catalytic subunit / Flap endonuclease 1 / DNA polymerase delta subunit 2 / DNA polymerase delta subunit 3 / DNA polymerase delta subunit 4
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.05 Å
AuthorsLancey C / Hamdan SM
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: Structure of the processive human Pol δ holoenzyme.
Authors: Claudia Lancey / Muhammad Tehseen / Vlad-Stefan Raducanu / Fahad Rashid / Nekane Merino / Timothy J Ragan / Christos G Savva / Manal S Zaher / Afnan Shirbini / Francisco J Blanco / Samir M ...Authors: Claudia Lancey / Muhammad Tehseen / Vlad-Stefan Raducanu / Fahad Rashid / Nekane Merino / Timothy J Ragan / Christos G Savva / Manal S Zaher / Afnan Shirbini / Francisco J Blanco / Samir M Hamdan / Alfredo De Biasio /
Abstract: In eukaryotes, DNA polymerase δ (Pol δ) bound to the proliferating cell nuclear antigen (PCNA) replicates the lagging strand and cooperates with flap endonuclease 1 (FEN1) to process the Okazaki ...In eukaryotes, DNA polymerase δ (Pol δ) bound to the proliferating cell nuclear antigen (PCNA) replicates the lagging strand and cooperates with flap endonuclease 1 (FEN1) to process the Okazaki fragments for their ligation. We present the high-resolution cryo-EM structure of the human processive Pol δ-DNA-PCNA complex in the absence and presence of FEN1. Pol δ is anchored to one of the three PCNA monomers through the C-terminal domain of the catalytic subunit. The catalytic core sits on top of PCNA in an open configuration while the regulatory subunits project laterally. This arrangement allows PCNA to thread and stabilize the DNA exiting the catalytic cleft and recruit FEN1 to one unoccupied monomer in a toolbelt fashion. Alternative holoenzyme conformations reveal important functional interactions that maintain PCNA orientation during synthesis. This work sheds light on the structural basis of Pol δ's activity in replicating the human genome.
History
DepositionDec 10, 2019-
Header (metadata) releaseDec 18, 2019-
Map releaseDec 18, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0073
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0073
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tnz
  • Surface level: 0.0073
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10540.png

Downloads & links

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Map

FileDownload / File: emd_10540.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.87 Å/pix.
x 400 pix.
= 348. Å		0.87 Å/pix.
x 400 pix.
= 348. Å		0.87 Å/pix.
x 400 pix.
= 348. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.87 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0073 / Movie #1: 0.0073
Minimum - Maximum-0.013152464 - 0.053721745
Average (Standard dev.)0.00010589942 (±0.00095735927)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 348.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.870.870.87
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z348.000348.000348.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0130.0540.000

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Supplemental data

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Sample components

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Entire : Toolbelt

EntireName: Toolbelt
Components
  • Complex: Toolbelt
    • Complex: DNA polymerase
      • Protein or peptide: DNA polymerase delta catalytic subunit
      • Protein or peptide: DNA polymerase delta subunit 2
      • Protein or peptide: DNA polymerase delta subunit 3
      • Protein or peptide: DNA polymerase delta subunit 4
    • Complex: Proliferating cell nuclear antigen, flap endonuclease
      • Protein or peptide: Proliferating cell nuclear antigen
      • Protein or peptide: Flap endonuclease 1
    • Complex: DNA primer, template
      • DNA: DNA primer
      • DNA: DNA template
  • Ligand: ZINC ION
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: THYMIDINE-5'-TRIPHOSPHATE

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Supramolecule #1: Toolbelt

SupramoleculeName: Toolbelt / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6, #8

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Supramolecule #2: DNA polymerase

SupramoleculeName: DNA polymerase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Proliferating cell nuclear antigen, flap endonuclease

SupramoleculeName: Proliferating cell nuclear antigen, flap endonuclease / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: DNA primer, template

SupramoleculeName: DNA primer, template / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #7-#8
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: DNA polymerase delta catalytic subunit

