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- EMDB-9250: CENP-A nucleosome bound by two copies of CENP-C(CD) and one copy ... -

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Basic information

Entry
Database: EMDB / ID: EMD-9250
TitleCENP-A nucleosome bound by two copies of CENP-C(CD) and one copy CENP-N(NT)
Map dataCENP-A nucleosome bound by two copies of CENP-C(CD) and one copy CENP-N(NT)
Sample
  • Organelle or cellular component: CENP-A chromatin complex bound with CENP-C and CENP-N of CCAN kinetochore components
    • Protein or peptide: Histone H3-like centromeric protein A
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-C
    • Protein or peptide: Histone H2B type 2-F
    • DNA: DNA/RNA (147-MER)
    • DNA: DNA/RNA (147-MER)
    • Protein or peptide: Centromere protein C
    • Protein or peptide: Centromere protein N
Keywordscentromere / CENP-A / kinetochore / nucleosome / NUCLEAR PROTEIN
Function / homology
Function and homology information


spindle attachment to meiosis I kinetochore / inner kinetochore / centromeric DNA binding / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / kinetochore assembly / condensed chromosome, centromeric region / establishment of mitotic spindle orientation / mitotic cytokinesis ...spindle attachment to meiosis I kinetochore / inner kinetochore / centromeric DNA binding / CENP-A containing chromatin assembly / protein localization to chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / kinetochore assembly / condensed chromosome, centromeric region / establishment of mitotic spindle orientation / mitotic cytokinesis / chromosome, centromeric region / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / pericentric heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / Resolution of Sister Chromatid Cohesion / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere organization / RNA Polymerase I Promoter Opening / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / HCMV Late Events / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / PRC2 methylates histones and DNA / Defective pyroptosis / chromosome segregation / RHO GTPases Activate Formins / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / kinetochore / PKMTs methylate histone lysines / RMTs methylate histone arginines / Meiotic recombination / Pre-NOTCH Transcription and Translation / nucleosome assembly / Activation of anterior HOX genes in hindbrain development during early embryogenesis / HCMV Early Events / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / Separation of Sister Chromatids / UCH proteinases / nucleosome / mitotic cell cycle / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Processing of DNA double-strand break ends / HATs acetylate histones / midbody / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / nuclear body / Ub-specific processing proteases / Amyloid fiber formation / protein heterodimerization activity / cell division / negative regulation of cell population proliferation / chromatin binding / protein-containing complex / DNA binding / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / identical protein binding / nucleus / cytosol
Similarity search - Function
CENP-C, middle DNMT3B-binding domain / Centromere assembly component CENP-C middle DNMT3B-binding region / Kinetochore assembly subunit CENP-C, N-terminal domain / Kinetochore assembly subunit CENP-C N-terminal / Mif2/CENP-C cupin domain / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C like / Centromere protein Chl4/mis15/CENP-N / Kinetochore protein CHL4 like / RmlC-like cupin domain superfamily ...CENP-C, middle DNMT3B-binding domain / Centromere assembly component CENP-C middle DNMT3B-binding region / Kinetochore assembly subunit CENP-C, N-terminal domain / Kinetochore assembly subunit CENP-C N-terminal / Mif2/CENP-C cupin domain / Centromere protein C/Mif2/cnp3 / Mif2/CENP-C like / Centromere protein Chl4/mis15/CENP-N / Kinetochore protein CHL4 like / RmlC-like cupin domain superfamily / 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. / Histone H4 / Histone H4 / RmlC-like jelly roll fold / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H3-like centromeric protein A / Histone H4 / Centromere protein C / Histone H2B type 2-F / Histone H2A type 1-C / Centromere protein N
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsAllu PK / Black BE
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM123233 GM130302 United States
CitationJournal: Curr Biol / Year: 2019
Title: Structure of the Human Core Centromeric Nucleosome Complex.
Authors: Praveen Kumar Allu / Jennine M Dawicki-McKenna / Trevor Van Eeuwen / Moriya Slavin / Merav Braitbard / Chen Xu / Nir Kalisman / Kenji Murakami / Ben E Black /
Abstract: Centromeric nucleosomes are at the interface of the chromosome and the kinetochore that connects to spindle microtubules in mitosis. The core centromeric nucleosome complex (CCNC) harbors the ...Centromeric nucleosomes are at the interface of the chromosome and the kinetochore that connects to spindle microtubules in mitosis. The core centromeric nucleosome complex (CCNC) harbors the histone H3 variant, CENP-A, and its binding proteins, CENP-C (through its central domain; CD) and CENP-N (through its N-terminal domain; NT). CENP-C can engage nucleosomes through two domains: the CD and the CENP-C motif (CM). CENP-C is part of the CCNC by virtue of its high specificity for CENP-A nucleosomes and ability to stabilize CENP-A at the centromere. CENP-C is thought to engage a neighboring nucleosome, either one containing conventional H3 or CENP-A, and a crystal structure of a nucleosome complex containing two copies of CENP-C was reported. Recent structures containing a single copy of CENP-N bound to the CENP-A nucleosome in the absence of CENP-C were reported. Here, we find that one copy of CENP-N is lost for every two copies of CENP-C on centromeric chromatin just prior to kinetochore formation. We present the structures of symmetric and asymmetric forms of the CCNC that vary in CENP-N stoichiometry. Our structures explain how the central domain of CENP-C achieves its high specificity for CENP-A nucleosomes and how CENP-C and CENP-N sandwich the histone H4 tail. The natural centromeric DNA path in our structures corresponds to symmetric surfaces for CCNC assembly, deviating from what is observed in prior structures using artificial sequences. At mitosis, we propose that CCNC asymmetry accommodates its asymmetric connections at the chromosome/kinetochore interface. VIDEO ABSTRACT.
History
DepositionOct 23, 2018-
Header (metadata) releaseNov 7, 2018-
Map releaseJul 24, 2019-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
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  • Atomic models: PDB-6muo
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9250.png

