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- EMDB-42287: Cryo-EM map of human clmap-clamp loader ATAD5-RFC-gapped PCNA com... -

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Basic information

Entry
Database: EMDB / ID: EMD-42287
TitleCryo-EM map of human clmap-clamp loader ATAD5-RFC-gapped PCNA complex in intermediate state 3
Map dataFinal sharpen cryo-EM map
Sample
  • Complex: ATAD5-RFC-gapped PCNA
    • Protein or peptide: ATPase family AAA domain-containing protein 5
    • Protein or peptide: Replication factor C subunit 2
    • Protein or peptide: Replication factor C subunit 5
    • Protein or peptide: Replication factor C subunit 4
    • Protein or peptide: Replication factor C subunit 3
    • Protein or peptide: Proliferating cell nuclear antigen
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsAAA ATPase / Clamp unloader / MOTOR PROTEIN
Function / homology
Function and homology information


DNA clamp unloader activity / positive regulation of cell cycle G2/M phase transition / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / response to organophosphorus / nuclear DNA replication / Ctf18 RFC-like complex / Rad17 RFC-like complex / mitotic telomere maintenance via semi-conservative replication ...DNA clamp unloader activity / positive regulation of cell cycle G2/M phase transition / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / response to organophosphorus / nuclear DNA replication / Ctf18 RFC-like complex / Rad17 RFC-like complex / mitotic telomere maintenance via semi-conservative replication / Elg1 RFC-like complex / DNA replication factor C complex / purine-specific mismatch base pair DNA N-glycosylase activity / positive regulation of isotype switching to IgG isotypes / positive regulation of DNA-directed DNA polymerase activity / nuclear lamina / MutLalpha complex binding / Polymerase switching / DNA clamp loader activity / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / PCNA complex / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / isotype switching / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / Removal of the Flap Intermediate from the C-strand / replisome / regulation of mitotic cell cycle phase transition / DNA duplex unwinding / response to L-glutamate / HDR through Single Strand Annealing (SSA) / DNA strand elongation involved in DNA replication / Impaired BRCA2 binding to RAD51 / histone acetyltransferase binding / DNA synthesis involved in DNA repair / DNA polymerase processivity factor activity / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / G1/S-Specific Transcription / leading strand elongation / replication fork processing / response to dexamethasone / nuclear replication fork / Presynaptic phase of homologous DNA pairing and strand exchange / SUMOylation of DNA replication proteins / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / cyclin-dependent protein kinase holoenzyme complex / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / signal transduction in response to DNA damage / ATP-dependent activity, acting on DNA / mismatch repair / translesion synthesis / Activation of ATR in response to replication stress / response to cadmium ion / DNA polymerase binding / positive regulation of B cell proliferation / epithelial cell differentiation / positive regulation of DNA repair / Translesion synthesis by REV1 / base-excision repair, gap-filling / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / replication fork / positive regulation of DNA replication / male germ cell nucleus / liver regeneration / nuclear estrogen receptor binding / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / Dual Incision in GG-NER / receptor tyrosine kinase binding / DNA-templated DNA replication / cellular response to hydrogen peroxide / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / cellular response to xenobiotic stimulus / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / cell population proliferation / DNA replication / damaged DNA binding / chromosome, telomeric region / nuclear body / DNA repair / centrosome / chromatin binding / chromatin
Similarity search - Function
Replication factor C, C-terminal / Replication factor C C-terminal domain / : / DNA polymerase III, delta subunit / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / Proliferating cell nuclear antigen signature 2. / 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 ...Replication factor C, C-terminal / Replication factor C C-terminal domain / : / DNA polymerase III, delta subunit / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / Proliferating cell nuclear antigen signature 2. / 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 / : / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Proliferating cell nuclear antigen / Replication factor C subunit 4 / Replication factor C subunit 2 / Replication factor C subunit 5 / Replication factor C subunit 3 / ATPase family AAA domain-containing protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsWang F / He Q / Li H
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131754 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115809 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: To Be Published
Title: Cryo-EM map of human clmap-clamp loader ATAD5-RFC-closed PCNA complex
Authors: Wang F / He Q / Li H / O'Donnel ME
History
DepositionOct 10, 2023-
Header (metadata) releaseMay 29, 2024-
Map releaseMay 29, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42287.png

