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- EMDB-76028: Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex... -

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Entry
Database: EMDB / ID: EMD-76028
TitleCryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (motor focused)
Map data
Sample
  • Complex: Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (motor focused)
    • Protein or peptide: Nuclear protein localization protein 4 homolog
    • Protein or peptide: Ubiquitin
    • Protein or peptide: FAS-associated factor 1
    • Protein or peptide: Ubiquitin recognition factor in ER-associated degradation protein 1
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsERAD / ubiquitin / AAA+ ATPase / unfoldase / HYDROLASE
Function / homology
Function and homology information


UFD1-NPL4 complex / Fas signaling pathway / negative regulation of RIG-I signaling pathway / ooplasm / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / CD95 death-inducing signaling complex / flavin adenine dinucleotide catabolic process / protein kinase regulator activity / VCP-NSFL1C complex / endoplasmic reticulum stress-induced pre-emptive quality control ...UFD1-NPL4 complex / Fas signaling pathway / negative regulation of RIG-I signaling pathway / ooplasm / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / CD95 death-inducing signaling complex / flavin adenine dinucleotide catabolic process / protein kinase regulator activity / VCP-NSFL1C complex / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / BAT3 complex binding / cytoplasmic ubiquitin ligase complex / cellular response to arsenite ion / protein-DNA covalent cross-linking repair / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / cytoplasm protein quality control / positive regulation of oxidative phosphorylation / response to insecticide / aggresome assembly / ubiquitin-modified protein reader activity / regulation of protein localization to chromatin / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / cellular response to misfolded protein / positive regulation of mitochondrial membrane potential / vesicle-fusing ATPase / K48-linked polyubiquitin modification-dependent protein binding / nuclear outer membrane-endoplasmic reticulum membrane network / K63-linked polyubiquitin modification-dependent protein binding / NAD+ metabolic process / regulation of aerobic respiration / retrograde protein transport, ER to cytosol / perinuclear theca / stress granule disassembly / ATPase complex / negative regulation of type I interferon production / ubiquitin-specific protease binding / Golgi organization / regulation of synapse organization / ciliary transition zone / regulation of protein catabolic process / positive regulation of ATP biosynthetic process / intracellular membrane-bounded organelle / ubiquitin-like protein ligase binding / RHOH GTPase cycle / MHC class I protein binding / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / autophagosome maturation / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / negative regulation of hippo signaling / HSF1 activation / endoplasmic reticulum to Golgi vesicle-mediated transport / Viral mRNA Translation / polyubiquitin modification-dependent protein binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / NF-kappaB binding / GTP hydrolysis and joining of the 60S ribosomal subunit / regulation of cell adhesion / L13a-mediated translational silencing of Ceruloplasmin expression / interstrand cross-link repair / Major pathway of rRNA processing in the nucleolus and cytosol / ATP metabolic process / translesion synthesis / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Attachment and Entry / Protein methylation / negative regulation of protein localization to chromatin / endoplasmic reticulum unfolded protein response / ERAD pathway / heat shock protein binding / proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / lipid droplet / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex
Similarity search - Function
Nuclear pore localisation protein Npl4, ubiquitin-like domain / Nuclear pore localisation protein NPL4 / FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / : / Fas-associated factor 1 / UAS / : / UAS / Ubiquitin fusion degradation protein Ufd1-like ...Nuclear pore localisation protein Npl4, ubiquitin-like domain / Nuclear pore localisation protein NPL4 / FAS-associated factor 1-like, UBX domain / FAF1, UBA-like domain / : / Fas-associated factor 1 / UAS / : / UAS / Ubiquitin fusion degradation protein Ufd1-like / Ufd1-like, Nn domain / : / : / Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 1 / Ubiquitin fusion degradation protein UFD1, N-terminal subdomain 2 / NPL4, zinc-binding putative / NPL4 family, putative zinc binding region / Nuclear pore localisation protein NPL4, C-terminal / Nuclear protein localization protein 4 / NPL4 family / Domain present in ubiquitin-regulatory proteins / UBX domain / UBX domain / UBX domain profile. / UBA-like domain / Zinc finger domain / AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / : / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / Zinc finger RanBP2 type profile. / Zinc finger, RanBP2-type superfamily / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type / CDC48 domain 2-like superfamily / Aspartate decarboxylase-like domain superfamily / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / MPN domain / MPN domain profile. / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Thioredoxin-like superfamily / Ubiquitin-like domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Transitional endoplasmic reticulum ATPase / Ubiquitin-ribosomal protein eL40 fusion protein / Nuclear protein localization protein 4 homolog / Ubiquitin recognition factor in ER-associated degradation protein 1 / FAS-associated factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.58 Å
AuthorsLiao Z / Arkinson C / Martin A
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: bioRxiv / Year: 2025
Title: Faf1 accelerates p97-mediated protein unfolding by promoting ubiquitin engagement.
Authors: Zengwei Liao / Connor Arkinson / Andreas Martin /
Abstract: P97/VCP is a protein unfoldase of the AAA+ ATPase family that plays essential roles in numerous cellular processes, including ER-associated degradation and DNA replication. P97 utilizes various ...P97/VCP is a protein unfoldase of the AAA+ ATPase family that plays essential roles in numerous cellular processes, including ER-associated degradation and DNA replication. P97 utilizes various cofactors to process different substrates. For unfolding of proteins that are modified with K48-linked ubiquitin chains, p97 works with the heterodimeric cofactor Ufd1-Npl4, and the cofactor Faf1 was shown to enhance this activity in the context of replisome disassembly, yet the underlying mechanisms remain unknown. Here, we employ an reconstituted system with human components for biochemical experiments, mutational studies, FRET-based assays, and cryo-EM structure determination to reveal that Faf1 plays a generic role in accelerating ubiquitin-dependent substrate processing by promoting the unfolding of an initiator ubiquitin and its engagement by the ATPase motor. Faf1 thereby uses its p97-bound C-terminal UBX domain to anchor a long helix that braces the UT3 domain of Ufd1 and apparently stabilizes the Ufd1-Npl4 cofactor for ubiquitin unfolding. Our findings demonstrate how p97 works simultaneously with several cofactors to facilitate the unfolding of ubiquitinated proteins, indicating more complex regulatory mechanisms for substrate selection than for the simpler Cdc48 ortholog in yeast.
History
DepositionMar 11, 2026-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76028.png