Downloads & links

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Map

FileDownload / File: emd_9250.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCENP-A nucleosome bound by two copies of CENP-C(CD) and one copy CENP-N(NT)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 200 pix.
= 212. Å		1.06 Å/pix.
x 200 pix.
= 212. Å		1.06 Å/pix.
x 200 pix.
= 212. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.09117952 - 0.10781192
Average (Standard dev.)0.0005523025 (±0.0044145933)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 211.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z212.000212.000212.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0910.1080.001

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Supplemental data

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Additional map: CENP-A nucleosome bound by two copies of CENP-C(CD)...

Fileemd_9250_additional.map
AnnotationCENP-A nucleosome bound by two copies of CENP-C(CD) and one copy CENP-N(NT)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CENP-A chromatin complex bound with CENP-C and CENP-N of CCAN kin...

EntireName: CENP-A chromatin complex bound with CENP-C and CENP-N of CCAN kinetochore components
Components
  • Organelle or cellular component: CENP-A chromatin complex bound with CENP-C and CENP-N of CCAN kinetochore components
    • Protein or peptide: Histone H3-like centromeric protein A
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-C
    • Protein or peptide: Histone H2B type 2-F
    • DNA: DNA/RNA (147-MER)
    • DNA: DNA/RNA (147-MER)
    • Protein or peptide: Centromere protein C
    • Protein or peptide: Centromere protein N

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Supramolecule #1: CENP-A chromatin complex bound with CENP-C and CENP-N of CCAN kin...

SupramoleculeName: CENP-A chromatin complex bound with CENP-C and CENP-N of CCAN kinetochore components
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#8
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 276 KDa

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Macromolecule #1: Histone H3-like centromeric protein A

MacromoleculeName: Histone H3-like centromeric protein A / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.993037 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
HQHSRRRQGW LKEIRKLQKS THLLIRKLPF SRLAREICVK FTRGVDFNWQ AQALLALQEA AEAFLVHLFE DAYLLTLHAG RVTLFPKDV QLARRIRGLE EGL

UniProtKB: Histone H3-like centromeric protein A

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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: Homo sapiens (human)
Molecular weightTheoretical: 10.604521 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
KGLGKGGAKR HRKVLRDNIQ GITKPAIRRL ARRGGVKRIS GLIYEETRGV LKVFLENVIR DAVTYTEHAK RKTVTAMDVV YALKRQGRT LYGFG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1-C

MacromoleculeName: Histone H2A type 1-C / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.494393 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
KAKSRSSRAG LQFPVGRVHR LLRKGNYAER VGAGAPVYLA AVLEYLTAEI LELAGNAARD NKKTRIIPRH LQLAIRNDEE LNKLLGRVT IAQGGVLPNI QSVLLP

UniProtKB: Histone H2A type 1-C

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Macromolecule #4: Histone H2B type 2-F

MacromoleculeName: Histone H2B type 2-F / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.249723 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
RKESYSVYVY KVLKQVHPDT GISSKAMGIM NSFVNDIFER IAGEASRLAH YNKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTKY TSS

UniProtKB: Histone H2B type 2-F

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Macromolecule #7: Centromere protein C

MacromoleculeName: Centromere protein C / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.508834 KDa
SequenceString:
TKSRRISRRP SDWWVVKSEE

UniProtKB: Centromere protein C

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Macromolecule #8: Centromere protein N

MacromoleculeName: Centromere protein N / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.052885 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MDETVAEFIK RTILKIPMNE LTTILKAWDF LSENQLQTVN FRQRKESVVQ HLIHLCEEKR ASISDAALLD IIYMQFHQHQ KVWDVFQMS KGPGEDVDLF DMKQFKNSFK KILQRALKNV TVSFRETEEN AVWIRIAWGT QYTKPNQYKP TYVVYYSQTP Y AFTSSSML ...String:
MDETVAEFIK RTILKIPMNE LTTILKAWDF LSENQLQTVN FRQRKESVVQ HLIHLCEEKR ASISDAALLD IIYMQFHQHQ KVWDVFQMS KGPGEDVDLF DMKQFKNSFK KILQRALKNV TVSFRETEEN AVWIRIAWGT QYTKPNQYKP TYVVYYSQTP Y AFTSSSML RRNTPLLGQA LTIASKHHQI VKMDLRSRYL DSLKAIVFKQ YNQT

