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- EMDB-25777: Structure of VRK1 C-terminal tail bound to nucleosome core particle -

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Basic information

Entry
Database: EMDB / ID: EMD-25777
TitleStructure of VRK1 C-terminal tail bound to nucleosome core particle
Map dataMap of crosslinked VRK1-nucleosome complex
Sample
  • Complex: Structure of VRK1 C-terminal tail bound to nucleosome core particle
    • Complex: Histone H3.2, Histone H4, Histone H2A type 1, Histone H2B type 1-C/E/F/G/I, Serine/threonine-protein kinase VRK1
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B type 1-C/E/F/G/I
      • Protein or peptide: Serine/threonine-protein kinase VRK1
    • Complex: DNA
      • DNA: WIDOM 601 DNA (185-MER)
      • DNA: WIDOM 601 DNA (185-MER)
Keywordsnucleosome / chromatin / NUCLEAR PROTEIN / STRUCTURAL PROTEIN-DNA-TRANSFERASE complex
Function / homology
Function and homology information


Golgi disassembly / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / histone H3S10 kinase activity / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin ...Golgi disassembly / histone H3T3 kinase activity / Nuclear Envelope Breakdown / positive regulation of protein localization to chromatin / mitotic nuclear membrane disassembly / Golgi stack / Initiation of Nuclear Envelope (NE) Reformation / histone H3S10 kinase activity / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / 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 / 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 / Interleukin-7 signaling / 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 / innate immune response in mucosa / PRC2 methylates histones and DNA / Defective pyroptosis / 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 / NoRC negatively regulates rRNA expression / G2/M DNA damage checkpoint / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / DNA Damage/Telomere Stress Induced Senescence / Metalloprotease DUBs / 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 / UCH proteinases / nucleosome / antimicrobial humoral immune response mediated by antimicrobial peptide / E3 ubiquitin ligases ubiquitinate target proteins / 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 / Factors involved in megakaryocyte development and platelet production / kinase activity / Processing of DNA double-strand break ends / HATs acetylate histones / antibacterial humoral response / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / protein autophosphorylation / non-specific serine/threonine protein kinase / Ub-specific processing proteases / protein kinase activity / defense response to Gram-positive bacterium / Amyloid fiber formation / protein heterodimerization activity / cell division / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / nucleolus / protein kinase binding / enzyme binding / signal transduction / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / membrane / identical protein binding
Similarity search - Function
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 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 / 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 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Histone H2A type 1 / Histone H4 / Histone H2B type 1-C/E/F/G/I / Histone H3.2 / Serine/threonine-protein kinase VRK1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsSpangler CJ / Budziszewski GR
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133498 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM119999 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)F99CA253730 United States
CitationJournal: Nucleic Acids Res / Year: 2022
Title: Multivalent DNA and nucleosome acidic patch interactions specify VRK1 mitotic localization and activity.
Authors: Gabrielle R Budziszewski / Yani Zhao / Cathy J Spangler / Katarzyna M Kedziora / Michael R Williams / Dalal N Azzam / Aleksandra Skrajna / Yuka Koyama / Andrew P Cesmat / Holly C Simmons / ...Authors: Gabrielle R Budziszewski / Yani Zhao / Cathy J Spangler / Katarzyna M Kedziora / Michael R Williams / Dalal N Azzam / Aleksandra Skrajna / Yuka Koyama / Andrew P Cesmat / Holly C Simmons / Eyla C Arteaga / Joshua D Strauss / Dmitri Kireev / Robert K McGinty /
Abstract: A key role of chromatin kinases is to phosphorylate histone tails during mitosis to spatiotemporally regulate cell division. Vaccinia-related kinase 1 (VRK1) is a serine-threonine kinase that ...A key role of chromatin kinases is to phosphorylate histone tails during mitosis to spatiotemporally regulate cell division. Vaccinia-related kinase 1 (VRK1) is a serine-threonine kinase that phosphorylates histone H3 threonine 3 (H3T3) along with other chromatin-based targets. While structural studies have defined how several classes of histone-modifying enzymes bind to and function on nucleosomes, the mechanism of chromatin engagement by kinases is largely unclear. Here, we paired cryo-electron microscopy with biochemical and cellular assays to demonstrate that VRK1 interacts with both linker DNA and the nucleosome acidic patch to phosphorylate H3T3. Acidic patch binding by VRK1 is mediated by an arginine-rich flexible C-terminal tail. Homozygous missense and nonsense mutations of this acidic patch recognition motif in VRK1 are causative in rare adult-onset distal spinal muscular atrophy. We show that these VRK1 mutations interfere with nucleosome acidic patch binding, leading to mislocalization of VRK1 during mitosis, thus providing a potential new molecular mechanism for pathogenesis.
History
DepositionDec 21, 2021-
Header (metadata) releaseMay 4, 2022-
Map releaseMay 4, 2022-
UpdateFeb 28, 2024-
Current statusFeb 28, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25777.png