MacromoleculeName: DNA polymerase delta catalytic subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 123.785922 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MDGKRRPGPG PGVPPKRARG GLWDDDDAPR PSQFEEDLAL MEEMEAEHRL QEQEEEELQS VLEGVADGQV PPSAIDPRWL RPTPPALDP QTEPLIFQQL EIDHYVGPAQ PVPGGPPPSR GSVPVLRAFG VTDEGFSVCC HIHGFAPYFY TPAPPGFGPE H MGDLQREL ...String:
MDGKRRPGPG PGVPPKRARG GLWDDDDAPR PSQFEEDLAL MEEMEAEHRL QEQEEEELQS VLEGVADGQV PPSAIDPRWL RPTPPALDP QTEPLIFQQL EIDHYVGPAQ PVPGGPPPSR GSVPVLRAFG VTDEGFSVCC HIHGFAPYFY TPAPPGFGPE H MGDLQREL NLAISRDSRG GRELTGPAVL AVELCSRESM FGYHGHGPSP FLRITVALPR LVAPARRLLE QGIRVAGLGT PS FAPYEAN VDFEIRFMVD TDIVGCNWLE LPAGKYALRL KEKATQCQLE ADVLWSDVVS HPPEGPWQRI APLRVLSFDI ECA GRKGIF PEPERDPVIQ ICSLGLRWGE PEPFLRLALT LRPCAPILGA KVQSYEKEED LLQAWSTFIR IMDPDVITGY NIQN FDLPY LISRAQTLKV QTFPFLGRVA GLCSNIRDSS FQSKQTGRRD TKVVSMVGRV QMDMLQVLLR EYKLRSYTLN AVSFH FLGE QKEDVQHSII TDLQNGNDQT RRRLAVYCLK DAYLPLRLLE RLMVLVNAVE MARVTGVPLS YLLSRGQQVK VVSQLL RQA MHEGLLMPVV KSEGGEDYTG ATVIEPLKGY YDVPIATLDF SSLYPSIMMA HNLCYTTLLR PGTAQKLGLT EDQFIRT PT GDEFVKTSVR KGLLPQILEN LLSARKRAKA ELAKETDPLR RQVLDGRQLA LKVSANSVYG FTGAQVGKLP CLEISQSV T GFGRQMIEKT KQLVESKYTV ENGYSTSAKV VYGDTDSVMC RFGVSSVAEA MALGREAADW VSGHFPSPIR LEFEKVYFP YLLISKKRYA GLLFSSRPDA HDRMDCKGLE AVRRDNCPLV ANLVTASLRR LLIDRDPEGA VAHAQDVISD LLCNRIDISQ LVITKELTR AASDYAGKQA HVELAERMRK RDPGSAPSLG DRVPYVIISA AKGVAAYMKS EDPLFVLEHS LPIDTQYYLE Q QLAKPLLR IFEPILGEGR AEAVLLRGDH TRCKTVLTGK VGGLLAFAKR RNCCIGCRTV LSHQGAVCEF CQPRESELYQ KE VSHLNAL EERFSRLWTQ CQRCQGSLHE DVICTSRDCP IFYMRKKVRK DLEDQEQLLR RFGPPGPEAW

UniProtKB: DNA polymerase delta catalytic subunit

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Macromolecule #2: DNA polymerase delta subunit 2