UniProtKB: Centromere protein N

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Macromolecule #5: DNA/RNA (147-MER)

MacromoleculeName: DNA/RNA (147-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.141918 KDa
SequenceString: (DA)(DT)(DC)(DA)(DA)(DA)(DT)(DA)(DT)(DC) (DC)(DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA) (DT)(DT)(DC)(DT)(DA)(DC)(DC)(DA)(DA) (DA)(DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT) (DG) (DG)(DA)(DA)(DA)(DC)(DT) ...String:
(DA)(DT)(DC)(DA)(DA)(DA)(DT)(DA)(DT)(DC) (DC)(DA)(DC)(DC)(DT)(DG)(DC)(DA)(DG)(DA) (DT)(DT)(DC)(DT)(DA)(DC)(DC)(DA)(DA) (DA)(DA)(DG)(DT)(DG)(DT)(DA)(DT)(DT)(DT) (DG) (DG)(DA)(DA)(DA)(DC)(DT)(DG)(DC) (DT)(DC)(DC)(DA)(DT)(DC)(DA)(DA)(DA)(DA) (DG)(DG) (DC)(DA)(DT)(DG)(DT)(DT)(DC) (DA)(DG)(DC)(DT)(DC)(DT)(DG)(DT)(DG)(DA) (DG)(DT)(DG) (DA)(DA)(DA)(DC)(DT)(DC) (DC)(DA)(DT)(DC)(DA)(DT)(DC)(DA)(DC)(DA) (DA)(DA)(DG)(DA) (DA)(DT)(DA)(DT)(DT) (DC)(DT)(DG)(DA)(DG)(DA)(DA)(DT)(DG)(DC) (DT)(DT)(DC)(DC)(DG) (DT)(DT)(DT)(DG) (DC)(DC)(DT)(DT)(DT)(DT)(DA)(DT)(DA)(DT) (DG)(DA)(DA)(DC)(DT)(DT) (DC)(DC)(DT) (DC)(DG)(DA)(DT)

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Macromolecule #6: DNA/RNA (147-MER)

MacromoleculeName: DNA/RNA (147-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.582188 KDa
SequenceString: (DA)(DT)(DC)(DG)(DA)(DG)(DG)(DA)(DA)(DG) (DT)(DT)(DC)(DA)(DT)(DA)(DT)(DA)(DA)(DA) (DA)(DG)(DG)(DC)(DA)(DA)(DA)(DC)(DG) (DG)(DA)(DA)(DG)(DC)(DA)(DT)(DT)(DC)(DT) (DC) (DA)(DG)(DA)(DA)(DT)(DA) ...String:
(DA)(DT)(DC)(DG)(DA)(DG)(DG)(DA)(DA)(DG) (DT)(DT)(DC)(DA)(DT)(DA)(DT)(DA)(DA)(DA) (DA)(DG)(DG)(DC)(DA)(DA)(DA)(DC)(DG) (DG)(DA)(DA)(DG)(DC)(DA)(DT)(DT)(DC)(DT) (DC) (DA)(DG)(DA)(DA)(DT)(DA)(DT)(DT) (DC)(DT)(DT)(DT)(DG)(DT)(DG)(DA)(DT)(DG) (DA)(DT) (DG)(DG)(DA)(DG)(DT)(DT)(DT) (DC)(DA)(DC)(DT)(DC)(DA)(DC)(DA)(DG)(DA) (DG)(DC)(DT) (DG)(DA)(DA)(DC)(DA)(DT) (DG)(DC)(DC)(DT)(DT)(DT)(DT)(DG)(DA)(DT) (DG)(DG)(DA)(DG) (DC)(DA)(DG)(DT)(DT) (DT)(DC)(DC)(DA)(DA)(DA)(DT)(DA)(DC)(DA) (DC)(DT)(DT)(DT)(DT) (DG)(DG)(DT)(DA) (DG)(DA)(DA)(DT)(DC)(DT)(DG)(DC)(DA)(DG) (DG)(DT)(DG)(DG)(DA)(DT) (DA)(DT)(DT) (DT)(DG)(DA)(DT)

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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

Concentration0.5 mg/mL
BufferpH: 7.5 / Details: 10 mM HEPES, 50 mN NaCl, 1 mM EDTA, 1mM DTT
GridModel: C-flat-1.2/1.3 4C / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 30.0 kPa / Details: unspecified
VitrificationCryogen name: ETHANE / Instrument: LEICA EM CPC / Details: Blot for 8 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 2 / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3an2

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationSoftware - Name: RELION (ver. 2.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 113950
FSC plot (resolution estimation)

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