Downloads & links

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Map

FileDownload / File: emd_76028.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.48 Å/pix.
x 256 pix.
= 378.24 Å		1.48 Å/pix.
x 256 pix.
= 378.24 Å		1.48 Å/pix.
x 256 pix.
= 378.24 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4775 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.133
Minimum - Maximum-0.47115424 - 1.3323418
Average (Standard dev.)0.0006731931 (±0.034184936)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 378.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Sharpened by CryoSPARC

Fileemd_76028_additional_1.map
AnnotationSharpened by CryoSPARC
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Additional map: Sharpened by DeepEMhancer

Fileemd_76028_additional_2.map
AnnotationSharpened by DeepEMhancer
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Half map: #2

Fileemd_76028_half_map_1.map
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Half map: #1

Fileemd_76028_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex...

EntireName: Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (motor focused)
Components
  • Complex: Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (motor focused)
    • Protein or peptide: Nuclear protein localization protein 4 homolog
    • Protein or peptide: Ubiquitin
    • Protein or peptide: FAS-associated factor 1
    • Protein or peptide: Ubiquitin recognition factor in ER-associated degradation protein 1
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex...

SupramoleculeName: Cryo-EM structure of substrate engaged p97-Ufd1-NPL4-Faf1 complex (motor focused)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 700 kDa/nm

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Macromolecule #1: Nuclear protein localization protein 4 homolog

MacromoleculeName: Nuclear protein localization protein 4 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 68.373172 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MGGGAESIII RVQSPDGVKR ITATKRETAA TFLKKVAKEF GFQNNGFSVY INRNKTGEIT ASSNKSLNLL KIKHGDLLFL FPSSLAGPS SEMETSVPPG FKVFGAPNVV EDEIDQYLSK QDGKIYRSRD PQLCRHGPLG KCVHCVPLEP FDEDYLNHLE P PVKHMSFH ...String:
MGGGAESIII RVQSPDGVKR ITATKRETAA TFLKKVAKEF GFQNNGFSVY INRNKTGEIT ASSNKSLNLL KIKHGDLLFL FPSSLAGPS SEMETSVPPG FKVFGAPNVV EDEIDQYLSK QDGKIYRSRD PQLCRHGPLG KCVHCVPLEP FDEDYLNHLE P PVKHMSFH AYIRKLTGGA DKGKFVALEN ISCKIKSGCE GHLPWPNGIC TKCQPSAITL NRQKYRHVDN IMFENHTVAD RF LDFWRKT GNQHFGYLYG RYTEHKDIPL GIRAEVAAIY EPPQIGTQNS LELLEDPKAE VVDEIAAKLG LRKVGWIFTD LVS EDTRKG TVRYSRNKDT YFLSSEECIT AGDFQNKHPN MCRLSPDGHF GSKFVTAVAT GGPDNQVHFE GYQVSNQCMA LVRD ECLLP CKDAPELGYA KESSSEQYVP DVFYKDVDKF GNEITQLARP LPVEYLIIDI TTTFPKDPVY TFSISQNPFP IENRD VLGE TQDFHSLATY LSQNTSSVFL DTISDFHLLL FLVTNEVMPL QDSISLLLEA VRTRNEELAQ TWKRSEQWAT IEQLCS TVG GQLPGLHEYG AVGGSTHTAT AAMWACQHCT FMNQPGTGHC EMCSLPRT

UniProtKB: Nuclear protein localization protein 4 homolog

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Macromolecule #2: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.576831 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Ubiquitin-ribosomal protein eL40 fusion protein

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Macromolecule #3: FAS-associated factor 1

