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- PDB-8uxq: Structure of Heterochromatin Protein 1 (HP1) alpha in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8uxq
TitleStructure of Heterochromatin Protein 1 (HP1) alpha in complex with an H2A.Z nucleosome
Components
  • (DNA Widom601 (208bp) ...) x 2
  • Chromobox protein homolog 5
  • Histone H2A.Z
  • Histone H2B 1.1
  • Histone H3.2
  • Histone H4
KeywordsSTRUCTURAL PROTEIN / heterochromatin / nucleosome / chromatin / GENE REGULATION
Function / homology
Function and homology information


chromocenter / histone methyltransferase complex / Transcriptional Regulation by E2F6 / site of DNA damage / histone deacetylase complex / RNA polymerase II core promoter sequence-specific DNA binding / ribonucleoprotein complex binding / heterochromatin / pericentric heterochromatin / nucleosomal DNA binding ...chromocenter / histone methyltransferase complex / Transcriptional Regulation by E2F6 / site of DNA damage / histone deacetylase complex / RNA polymerase II core promoter sequence-specific DNA binding / ribonucleoprotein complex binding / heterochromatin / pericentric heterochromatin / nucleosomal DNA binding / transcription repressor complex / methylated histone binding / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by KRAB-ZFP proteins / cellular response to estradiol stimulus / euchromatin / heterochromatin formation / kinetochore / histone deacetylase binding / cellular response to insulin stimulus / structural constituent of chromatin / nucleosome / nucleosome assembly / nuclear envelope / chromatin organization / Factors involved in megakaryocyte development and platelet production / protein-macromolecule adaptor activity / DNA-binding transcription factor binding / chromosome, telomeric region / ribonucleoprotein complex / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / DNA damage response / chromatin binding / protein-containing complex binding / nucleolus / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / : / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. ...Chromo shadow domain / Chromo shadow domain / Chromo Shadow Domain / : / Chromo domain subgroup / Chromo domain, conserved site / Chromo domain signature. / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / Chromo-like 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. / 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 / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B 1.1 / Histone H2A.Z / Chromobox protein homolog 5 / Histone H4 / Histone H3.2
Similarity search - Component
Biological speciesHomo sapiens (human)
Xenopus laevis (African clawed frog)
Mus musculus (house mouse)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.3 Å
AuthorsTan, D. / Sokolova, V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133611 United States
National Science Foundation (NSF, United States)1942049 United States
CitationJournal: To Be Published
Title: Structure of human HP1 in complex with H2A.Z nucleosome
Authors: Tan, D. / Sokolova, V.
History
DepositionNov 9, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chromobox protein homolog 5
C: Chromobox protein homolog 5
E: Histone H3.2
F: Histone H4
G: Histone H2A.Z
H: Histone H2B 1.1
K: Histone H3.2
L: Histone H4
M: Histone H2A.Z
N: Histone H2B 1.1
I: DNA Widom601 (208bp) strand1
J: DNA Widom601 (208bp) strand2


Theoretical massNumber of molelcules
Total (without water)281,47912
Polymers281,47912
Non-polymers00
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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Protein , 5 types, 10 molecules ACEKFLGMHN

#1: Protein Chromobox protein homolog 5 / Antigen p25 / Heterochromatin protein 1 homolog alpha / HP1 alpha


Mass: 22651.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CBX5, HP1A / Production host: Escherichia coli (E. coli) / References: UniProt: P45973
#2: Protein Histone H3.2 / Histone H3


Mass: 15303.930 Da / Num. of mol.: 2 / Mutation: C110A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#3: Protein Histone H4


Mass: 11263.231 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#4: Protein Histone H2A.Z / H2A/z


Mass: 13450.601 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2az1, H2afz, H2az / Production host: Escherichia coli (E. coli) / References: UniProt: P0C0S6
#5: Protein Histone H2B 1.1 / H2B1.1


Mass: 13848.097 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281

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DNA Widom601 (208bp) ... , 2 types, 2 molecules IJ

#6: DNA chain DNA Widom601 (208bp) strand1


Mass: 64456.039 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#7: DNA chain DNA Widom601 (208bp) strand2


Mass: 63988.711 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Details

Has ligand of interestY

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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: HP1alpha dimer bound to H2A.Z nucleosome / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightValue: 0.288 MDa / Experimental value: NO
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 39.2 K

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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 / Calibrated magnification: 81000 X / Nominal defocus max: 2250 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
7MDFFmodel fitting
9MDFFmodel refinement
12RELION4classification
13RELION43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 74257 / Algorithm: BACK PROJECTION / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Atomic model buildingAccession code: P45973 / Source name: AlphaFold / Type: in silico model

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