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- PDB-8xgc: Structure of yeast replisome associated with FACT and histone hex... -

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Entry
Database: PDB / ID: 8xgc
TitleStructure of yeast replisome associated with FACT and histone hexamer, Composite map
Components
  • (DNA polymerase epsilon ...) x 2
  • (DNA replication complex GINS protein ...) x 4
  • (DNA replication licensing factor ...) x 5
  • (FACT complex subunit ...) x 2
  • Cell division control protein 45
  • Chromosome segregation in meiosis protein 3
  • DNA (39-MER)
  • DNA (51-MER)
  • DNA polymerase alpha-binding protein
  • Histone H2A.1
  • Histone H2B.2
  • Histone H3
  • Histone H4
  • Mediator of replication checkpoint protein 1
  • Minichromosome maintenance protein 5
  • Topoisomerase 1-associated factor 1
KeywordsREPLICATION / Replisome / FACT / histone hexamer
Function / homology
Function and homology information


Regulation of TP53 Activity through Phosphorylation / regulation of sister chromatid cohesion / : / establishment of sister chromatid cohesion / DNA-templated DNA replication maintenance of fidelity / gene conversion / FACT complex / Unwinding of DNA / maintenance of DNA repeat elements / regulation of nuclear cell cycle DNA replication ...Regulation of TP53 Activity through Phosphorylation / regulation of sister chromatid cohesion / : / establishment of sister chromatid cohesion / DNA-templated DNA replication maintenance of fidelity / gene conversion / FACT complex / Unwinding of DNA / maintenance of DNA repeat elements / regulation of nuclear cell cycle DNA replication / DNA replication initiation / replication fork arrest / Cul8-RING ubiquitin ligase complex / meiotic chromosome segregation / HATs acetylate histones / RNA polymerase I upstream activating factor complex / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / epsilon DNA polymerase complex / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / nuclear DNA replication / regulation of chromatin organization / premeiotic DNA replication / Assembly of the ORC complex at the origin of replication / HDACs deacetylate histones / replication fork protection complex / SUMO binding / pre-replicative complex assembly involved in nuclear cell cycle DNA replication / anaphase-promoting complex binding / nucleotide-excision repair, DNA gap filling / mitotic DNA replication / Activation of the pre-replicative complex / DNA replication checkpoint signaling / CMG complex / establishment of mitotic sister chromatid cohesion / nuclear pre-replicative complex / DNA replication proofreading / nucleosome organization / Termination of translesion DNA synthesis / Activation of ATR in response to replication stress / DNA replication preinitiation complex / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / single-stranded DNA 3'-5' DNA exonuclease activity / MCM complex / mitotic DNA replication checkpoint signaling / Oxidative Stress Induced Senescence / double-strand break repair via break-induced replication / mitotic DNA replication initiation / cellular response to osmotic stress / RMTs methylate histone arginines / single-stranded DNA helicase activity / mitotic intra-S DNA damage checkpoint signaling / SUMOylation of chromatin organization proteins / regulation of DNA-templated DNA replication initiation / silent mating-type cassette heterochromatin formation / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / mitotic sister chromatid cohesion / TP53 Regulates Transcription of DNA Repair Genes / nuclear chromosome / RNA Polymerase II Pre-transcription Events / 3'-5' DNA helicase activity / DNA strand elongation involved in DNA replication / leading strand elongation / RNA Polymerase I Promoter Escape / mitotic G2 DNA damage checkpoint signaling / positive regulation of transcription by RNA polymerase I / nucleolar large rRNA transcription by RNA polymerase I / replication fork processing / nuclear replication fork / Estrogen-dependent gene expression / rRNA transcription / DNA replication origin binding / Dual incision in TC-NER / positive regulation of RNA polymerase II transcription preinitiation complex assembly / DNA replication initiation / Ub-specific processing proteases / positive regulation of transcription initiation by RNA polymerase II / error-prone translesion synthesis / subtelomeric heterochromatin formation / base-excision repair, gap-filling / telomere maintenance / DNA helicase activity / nuclear periphery / replication fork / meiotic cell cycle / transcription elongation by RNA polymerase II / helicase activity / base-excision repair / double-strand break repair via nonhomologous end joining / DNA-templated DNA replication / structural constituent of chromatin / nucleosome / heterochromatin formation
Similarity search - Function
DNA replication checkpoint mediator, MRC1 domain / MRC1-like domain / : / SSRP1 PH domain / Claspin / FACT complex subunit Spt16, peptidase M24-like domain / : / FACT complex subunit SPT16, C-terminal domain / FACT complex subunit SSRP1/POB3 / SSRP1, dimerization domain ...DNA replication checkpoint mediator, MRC1 domain / MRC1-like domain / : / SSRP1 PH domain / Claspin / FACT complex subunit Spt16, peptidase M24-like domain / : / FACT complex subunit SPT16, C-terminal domain / FACT complex subunit SSRP1/POB3 / SSRP1, dimerization domain / FACT complex subunit SSRP1/POB3, N-terminal PH domain / SSRP1 domain superfamily / : / Structure-specific recognition protein (SSRP1) / POB3-like N-terminal PH domain / : / FACT complex subunit SPT16 PH-like domain / FACT complex subunit Spt16 domain / FACT complex subunit (SPT16/CDC68) / FACT complex subunit (SPT16/CDC68) / FACT complex subunit Spt16, N-terminal lobe domain / FACT complex subunit Spt16 / FACT complex subunit SPT16 N-terminal lobe domain / FACT complex subunit SPT16 N-terminal lobe domain / Chromosome segregation in meiosis protein 3 / TIPIN/Csm3/Swi3 / Replication Fork Protection Component Swi3 / DNA polymerase epsilon, subunit B / Timeless, N-terminal / Timeless / Timeless protein / Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain / Histone chaperone Rttp106-like, middle domain / Histone chaperone Rttp106-like / : / DNA polymerase alpha-binding protein Ctf4, C-terminal domain / Minichromosome loss protein Mcl1, middle region / Minichromosome loss protein, Mcl1, middle region / : / : / DNA polymerase epsilon catalytic subunit A, thumb domain / Zinc finger domain of DNA polymerase-epsilon / : / PSF1 C-terminal domain / DNA polymerase epsilon, catalytic subunit A, C-terminal / DNA polymerase epsilon catalytic subunit / Domain of unknown function (DUF1744) / DUF1744 / : / PSF3 N-terminal domain / CDC45 family / 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 / Creatinase/Aminopeptidase P/Spt16, N-terminal / DNA polymerase alpha/delta/epsilon, subunit B / DNA polymerase alpha/epsilon subunit B / : / MCM5, C-terminal domain / 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 / DNA polymerase family B, thumb domain / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / DNA polymerase family B, exonuclease domain / DNA-directed DNA polymerase, family B, exonuclease domain
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / DNA replication licensing factor MCM2 / Histone H3 / DNA replication licensing factor MCM7 / Histone H2B.2 / Histone H4 / Histone H2A.1 / DNA polymerase epsilon catalytic subunit A ...ADENOSINE-5'-DIPHOSPHATE / DNA / DNA (> 10) / DNA replication licensing factor MCM2 / Histone H3 / DNA replication licensing factor MCM7 / Histone H2B.2 / Histone H4 / Histone H2A.1 / DNA polymerase epsilon catalytic subunit A / DNA replication licensing factor MCM3 / DNA polymerase epsilon subunit B / Mediator of replication checkpoint protein 1 / Minichromosome maintenance protein 5 / DNA replication licensing factor MCM4 / FACT complex subunit SPT16 / DNA replication licensing factor MCM6 / Topoisomerase 1-associated factor 1 / DNA polymerase alpha-binding protein / DNA replication complex GINS protein SLD5 / FACT complex subunit POB3 / Chromosome segregation in meiosis protein 3 / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsLi, N. / Gao, Y. / Yu, D. / Gao, N. / Zhai, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nature / Year: 2024
Title: Parental histone transfer caught at the replication fork.
Authors: Ningning Li / Yuan Gao / Yujie Zhang / Daqi Yu / Jianwei Lin / Jianxun Feng / Jian Li / Zhichun Xu / Yingyi Zhang / Shangyu Dang / Keda Zhou / Yang Liu / Xiang David Li / Bik Kwoon Tye / ...Authors: Ningning Li / Yuan Gao / Yujie Zhang / Daqi Yu / Jianwei Lin / Jianxun Feng / Jian Li / Zhichun Xu / Yingyi Zhang / Shangyu Dang / Keda Zhou / Yang Liu / Xiang David Li / Bik Kwoon Tye / Qing Li / Ning Gao / Yuanliang Zhai /
Abstract: In eukaryotes, DNA compacts into chromatin through nucleosomes. Replication of the eukaryotic genome must be coupled to the transmission of the epigenome encoded in the chromatin. Here we report cryo- ...In eukaryotes, DNA compacts into chromatin through nucleosomes. Replication of the eukaryotic genome must be coupled to the transmission of the epigenome encoded in the chromatin. Here we report cryo-electron microscopy structures of yeast (Saccharomyces cerevisiae) replisomes associated with the FACT (facilitates chromatin transactions) complex (comprising Spt16 and Pob3) and an evicted histone hexamer. In these structures, FACT is positioned at the front end of the replisome by engaging with the parental DNA duplex to capture the histones through the middle domain and the acidic carboxyl-terminal domain of Spt16. The H2A-H2B dimer chaperoned by the carboxyl-terminal domain of Spt16 is stably tethered to the H3-H4 tetramer, while the vacant H2A-H2B site is occupied by the histone-binding domain of Mcm2. The Mcm2 histone-binding domain wraps around the DNA-binding surface of one H3-H4 dimer and extends across the tetramerization interface of the H3-H4 tetramer to the binding site of Spt16 middle domain before becoming disordered. This arrangement leaves the remaining DNA-binding surface of the other H3-H4 dimer exposed to additional interactions for further processing. The Mcm2 histone-binding domain and its downstream linker region are nested on top of Tof1, relocating the parental histones to the replisome front for transfer to the newly synthesized lagging-strand DNA. Our findings offer crucial structural insights into the mechanism of replication-coupled histone recycling for maintaining epigenetic inheritance.
History
DepositionDec 15, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
2: DNA replication licensing factor MCM2
3: DNA replication licensing factor MCM3
4: DNA replication licensing factor MCM4
5: Minichromosome maintenance protein 5
6: DNA replication licensing factor MCM6
7: DNA replication licensing factor MCM7
8: DNA polymerase epsilon catalytic subunit A
9: DNA polymerase epsilon subunit B
A: DNA replication complex GINS protein PSF1
B: DNA replication complex GINS protein PSF2
C: DNA replication complex GINS protein PSF3
D: DNA replication complex GINS protein SLD5
E: Cell division control protein 45
F: DNA polymerase alpha-binding protein
G: DNA polymerase alpha-binding protein
H: DNA polymerase alpha-binding protein
I: Topoisomerase 1-associated factor 1
J: Chromosome segregation in meiosis protein 3
K: Mediator of replication checkpoint protein 1
L: FACT complex subunit SPT16
M: FACT complex subunit POB3
N: Histone H3
O: Histone H4
P: Histone H2A.1
Q: Histone H2B.2
R: Histone H3
S: Histone H4
X: DNA (51-MER)
Y: DNA (39-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,034,40541
Polymers2,031,81229
Non-polymers2,59412
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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DNA replication licensing factor ... , 5 types, 5 molecules 23467

