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- EMDB-30456: NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp N... -

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Basic information

Entry
Database: EMDB / ID: EMD-30456
TitleNSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode)
Map data
Sample
  • Complex: NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode)
    • Complex: Histone H3, H4, H2A, H2B
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: DNA
      • DNA: DNA (168-MER)
      • DNA: DNA (168-MER)
    • Complex: NSD3
      • Protein or peptide: Histone-lysine N-methyltransferase NSD3
  • Ligand: S-ADENOSYLMETHIONINE
  • Ligand: ZINC ION
Keywordsnucleosome complex / histone methyltransferase / DNA / Gene reguration / GENE REGULATION
Function / homology
Function and homology information


[histone H3]-lysine4 N-dimethyltransferase / [histone H3]-lysine27 N-dimethyltransferase / histone H3K4 dimethyltransferase activity / histone H3K27 dimethyltransferase activity / histone H3K27 trimethyltransferase activity / histone H3K36 methyltransferase activity / transcription regulator activator activity / histone H3 methyltransferase activity / PKMTs methylate histone lysines / structural constituent of chromatin ...[histone H3]-lysine4 N-dimethyltransferase / [histone H3]-lysine27 N-dimethyltransferase / histone H3K4 dimethyltransferase activity / histone H3K27 dimethyltransferase activity / histone H3K27 trimethyltransferase activity / histone H3K36 methyltransferase activity / transcription regulator activator activity / histone H3 methyltransferase activity / PKMTs methylate histone lysines / structural constituent of chromatin / nucleosome / nucleosome assembly / methylation / protein heterodimerization activity / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / DNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
: / : / : / : / : / : / NSD, Cys-His rich domain / NSD Cys-His rich domain / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger / Histone-lysine N-methyltransferase NSD-like, variant PHD zinc finger ...: / : / : / : / : / : / NSD, Cys-His rich domain / NSD Cys-His rich domain / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger / Histone-lysine N-methyltransferase NSD-like, variant PHD zinc finger / Histone-lysine N-methyltransferase NSD-like, PHD zinc finger 1 / : / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / Zinc finger PHD-type signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Zinc finger, FYVE/PHD-type / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H2A / Histone H2B / Histone H3 / Histone-lysine N-methyltransferase NSD3
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / Homo sapiens (human) / Xenopus tropicalis (tropical clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.15 Å
AuthorsLi W / Tian W
Funding support China, United States, 6 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31870725 China
National Natural Science Foundation of China (NSFC)31570729 China
Other governmentFundamental Research Funds for the Central Universities (2017EYT19) China
Other governmentMemorial Sloan-Kettering Cancer Center Core grant P30CA008748 United States
National Institutes of Health/National Library of Medicine (NIH/NLM)R01GM079641 United States
Other governmentBasic Research grant from Shenzhen government (JCYJ20180302174213122) China
CitationJournal: Nature / Year: 2021
Title: Molecular basis of nucleosomal H3K36 methylation by NSD methyltransferases.
Authors: Wanqiu Li / Wei Tian / Gang Yuan / Pujuan Deng / Deepanwita Sengupta / Zhongjun Cheng / Yinghua Cao / Jiahao Ren / Yan Qin / Yuqiao Zhou / Yulin Jia / Or Gozani / Dinshaw J Patel / Zhanxin Wang /
Abstract: Histone methyltransferases of the nuclear receptor-binding SET domain protein (NSD) family, including NSD1, NSD2 and NSD3, have crucial roles in chromatin regulation and are implicated in oncogenesis. ...Histone methyltransferases of the nuclear receptor-binding SET domain protein (NSD) family, including NSD1, NSD2 and NSD3, have crucial roles in chromatin regulation and are implicated in oncogenesis. NSD enzymes exhibit an autoinhibitory state that is relieved by binding to nucleosomes, enabling dimethylation of histone H3 at Lys36 (H3K36). However, the molecular basis that underlies this mechanism is largely unknown. Here we solve the cryo-electron microscopy structures of NSD2 and NSD3 bound to mononucleosomes. We find that binding of NSD2 and NSD3 to mononucleosomes causes DNA near the linker region to unwrap, which facilitates insertion of the catalytic core between the histone octamer and the unwrapped segment of DNA. A network of DNA- and histone-specific contacts between NSD2 or NSD3 and the nucleosome precisely defines the position of the enzyme on the nucleosome, explaining the specificity of methylation to H3K36. Intermolecular contacts between NSD proteins and nucleosomes are altered by several recurrent cancer-associated mutations in NSD2 and NSD3. NSDs that contain these mutations are catalytically hyperactive in vitro and in cells, and their ectopic expression promotes the proliferation of cancer cells and the growth of xenograft tumours. Together, our research provides molecular insights into the nucleosome-based recognition and histone-modification mechanisms of NSD2 and NSD3, which could lead to strategies for therapeutic targeting of proteins of the NSD family.
History
DepositionAug 14, 2020-
Header (metadata) releaseOct 21, 2020-
Map releaseOct 21, 2020-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0184
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0184
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7crq
  • Surface level: 0.0184
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30456.png