MacromoleculeName: FAS-associated factor 1 / type: protein_or_peptide / ID: 3 / Details: FH-UBX fragment / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.495 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
PLGMAAMEIF TAQQQEDIKD EDEREARENV KREQDEAYRL SLEADRAKRE AHEREMAEQF RLEQIRKEQE EEREAIRLSL EQALPPEPK EENAEPVSKL RIRTPSGEFL ERRFLASNKL QIVFDFVASK GFPWDEYKLL STFPRRDVTQ LDPNKSLLEV K LFPQETLF LEAKE

UniProtKB: FAS-associated factor 1

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Macromolecule #4: Ubiquitin recognition factor in ER-associated degradation protein 1

MacromoleculeName: Ubiquitin recognition factor in ER-associated degradation protein 1
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 35.373188 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MFSFNMFDHP IPRVFQNRFS TQYRCFSVSM LAGPNDRSDV EKGGKIIMPP SALDQLSRLN ITYPMLFKLT NKNSDRMTHC GVLEFVADE GICYLPHWMM QNLLLEEGGL VQVESVNLQV ATYSKFQPQS PDFLDITNPK AVLENALRNF ACLTTGDVIA I NYNEKIYE ...String:
MFSFNMFDHP IPRVFQNRFS TQYRCFSVSM LAGPNDRSDV EKGGKIIMPP SALDQLSRLN ITYPMLFKLT NKNSDRMTHC GVLEFVADE GICYLPHWMM QNLLLEEGGL VQVESVNLQV ATYSKFQPQS PDFLDITNPK AVLENALRNF ACLTTGDVIA I NYNEKIYE LRVMETKPDK AVSIIECDMN VDFDAPLGYK EPERQVQHEE STEGEADHSG YAGELGFRAF SGSGNRLDGK KK GVEPSPS PIKPGDIKRG IPNYEFKLGK ITFIRNSRPL VKKVEEDEAG GRFVAFSGEG QSLRKKGRKP HHHHHH

UniProtKB: Ubiquitin recognition factor in ER-associated degradation protein 1

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Macromolecule #5: Transitional endoplasmic reticulum ATPase

MacromoleculeName: Transitional endoplasmic reticulum ATPase / type: protein_or_peptide / ID: 5 / Number of copies: 6 / Enantiomer: LEVO / EC number: vesicle-fusing ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 91.177781 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MASGADSKGD DLSTAILKQK NRPNRLIVDE AINEDNSVVS LSQPKMDELQ LFRGDTVLLK GKKRREAVCI VLSDDTCSDE KIRMNRVVR NNLRVRLGDV ISIQPCPDVK YGKRIHVLPI DDTVEGITGN LFEVYLKPYF LEAYRPIRKG DIFLVRGGMR A VEFKVVET ...String:
MASGADSKGD DLSTAILKQK NRPNRLIVDE AINEDNSVVS LSQPKMDELQ LFRGDTVLLK GKKRREAVCI VLSDDTCSDE KIRMNRVVR NNLRVRLGDV ISIQPCPDVK YGKRIHVLPI DDTVEGITGN LFEVYLKPYF LEAYRPIRKG DIFLVRGGMR A VEFKVVET DPSPYCIVAP DTVIHCEGEP IKREDEEESL NEVGYDDIGG CRKQLAQIKE MVELPLRHPA LFKAIGVKPP RG ILLYGPP GTGKTLIARA VANETGAFFF LINGPEIMSK LAGESESNLR KAFEEAEKNA PAIIFIDELD AIAPKREKTH GEV ERRIVS QLLTLMDGLK QRAHVIVMAA TNRPNSIDPA LRRFGRFDRE VDIGIPDATG RLEILQIHTK NMKLADDVDL EQVA NETHG HVGADLAALC SEAALQAIRK KMDLIDLEDE TIDAEVMNSL AVTMDDFRWA LSQSNPSALR ETVVEVPQVT WEDIG GLED VKRELQELVQ YPVEHPDKFL KFGMTPSKGV LFYGPPGCGK TLLAKAIANE CQANFISIKG PELLTMWFGE SEANVR EIF DKARQAAPCV LFFDELDSIA KARGGNIGDG GGAADRVINQ ILTEMDGMST KKNVFIIGAT NRPDIIDPAI LRPGRLD QL IYIPLPDEKS RVAILKANLR KSPVAKDVDL EFLAKMTNGF SGADLTEICQ RACKLAIRES IESEIRRERE RQTNPSAM E VEEDDPVPEI RRDHFEEAMR FARRSVSDND IRKYEMFAQT LQQSRGFGSF RFPSGNQGGA GPSQGSGGGT GGSVYTEDN DDDLYGVDKL AAALEHHHHH H

UniProtKB: Transitional endoplasmic reticulum ATPase

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Macromolecule #6: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #7: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / 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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Macromolecule #8: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 9 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, 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: 7.6
Details: 50 mM HEPES, pH 7.6, 150 mM KCl, 5 mM MgCl2, 2 mM ATP
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 2 / Number real images: 17244 / 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 / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 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: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 102875
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC

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