Downloads & links

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Map

FileDownload / File: emd_42287.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal sharpen cryo-EM map
Voxel sizeX=Y=Z: 0.828 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.34486958 - 0.71341205
Average (Standard dev.)0.0008551307 (±0.026800176)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened Cryo-EM map by DeepEMhancer

Fileemd_42287_additional_1.map
AnnotationSharpened Cryo-EM map by DeepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened cryo-EM map

Fileemd_42287_additional_2.map
AnnotationUnsharpened cryo-EM map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_42287_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_42287_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ATAD5-RFC-gapped PCNA

EntireName: ATAD5-RFC-gapped PCNA
Components
  • Complex: ATAD5-RFC-gapped PCNA
    • Protein or peptide: ATPase family AAA domain-containing protein 5
    • Protein or peptide: Replication factor C subunit 2
    • Protein or peptide: Replication factor C subunit 5
    • Protein or peptide: Replication factor C subunit 4
    • Protein or peptide: Replication factor C subunit 3
    • Protein or peptide: Proliferating cell nuclear antigen
  • Ligand: MAGNESIUM ION
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: ATAD5-RFC-gapped PCNA

SupramoleculeName: ATAD5-RFC-gapped PCNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 320 KDa

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Macromolecule #1: ATPase family AAA domain-containing protein 5

MacromoleculeName: ATPase family AAA domain-containing protein 5 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 116.421094 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: FDESSQDTSE KSQDCDVQCK AKRDFLMSGL PDLLKRQIAK KAAALDVYNA VSTSFQRVVH VQQKDDGCCL WHLKPPSCPL LTKFKELNT KVIDLSKCGI ALGEFSTLNS KLKSGNSAAV FMRTRKEFTE EVRNLLLEEI RWSNPEFSLK KYFPLLLKKQ I EHQVLSSE ...String:
FDESSQDTSE KSQDCDVQCK AKRDFLMSGL PDLLKRQIAK KAAALDVYNA VSTSFQRVVH VQQKDDGCCL WHLKPPSCPL LTKFKELNT KVIDLSKCGI ALGEFSTLNS KLKSGNSAAV FMRTRKEFTE EVRNLLLEEI RWSNPEFSLK KYFPLLLKKQ I EHQVLSSE CHSKQELEAD VSHKETKRKL VEAENSKSKR KKPNEYSKNL EKTNRKSEEL SKRNNSSGIK LDSSKDSGTE DM LWTEKYQ PQTASELIGN ELAIKKLHSW LKDWKRRAEL EERQNLKGKR DEKHEDFSGG IDFKGSSDDE EESRLCNTVL ITG PTGVGK TAAVYACAQE LGFKIFEVNA SSQRSGRQIL SQLKEATQSH QVDKQGVNSQ KPCFFNSYYI GKSPKKISSP KKVV TSPRK VPPPSPKSSG PKRALPPKTL ANYFKVSPKP KNNEEIGMLL ENNKGIKNSF EQKQITQTKS TNATNSNVKD VGAEE PSRK NATSLILFEE VDVIFDEDAG FLNAIKTFMA TTKRPVILTT SDPTFSLMFD GCFEEIKFST PSLLNVASYL QMICLT ENF RTDVKDFVTL LTANTCDIRK SILYLQFWIR SGGGVLEERP LTLYRGNSRN VQLVCSEHGL DNKIYPKNTK KKRVDLP KC DSGCAETLFG LKNIFSPSED LFSFLKHKIT MKEEWHKFIQ LLTEFQMRNV DFLYSNLEFI LPLPVDTIPE TKNFCGPS V TVDASAATKS MNCLARKHSE REQPLKKSQK KKQKKTLVIL DDSDLFDTDL DFPDQSISLS SVSSSSNAEE SKTGDEESK ARDKGNNPET KKSIPCPPKT TAGKKCSALV SHCLNSLSEF MDNMSFLDAL LTDVREQNKY GRNDFSWTNG KVTSGLCDEF SLESNDGWT SQSSGELKAA AEALSFTKCS SAISKALETL NSCKKLGRDP TNDLTFYVSQ KRNNVYFSQS AANLDNAWKR I SVIKSVFS SRSLLYVGNR QASIIEYLPT LRNICKTEKL KEQGKSKRRF LHYFEGIHLD IPKETVNTLA ADFP