Downloads & links

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Map

FileDownload / File: emd_30456.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 216 pix.
= 233.28 Å		1.08 Å/pix.
x 216 pix.
= 233.28 Å		1.08 Å/pix.
x 216 pix.
= 233.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0184 / Movie #1: 0.0184
Minimum - Maximum-0.1267722 - 0.21992825
Average (Standard dev.)0.00046952371 (±0.006824801)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions216216216
Spacing216216216
CellA=B=C: 233.28001 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.081.081.08
M x/y/z216216216
origin x/y/z0.0000.0000.000
length x/y/z233.280233.280233.280
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ304304304
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS216216216
D min/max/mean-0.1270.2200.000

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Supplemental data

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Sample components

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Entire : NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp N...

EntireName: NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode)
Components
  • Complex: NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode)
    • Complex: Histone H3, H4, H2A, H2B
      • Protein or peptide: Histone H3
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A
      • Protein or peptide: Histone H2B
    • Complex: DNA
      • DNA: DNA (168-MER)
      • DNA: DNA (168-MER)
    • Complex: NSD3
      • Protein or peptide: Histone-lysine N-methyltransferase NSD3
  • Ligand: S-ADENOSYLMETHIONINE
  • Ligand: ZINC ION

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Supramolecule #1: NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp N...

SupramoleculeName: NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Molecular weightTheoretical: 300 KDa

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Supramolecule #2: Histone H3, H4, H2A, H2B

SupramoleculeName: Histone H3, H4, H2A, H2B / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #4: NSD3

SupramoleculeName: NSD3 / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #7
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.223779 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGV(NLE)KPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQ DFK TDLRFQSSAV (NLE)ALQEASEAY LVGLFEDTNL CGIHAKRVTI (NLE)PKDIQLARR IRGERA

UniProtKB: Histone H3

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.978241 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

UniProtKB: Histone H2A

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Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus tropicalis (tropical clawed frog)
Molecular weightTheoretical: 13.524752 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTKYT SAK

UniProtKB: Histone H2B

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Macromolecule #7: Histone-lysine N-methyltransferase NSD3

MacromoleculeName: Histone-lysine N-methyltransferase NSD3 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
EC number: Transferases; Transferring one-carbon groups; Methyltransferases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 85.454359 KDa
Recombinant expressionOrganism: Baculovirus transfer vector pFASTBAC1
SequenceString: VSDVQSMDSS LSRRGTGMSK KDTVCQICES SGDSLIPCEG ECCKHFHLEC LGLASLPDSK FICMECKTGQ HPCFSCKVSG KDVKRCSVG ACGKFYHEAC VRKFPTAIFE SKGFRCPQHC CSACSMEKDI HKASKGRMMR CLRCPVAYHS GDACIAAGSM L VSSYILIC ...String:
VSDVQSMDSS LSRRGTGMSK KDTVCQICES SGDSLIPCEG ECCKHFHLEC LGLASLPDSK FICMECKTGQ HPCFSCKVSG KDVKRCSVG ACGKFYHEAC VRKFPTAIFE SKGFRCPQHC CSACSMEKDI HKASKGRMMR CLRCPVAYHS GDACIAAGSM L VSSYILIC SNHSKRSSNS SAVNVGFCFV CARGLIVQDH SDPMFSSYAY KSHYLLNESN RAELMKLPMI PSSSASKKKC EK GGRLLCC ESCPASFHPE CLSIEMPEGC WNCNDCKAGK KLHYKQIVWV KLGNYRWWPA EICNPRSVPL NIQGLKHDLG DFP VFFFGS HDYYWVHQGR VFPYVEGDKS FAEGQTSINK TFKKALEEAA KRFQELKAQR ESKEALEIEK NSRKPPPYKH IKAN KVIGK VQIQVADLSE IPRCNCKPAD ENPCGLESEC LNRMLQYECH PQVCPAGDRC QNQCFTKRLY PDAEIIKTER RGWGL RTKR SIKKGEFVNE YVGELIDKEE CRLRIKRAHE NSVTNFYMLT VTKDRIIDAG PKGNYSRFMN HSCNPNCEAQ KWTVNG DVR VGLFALCDIP AGMELTFNYN LDCLGNGRTE CHCGADNCSG FLGVRPKSAC ASTNEEKAKN AKLKQKRRKI KTEPKQM HE DYCFQCGDGG ELVMCDKKDC PKAYHLLCLN LTQPPYGKWE CPWHQCDECS SAAVSFCEFC PHSFCKDHEK GALVPSAL E GRLCCSEHDP MAPVSPEYWS KIKCKWESQD HGEEVKE

