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- EMDB-10539: Processive human polymerase delta holoenzyme -

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Basic information

Entry
Database: EMDB / ID: EMD-10539
TitleProcessive human polymerase delta holoenzyme
Map data
Sample
  • 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
      • Protein or peptide: Proliferating cell nuclear antigen
    • Complex: DNA primer, template
      • DNA: DNA primer
      • DNA: DNA template
  • Ligand: ZINC ION
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: THYMIDINE-5'-TRIPHOSPHATE
KeywordsProtein / REPLICATION
Function / homology
Function and homology information


delta DNA polymerase complex / DNA synthesis involved in UV-damage excision repair / zeta DNA polymerase complex / nucleotide-excision repair complex / Cytosolic iron-sulfur cluster assembly / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / nucleotide-excision repair, DNA gap filling ...delta DNA polymerase complex / DNA synthesis involved in UV-damage excision repair / zeta DNA polymerase complex / nucleotide-excision repair complex / Cytosolic iron-sulfur cluster assembly / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / nucleotide-excision repair, DNA gap filling / replisome / nuclear lamina / Polymerase switching / Processive synthesis on the lagging strand / DNA replication proofreading / PCNA complex / 3'-5'-DNA exonuclease activity / Removal of the Flap Intermediate / MutLalpha complex binding / Telomere C-strand (Lagging Strand) Synthesis / 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 / Polymerase switching on the C-strand of the telomere / mitotic DNA replication / response to L-glutamate / Processive synthesis on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / error-free translesion synthesis / response to dexamethasone / DNA biosynthetic process / DNA strand elongation involved in DNA replication / histone acetyltransferase binding / DNA synthesis involved in DNA repair / leading strand elongation / DNA polymerase processivity factor activity / G1/S-Specific Transcription / nuclear replication fork / response to UV / SUMOylation of DNA replication proteins / PCNA-Dependent Long Patch Base Excision Repair / response to cadmium ion / DNA repair-dependent chromatin remodeling / fatty acid homeostasis / error-prone translesion synthesis / cyclin-dependent protein kinase holoenzyme complex / estrous cycle / base-excision repair, gap-filling / mismatch repair / epithelial cell differentiation / DNA polymerase binding / liver regeneration / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / replication fork / replication fork processing / positive regulation of DNA replication / positive regulation of DNA repair / translesion synthesis / nuclear estrogen receptor binding / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / receptor tyrosine kinase binding / Recognition of DNA damage by PCNA-containing replication complex / DNA-templated DNA replication / cellular response to hydrogen peroxide / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / heart development / cellular response to UV / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / response to estradiol / E3 ubiquitin ligases ubiquitinate target proteins / 4 iron, 4 sulfur cluster binding / DNA-directed DNA polymerase / chromatin organization / damaged DNA binding / DNA-directed DNA polymerase activity / DNA replication / protein-macromolecule adaptor activity / chromosome, telomeric region / nucleotide binding / DNA repair / centrosome / chromatin binding / protein-containing complex binding / chromatin / enzyme binding / DNA binding / extracellular exosome / nucleoplasm / zinc ion binding / membrane / identical protein binding / nucleus
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 / DNA polymerase delta/II small subunit family / C4-type zinc-finger of DNA polymerase delta ...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 / 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 / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / Proliferating cell nuclear antigen signature 2. / : / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, C-terminal domain / 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, N-terminal domain / DNA polymerase family B, thumb domain / DNA-directed DNA polymerase, family B, multifunctional domain / DNA-directed DNA polymerase, family B, conserved site / DNA polymerase family B signature. / DNA polymerase family B / 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
DNA sliding clamp PCNA / DNA polymerase delta catalytic subunit / 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: 3.08 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-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0095
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0095
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6tny
  • Surface level: 0.0095
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10539.png

Downloads & links

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Map

FileDownload / File: emd_10539.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: 0.0095 / Movie #1: 0.0095
Minimum - Maximum-0.022090377 - 0.06058694
Average (Standard dev.)0.00009167447 (±0.0010096)
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-0.0220.0610.000

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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
      • Protein or peptide: Proliferating cell nuclear antigen
    • 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-#5, #7

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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

SupramoleculeName: Proliferating cell nuclear antigen / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5
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: #6-#7
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: DNA sliding clamp PCNA

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Macromolecule #6: DNA primer

MacromoleculeName: DNA primer / type: dna / ID: 6 / 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 #7: DNA template

MacromoleculeName: DNA template / type: dna / ID: 7 / 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 #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #9: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 9 / Number of copies: 1 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #10: THYMIDINE-5'-TRIPHOSPHATE

MacromoleculeName: THYMIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 10 / 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
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

CTF correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Relion initial model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 288920
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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