UniProtKB: ATPase family AAA domain-containing protein 5

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Macromolecule #2: Replication factor C subunit 2

MacromoleculeName: Replication factor C subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.203207 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: MEVEAVCGGA GEVEAQDSDP APAFSKAPGS AGHYELPWVE KYRPVKLNEI VGNEDTVSRL EVFAREGNVP NIIIAGPPGT GKTTSILCL ARALLGPALK DAMLELNASN DRGIDVVRNK IKMFAQQKVT LPKGRHKIII LDEADSMTDG AQQALRRTME I YSKTTRFA ...String:
MEVEAVCGGA GEVEAQDSDP APAFSKAPGS AGHYELPWVE KYRPVKLNEI VGNEDTVSRL EVFAREGNVP NIIIAGPPGT GKTTSILCL ARALLGPALK DAMLELNASN DRGIDVVRNK IKMFAQQKVT LPKGRHKIII LDEADSMTDG AQQALRRTME I YSKTTRFA LACNASDKII EPIQSRCAVL RYTKLTDAQI LTRLMNVIEK ERVPYTDDGL EAIIFTAQGD MRQALNNLQS TF SGFGFIN SENVFKVCDE PHPLLVKEMI QHCVNANIDE AYKILAHLWH LGYSPEDIIG NIFRVCKTFQ MAEYLKLEFI KEI GYTHMK IAEGVNSLLQ MAGLLARLCQ KTMAPVAS

UniProtKB: Replication factor C subunit 2

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Macromolecule #3: Replication factor C subunit 5

MacromoleculeName: Replication factor C subunit 5 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.545512 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: METSALKQQE QPAATKIRNL PWVEKYRPQT LNDLISHQDI LSTIQKFINE DRLPHLLLYG PPGTGKTSTI LACAKQLYKD KEFGSMVLE LNASDDRGID IIRGPILSFA STRTIFKKGF KLVILDEADA MTQDAQNALR RVIEKFTENT RFCLICNYLS K IIPALQSR ...String:
METSALKQQE QPAATKIRNL PWVEKYRPQT LNDLISHQDI LSTIQKFINE DRLPHLLLYG PPGTGKTSTI LACAKQLYKD KEFGSMVLE LNASDDRGID IIRGPILSFA STRTIFKKGF KLVILDEADA MTQDAQNALR RVIEKFTENT RFCLICNYLS K IIPALQSR CTRFRFGPLT PELMVPRLEH VVEEEKVDIS EDGMKALVTL SSGDMRRALN ILQSTNMAFG KVTEETVYTC TG HPLKSDI ANILDWMLNQ DFTTAYRNIT ELKTLKGLAL HDILTEIHLF VHRVDFPSSV RIHLLTKMAD IEYRLSVGTN EKI QLSSLI AAFQVTRDLI VAEA

UniProtKB: Replication factor C subunit 5

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Macromolecule #4: Replication factor C subunit 4