MacromoleculeName: DNA polymerase delta subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 51.338168 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MFSEQAAQRA HTLLSPPSAN NATFARVPVA TYTNSSQPFR LGERSFSRQY AHIYATRLIQ MRPFLENRAQ QHWGSGVGVK KLCELQPEE KCCVVGTLFK AMPLQPSILR EVSEEHNLLP QPPRSKYIHP DDELVLEDEL QRIKLKGTID VSKLVTGTVL A VFGSVRDD ...String:
MFSEQAAQRA HTLLSPPSAN NATFARVPVA TYTNSSQPFR LGERSFSRQY AHIYATRLIQ MRPFLENRAQ QHWGSGVGVK KLCELQPEE KCCVVGTLFK AMPLQPSILR EVSEEHNLLP QPPRSKYIHP DDELVLEDEL QRIKLKGTID VSKLVTGTVL A VFGSVRDD GKFLVEDYCF ADLAPQKPAP PLDTDRFVLL VSGLGLGGGG GESLLGTQLL VDVVTGQLGD EGEQCSAAHV SR VILAGNL LSHSTQSRDS INKAKYLTKK TQAASVEAVK MLDEILLQLS ASVPVDVMPG EFDPTNYTLP QQPLHPCMFP LAT AYSTLQ LVTNPYQATI DGVRFLGTSG QNVSDIFRYS SMEDHLEILE WTLRVRHISP TAPDTLGCYP FYKTDPFIFP ECPH VYFCG NTPSFGSKII RGPEDQTVLL VTVPDFSATQ TACLVNLRSL ACQPISFSGF GAEDDDLGGL GLGP

UniProtKB: DNA polymerase delta subunit 2

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Macromolecule #3: DNA polymerase delta subunit 3

MacromoleculeName: DNA polymerase delta subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.5285 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MWSHPQFEKA DQLYLENIDE FVTDQNKIVT YKWLSYTLGV HVNQAKQMLY DYVERKRKEN SGAQLHVTYL VSGSLIQNGH SCHKVAVVR EDKLEAVKSK LAVTASIHVY SIQKAMLKDS GPLFNTDYDI LKSNLQNCSK FSAIQCAAAV PRAPAESSSS S KKFEQSHL ...String:
MWSHPQFEKA DQLYLENIDE FVTDQNKIVT YKWLSYTLGV HVNQAKQMLY DYVERKRKEN SGAQLHVTYL VSGSLIQNGH SCHKVAVVR EDKLEAVKSK LAVTASIHVY SIQKAMLKDS GPLFNTDYDI LKSNLQNCSK FSAIQCAAAV PRAPAESSSS S KKFEQSHL HMSSETQANN ELTTNGHGPP ASKQVSQQPK GIMGMFASKA AAKTQETNKE TKTEAKEVTN ASAAGNKAPG KG NMMSNFF GKAAMNKFKV NLDSEQAVKE EKIVEQPTVS VTEPKLATPA GLKKSSKKAE PVKVLQKEKK RGKRVALSDD ETK ETENMR KKRRRIKLPE SDSSEDEVFP DSPGAYEAES PSPPPPPSPP LEPVPKTEPE PPSVKSSSGE NKRKRKRVLK SKTY LDGEG CIVTEKVYES ESCTDSEEEL NMKTSSVHRP PAMTVKKEPR EERKGPKKGT AALGKANRQV SITGFFQRK

UniProtKB: DNA polymerase delta subunit 3

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Macromolecule #4: DNA polymerase delta subunit 4

MacromoleculeName: DNA polymerase delta subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 16.274323 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString:
MHHHHHHSRA WRHPQFGGHH HHHHENLYFQ SGRKRLITDS YPVVKRREGP AGHSKGELAP ELGEEPQPRD EEEAELELLR QFDLAWQYG PCTGITRLQR WCRAKQMGLE PPPEVWQVLK THPGDPRFQC SLWHLYPL

UniProtKB: DNA polymerase delta subunit 4

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Macromolecule #5: Proliferating cell nuclear antigen

MacromoleculeName: Proliferating cell nuclear antigen / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.088061 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPHMFEARLV QGSILKKVLE ALKDLINEAC WDISSSGVNL QSMDSSHVSL VQLTLRSEGF DTYRCDRNLA MGVNLTSMSK ILKCAGNED IITLRAEDNA DTLALVFEAP NQEKVSDYEM KLMDLDVEQL GIPEQEYSCV VKMPSGEFAR ICRDLSHIGD A VVISCAKD ...String:
GPHMFEARLV QGSILKKVLE ALKDLINEAC WDISSSGVNL QSMDSSHVSL VQLTLRSEGF DTYRCDRNLA MGVNLTSMSK ILKCAGNED IITLRAEDNA DTLALVFEAP NQEKVSDYEM KLMDLDVEQL GIPEQEYSCV VKMPSGEFAR ICRDLSHIGD A VVISCAKD GVKFSASGEL GNGNIKLSQT SNVDKEEEAV TIEMNEPVQL TFALRYLNFF TKATPLSSTV TLSMSADVPL VV EYKIADM GHLKYYLAPK IEDEEGS