UniProtKB: Histone-lysine N-methyltransferase NSD3

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Macromolecule #5: DNA (168-MER)

MacromoleculeName: DNA (168-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 57.488551 KDa
SequenceString: (DA)(DT)(DC)(DG)(DG)(DG)(DT)(DG)(DA)(DT) (DG)(DC)(DC)(DC)(DG)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT) (DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG) (DA) (DG)(DG)(DC)(DC)(DG)(DC) ...String:
(DA)(DT)(DC)(DG)(DG)(DG)(DT)(DG)(DA)(DT) (DG)(DC)(DC)(DC)(DG)(DA)(DT)(DC)(DC)(DC) (DC)(DT)(DG)(DG)(DA)(DG)(DA)(DA)(DT) (DC)(DC)(DC)(DG)(DG)(DT)(DG)(DC)(DC)(DG) (DA) (DG)(DG)(DC)(DC)(DG)(DC)(DT)(DC) (DA)(DA)(DT)(DT)(DG)(DG)(DT)(DC)(DG)(DT) (DA)(DG) (DA)(DC)(DA)(DG)(DC)(DT)(DC) (DT)(DA)(DG)(DC)(DA)(DC)(DC)(DG)(DC)(DT) (DT)(DA)(DA) (DA)(DC)(DG)(DC)(DA)(DC) (DG)(DT)(DA)(DC)(DG)(DC)(DG)(DC)(DT)(DG) (DT)(DC)(DC)(DC) (DC)(DC)(DG)(DC)(DG) (DT)(DT)(DT)(DT)(DA)(DA)(DC)(DC)(DG)(DC) (DC)(DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT) (DT)(DA)(DC)(DT)(DC)(DC)(DC)(DT)(DA)(DG) (DT)(DC)(DT)(DC)(DC)(DA) (DG)(DG)(DC) (DA)(DC)(DG)(DT)(DG)(DT)(DC)(DA)(DG)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DC) (DA)(DT) (DC)(DC)(DT)(DG)(DT)(DT)(DC)(DC)(DA)(DG) (DT)(DG)(DC)(DC)(DG)(DG)(DT)(DG) (DT) (DC)(DG)(DC)(DG)(DA)(DT)

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Macromolecule #6: DNA (168-MER)

MacromoleculeName: DNA (168-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 57.982918 KDa
SequenceString: (DA)(DT)(DC)(DG)(DC)(DG)(DA)(DC)(DA)(DC) (DC)(DG)(DG)(DC)(DA)(DC)(DT)(DG)(DG)(DA) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA) (DC) (DA)(DC)(DG)(DT)(DG)(DC) ...String:
(DA)(DT)(DC)(DG)(DC)(DG)(DA)(DC)(DA)(DC) (DC)(DG)(DG)(DC)(DA)(DC)(DT)(DG)(DG)(DA) (DA)(DC)(DA)(DG)(DG)(DA)(DT)(DG)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DC)(DT)(DG)(DA) (DC) (DA)(DC)(DG)(DT)(DG)(DC)(DC)(DT) (DG)(DG)(DA)(DG)(DA)(DC)(DT)(DA)(DG)(DG) (DG)(DA) (DG)(DT)(DA)(DA)(DT)(DC)(DC) (DC)(DC)(DT)(DT)(DG)(DG)(DC)(DG)(DG)(DT) (DT)(DA)(DA) (DA)(DA)(DC)(DG)(DC)(DG) (DG)(DG)(DG)(DG)(DA)(DC)(DA)(DG)(DC)(DG) (DC)(DG)(DT)(DA) (DC)(DG)(DT)(DG)(DC) (DG)(DT)(DT)(DT)(DA)(DA)(DG)(DC)(DG)(DG) (DT)(DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC) (DT)(DG)(DT)(DC)(DT)(DA)(DC)(DG)(DA)(DC) (DC)(DA)(DA)(DT)(DT)(DG) (DA)(DG)(DC) (DG)(DG)(DC)(DC)(DT)(DC)(DG)(DG)(DC)(DA) (DC)(DC)(DG)(DG)(DG)(DA)(DT) (DT)(DC) (DT)(DC)(DC)(DA)(DG)(DG)(DG)(DG)(DA)(DT) (DC)(DG)(DG)(DG)(DC)(DA)(DT)(DC) (DA) (DC)(DC)(DC)(DG)(DA)(DT)

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Macromolecule #8: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 8 / Number of copies: 2 / Formula: SAM
Molecular weightTheoretical: 398.437 Da
Chemical component information

ChemComp-SAM:
S-ADENOSYLMETHIONINE

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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

Concentration0.3 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details: blotted for 3 s before being plunged into liquid ethane.
DetailsThe sample was monodisperse.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
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
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 281815
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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