#1: Protein DNA replication licensing factor MCM2


Mass: 98911.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q1S9
#2: Protein DNA replication licensing factor MCM3 / Minichromosome maintenance protein 3


Mass: 107653.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P24279, DNA helicase
#3: Protein DNA replication licensing factor MCM4 / Cell division control protein 54


Mass: 105138.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P30665, DNA helicase
#5: Protein DNA replication licensing factor MCM6 / Minichromosome maintenance protein 6


Mass: 113110.211 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53091, DNA helicase
#6: Protein DNA replication licensing factor MCM7


Mass: 95049.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A8H4BTB2

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Protein , 10 types, 14 molecules 5EFGHIJKNROSPQ

#4: Protein Minichromosome maintenance protein 5 / Cell division control protein 46


Mass: 86505.734 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P29496, DNA helicase
#13: Protein Cell division control protein 45


Mass: 74324.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q08032
#14: Protein DNA polymerase alpha-binding protein / Chromosome replication protein CHL15 / Chromosome transmission fidelity protein 4 / Protein POB1


Mass: 104543.391 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q01454
#15: Protein Topoisomerase 1-associated factor 1


Mass: 141296.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P53840
#16: Protein Chromosome segregation in meiosis protein 3


Mass: 36402.590 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04659
#17: Protein Mediator of replication checkpoint protein 1 / DNA replication checkpoint mediator MRC1


Mass: 124516.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P25588
#20: Protein Histone H3


Mass: 15391.007 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q536
#21: Protein Histone H4


Mass: 11395.390 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02309
#22: Protein Histone H2A.1


Mass: 14013.177 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P04911
#23: Protein Histone H2B.2


Mass: 14264.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P02294

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DNA polymerase epsilon ... , 2 types, 2 molecules 89

#7: Protein DNA polymerase epsilon catalytic subunit A / 3'-5' exodeoxyribonuclease / DNA polymerase II subunit A


Mass: 255992.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P21951, DNA-directed DNA polymerase, Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters
#8: Protein DNA polymerase epsilon subunit B / DNA polymerase II subunit 2


Mass: 78425.852 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P24482

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DNA replication complex GINS protein ... , 4 types, 4 molecules ABCD

#9: Protein DNA replication complex GINS protein PSF1 / Partner of Sld five 1


Mass: 24230.576 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12488
#10: Protein DNA replication complex GINS protein PSF2


Mass: 29341.074 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#11: Protein DNA replication complex GINS protein PSF3 / Partner of Sld five 3


Mass: 21977.135 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12146
#12: Protein DNA replication complex GINS protein SLD5


Mass: 33983.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q03406

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FACT complex subunit ... , 2 types, 2 molecules LM

#18: Protein FACT complex subunit SPT16 / Cell division control protein 68 / Facilitates chromatin transcription complex subunit SPT16 / ...Cell division control protein 68 / Facilitates chromatin transcription complex subunit SPT16 / Suppressor of Ty protein 16


Mass: 118776.984 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32558
#19: Protein FACT complex subunit POB3 / Facilitates chromatin transcription complex subunit POB3


Mass: 63068.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q04636

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DNA chain , 2 types, 2 molecules XY

#24: DNA chain DNA (51-MER)


Mass: 15689.072 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)
#25: DNA chain DNA (39-MER)


Mass: 11935.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast)

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Non-polymers , 2 types, 12 molecules

#26: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#27: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Endogenous replisomes / Type: COMPLEX / Entity ID: #1-#25 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 524000 / Symmetry type: POINT

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