UniProtKB: Proliferating cell nuclear antigen

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Macromolecule #6: Flap endonuclease 1

MacromoleculeName: Flap endonuclease 1 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.617039 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGIQGLAKLI ADVAPSAIRE NDIKSYFGRK VAIDASMSIY QFLIAVRQGG DVLQNEEGET TSHLMGMFYR TIRMMENGIK PVYVFDGKP PQLKSGELAK RSERRAEAEK QLQQAQAAGA EQEVEKFTKR LVKVTKQHND ECKHLLSLMG IPYLDAPSEA E ASCAALVK ...String:
MGIQGLAKLI ADVAPSAIRE NDIKSYFGRK VAIDASMSIY QFLIAVRQGG DVLQNEEGET TSHLMGMFYR TIRMMENGIK PVYVFDGKP PQLKSGELAK RSERRAEAEK QLQQAQAAGA EQEVEKFTKR LVKVTKQHND ECKHLLSLMG IPYLDAPSEA E ASCAALVK AGKVYAAATE DMACLTFGSP VLMRHLTASE AKKLPIQEFH LSRILQELGL NQEQFVDLCI LLGSDYCESI RG IGPKRAV DLIQKHKSIE EIVRRLDPNK YPVPENWLHK EAHQLFLEPE VLDPESVELK WSEPNEEELI KFMCGEKQFS EER IRSGVK RLSKSRQGST QGRLDDFFKV TGSLSSAKRK EPEPKGSTKK KAKTGAAGKF KRGK

UniProtKB: Flap endonuclease 1

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Macromolecule #7: DNA primer

MacromoleculeName: DNA primer / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 7.665987 KDa
SequenceString:
(DA)(DG)(DC)(DT)(DA)(DT)(DG)(DA)(DC)(DC) (DA)(DT)(DG)(DA)(DT)(DT)(DA)(DC)(DG)(DA) (DA)(DT)(DT)(DG)(DOC)

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Macromolecule #8: DNA template

MacromoleculeName: DNA template / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 11.677539 KDa
SequenceString:
(DC)(DT)(DG)(DC)(DA)(DC)(DG)(DA)(DA)(DT) (DT)(DA)(DA)(DG)(DC)(DA)(DA)(DT)(DT)(DC) (DG)(DT)(DA)(DA)(DT)(DC)(DA)(DT)(DG) (DG)(DT)(DC)(DA)(DT)(DA)(DG)(DC)(DT)

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #10: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 10 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #11: THYMIDINE-5'-TRIPHOSPHATE

MacromoleculeName: THYMIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 11 / Number of copies: 1 / Formula: TTP
Molecular weightTheoretical: 482.168 Da
Chemical component information

ChemComp-TTP:
THYMIDINE-5'-TRIPHOSPHATE

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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
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
100.0 mMCH3CO2KPotassium Acetate
10.0 mMCaCl2Calcium Chloride
0.02 %H(C2H4O)nO(C6H4)C9H19NP-40
0.4 mMC10H16N2O3SBiotin
1.0 mMC4H10O2S2Dithiothreitol
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 300 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsComplex separated by gel filtration

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 77.0 K / Max: 77.0 K
Specialist opticsPhase plate: OTHER
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 1 / Number real images: 5071 / Average exposure time: 3.0 sec. / Average electron dose: 44.0 e/Å2 / Details: Data were collected in super resolution mode
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 57471 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Relion initial model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 47291
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 8
FSC plot (resolution estimation)

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