MacromoleculeName: Replication factor C subunit 4 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.735711 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: MQAFLKGTSI STKPPLTKDR GVAASAGSSG ENKKAKPVPW VEKYRPKCVD EVAFQEEVVA VLKKSLEGAD LPNLLFYGPP GTGKTSTIL AAARELFGPE LFRLRVLELN ASDERGIQVV REKVKNFAQL TVSGSRSDGK PCPPFKIVIL DEADSMTSAA Q AALRRTME ...String:
MQAFLKGTSI STKPPLTKDR GVAASAGSSG ENKKAKPVPW VEKYRPKCVD EVAFQEEVVA VLKKSLEGAD LPNLLFYGPP GTGKTSTIL AAARELFGPE LFRLRVLELN ASDERGIQVV REKVKNFAQL TVSGSRSDGK PCPPFKIVIL DEADSMTSAA Q AALRRTME KESKTTRFCL ICNYVSRIIE PLTSRCSKFR FKPLSDKIQQ QRLLDIAKKE NVKISDEGIA YLVKVSEGDL RK AITFLQS ATRLTGGKEI TEKVITDIAG VIPAEKIDGV FAACQSGSFD KLEAVVKDLI DEGHAATQLV NQLHDVVVEN NLS DKQKSI ITEKLAEVDK CLADGADEHL QLISLCATVM QQLSQNC

UniProtKB: Replication factor C subunit 4

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Macromolecule #5: Replication factor C subunit 3

MacromoleculeName: Replication factor C subunit 3 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.614332 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: MSLWVDKYRP CSLGRLDYHK EQAAQLRNLV QCGDFPHLLV YGPSGAGKKT RIMCILRELY GVGVEKLRIE HQTITTPSKK KIEISTIAS NYHLEVNPSD AGNSDRVVIQ EMLKTVAQSQ QLETNSQRDF KVVLLTEVDK LTKDAQHALR RTMEKYMSTC R LILCCNST ...String:
MSLWVDKYRP CSLGRLDYHK EQAAQLRNLV QCGDFPHLLV YGPSGAGKKT RIMCILRELY GVGVEKLRIE HQTITTPSKK KIEISTIAS NYHLEVNPSD AGNSDRVVIQ EMLKTVAQSQ QLETNSQRDF KVVLLTEVDK LTKDAQHALR RTMEKYMSTC R LILCCNST SKVIPPIRSR CLAVRVPAPS IEDICHVLST VCKKEGLNLP SQLAHRLAEK SCRNLRKALL MCEACRVQQY PF TADQEIP ETDWEVYLRE TANAIVSQQT PQRLLEVRGR LYELLTHCIP PEIIMKGLLS ELLHNCDGQL KGEVAQMAAY YEH RLQLGS KAIYHLEAFV AKFMALYKKF MEDGLEGMMF

UniProtKB: Replication factor C subunit 3

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Macromolecule #6: Proliferating cell nuclear antigen

MacromoleculeName: Proliferating cell nuclear antigen / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.795752 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: MFEARLVQGS ILKKVLEALK DLINEACWDI SSSGVNLQSM DSSHVSLVQL TLRSEGFDTY RCDRNLAMGV NLTSMSKILK CAGNEDIIT LRAEDNADTL ALVFEAPNQE KVSDYEMKLM DLDVEQLGIP EQEYSCVVKM PSGEFARICR DLSHIGDAVV I SCAKDGVK ...String:
MFEARLVQGS ILKKVLEALK DLINEACWDI SSSGVNLQSM DSSHVSLVQL TLRSEGFDTY RCDRNLAMGV NLTSMSKILK CAGNEDIIT LRAEDNADTL ALVFEAPNQE KVSDYEMKLM DLDVEQLGIP EQEYSCVVKM PSGEFARICR DLSHIGDAVV I SCAKDGVK FSASGELGNG NIKLSQTSNV DKEEEAVTIE MNEPVQLTFA LRYLNFFTKA TPLSSTVTLS MSADVPLVVE YK IADMGHL KYYLAPKIED EEGS

UniProtKB: Proliferating cell nuclear antigen

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Macromolecule #7: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 7 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #8: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 8 / Number of copies: 3 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

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Macromolecule #9: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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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

Concentration1.0 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55855
FSC plot (resolution estimation)

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