Downloads & links

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Map

FileDownload / File: emd_25777.map.gz / Format: CCP4 / Size: 137.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of crosslinked VRK1-nucleosome complex
Voxel sizeX=Y=Z: 0.91 Å
Density
Contour LevelBy AUTHOR: 0.017
Minimum - Maximum-0.05580498 - 0.12431903
Average (Standard dev.)0.00012849456 (±0.0022779466)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions330330330
Spacing330330330
CellA=B=C: 300.30002 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Structure of VRK1 C-terminal tail bound to nucleosome core particle

EntireName: Structure of VRK1 C-terminal tail bound to nucleosome core particle
Components
  • Complex: Structure of VRK1 C-terminal tail bound to nucleosome core particle
    • Complex: Histone H3.2, Histone H4, Histone H2A type 1, Histone H2B type 1-C/E/F/G/I, Serine/threonine-protein kinase VRK1
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B type 1-C/E/F/G/I
      • Protein or peptide: Serine/threonine-protein kinase VRK1
    • Complex: DNA
      • DNA: WIDOM 601 DNA (185-MER)
      • DNA: WIDOM 601 DNA (185-MER)

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Supramolecule #1: Structure of VRK1 C-terminal tail bound to nucleosome core particle

SupramoleculeName: Structure of VRK1 C-terminal tail bound to nucleosome core particle
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7

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Supramolecule #2: Histone H3.2, Histone H4, Histone H2A type 1, Histone H2B type 1-...

SupramoleculeName: Histone H3.2, Histone H4, Histone H2A type 1, Histone H2B type 1-C/E/F/G/I, Serine/threonine-protein kinase VRK1
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4, #7
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: DNA

SupramoleculeName: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.289904 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVGLFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.2

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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: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.990342 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKA RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLGK VTIAQGGVLP NIQAVLLPKK TESHHKAKGK

UniProtKB: Histone H2A type 1

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Macromolecule #4: Histone H2B type 1-C/E/F/G/I

MacromoleculeName: Histone H2B type 1-C/E/F/G/I / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.806018 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSVY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSSK

UniProtKB: Histone H2B type 1-C/E/F/G/I

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Macromolecule #7: Serine/threonine-protein kinase VRK1

MacromoleculeName: Serine/threonine-protein kinase VRK1 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.696223 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSMPRVKAAQ AGRQSSAKRH LAEQFAVGEI ITDMAKKEWK VGLPIGQGGF GCIYLADMNS SESVGSDAPC VVKVEPSDNG PLFTELKFY QRAAKPEQIQ KWIRTRKLKY LGVPKYWGSG LHDKNGKSYR FMIMDRFGSD LQKIYEANAK RFSRKTVLQL S LRILDILE ...String:
GSMPRVKAAQ AGRQSSAKRH LAEQFAVGEI ITDMAKKEWK VGLPIGQGGF GCIYLADMNS SESVGSDAPC VVKVEPSDNG PLFTELKFY QRAAKPEQIQ KWIRTRKLKY LGVPKYWGSG LHDKNGKSYR FMIMDRFGSD LQKIYEANAK RFSRKTVLQL S LRILDILE YIHEHEYVHG DIKASNLLLN YKNPDQVYLV DYGLAYRYCP EGVHKEYKED PKRCHDGTIE FTSIDAHNGV AP SRRGDLE ILGYCMIQWL TGHLPWEDNL KDPKYVRDSK IRYRENIASL MDKCFPEKNK PGEIAKYMET VKLLDYTEKP LYE NLRDIL LQGLKAIGSK DDGKLDLSVV ENGGLKAKTI TKKRKKEIEE SKEPGVEDTE WSNTQTEEAI QTRSRTRKRV QK

UniProtKB: Serine/threonine-protein kinase VRK1

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Macromolecule #5: WIDOM 601 DNA (185-MER)

MacromoleculeName: WIDOM 601 DNA (185-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 57.400559 KDa
SequenceString: (DA)(DT)(DC)(DG)(DC)(DT)(DG)(DT)(DT)(DC) (DA)(DA)(DT)(DA)(DC)(DA)(DT)(DG)(DC)(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) ...String:
(DA)(DT)(DC)(DG)(DC)(DT)(DG)(DT)(DT)(DC) (DA)(DA)(DT)(DA)(DC)(DA)(DT)(DG)(DC)(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)(DC)(DG)(DG)(DC) (DC)(DG)(DC)(DG)(DT)(DA)(DT)(DA) (DG) (DG)(DG)(DA)(DT)

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Macromolecule #6: WIDOM 601 DNA (185-MER)

MacromoleculeName: WIDOM 601 DNA (185-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 56.831191 KDa
SequenceString: (DA)(DT)(DC)(DC)(DC)(DT)(DA)(DT)(DA)(DC) (DG)(DC)(DG)(DG)(DC)(DC)(DG)(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) ...String:
(DA)(DT)(DC)(DC)(DC)(DT)(DA)(DT)(DA)(DC) (DG)(DC)(DG)(DG)(DC)(DC)(DG)(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)(DG)(DC)(DA)(DT)(DG)(DT) (DA)(DT)(DT)(DG)(DA)(DA)(DC)(DA) (DG) (DC)(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

BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 8000 / Average electron dose: 52.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

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

6esf


Details: low pass filtered at 50 angstroms
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 460962
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7jo9


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-7tan:
Structure of VRK1 C-terminal tail bound to nucleosome core particle

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