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Basic information

Entry
Database: PDB / ID: 8q3e
TitleHigh Resolution Structure of Nucleosome Core with Bound Foamy Virus GAG Peptide
Components
  • (DNA (145-MER)) x 2
  • GLY-GLY-TYR-ASN-LEU-ARG-PRO-ARG-THR-TYR-GLN-PRO-GLN-ARG-TYR-GLY-GLY-GLY
  • Histone H2A type 1-B/E
  • Histone H2B type 1-K
  • Histone H3.1Histone H3
  • Histone H4
KeywordsDNA / Nucleosome / Viral protein / Metallopeptide conjugate / GAG peptide
Function / homology
Function and homology information


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 / epigenetic regulation of gene expression / 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 ...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 / epigenetic regulation of gene expression / 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 / gene expression / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / HATs acetylate histones / antibacterial humoral response / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / killing of cells of another organism / Estrogen-dependent gene expression / defense response to Gram-negative bacterium / chromosome, telomeric region / Ub-specific processing proteases / defense response to Gram-positive bacterium / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of cell population proliferation / protein-containing complex / DNA binding / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol
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
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B type 1-K / Histone H2A type 1-B/E / Histone H4 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
Human spumaretrovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.174 Å
AuthorsDe Falco, L. / Batchelor, L.K. / Dyson, P.J. / Davey, C.A.
Funding support Singapore, 5items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)MOE2015-T2-2-089 Singapore
Ministry of Education (MoE, Singapore)MOE-T2EP30121-0005 Singapore
Ministry of Education (MoE, Singapore)2017-T1-002-020 Singapore
Ministry of Education (MoE, Singapore)2020-T1-001-128 Singapore
Ministry of Education (MoE, Singapore)2021-T1-001-014 Singapore
CitationJournal: Rsc Adv / Year: 2024
Title: Viral peptide conjugates for metal-warhead delivery to chromatin.
Authors: Batchelor, L.K. / De Falco, L. / Dyson, P.J. / Davey, C.A.
History
DepositionAug 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
MMM: GLY-GLY-TYR-ASN-LEU-ARG-PRO-ARG-THR-TYR-GLN-PRO-GLN-ARG-TYR-GLY-GLY-GLY
AAA: Histone H3.1
BBB: Histone H4
CCC: Histone H2A type 1-B/E
DDD: Histone H2B type 1-K
EEE: Histone H3.1
FFF: Histone H4
GGG: Histone H2A type 1-B/E
HHH: Histone H2B type 1-K
III: DNA (145-MER)
JJJ: DNA (145-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,29612
Polymers179,27211
Non-polymers241
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.168, 109.638, 183.557
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 8 molecules AAAEEEBBBFFFCCCGGGDDDHHH

#2: Protein Histone H3.1 / Histone H3 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 11504.476 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, ...Gene: H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
Production host: Escherichia coli (E. coli) / References: UniProt: P68431
#3: Protein Histone H4 /


Mass: 9990.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, ...Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4C16, H4-16, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#4: Protein Histone H2A type 1-B/E / Histone H2A.2 / Histone H2A/a / Histone H2A/m


Mass: 11766.779 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2AC4, H2AFM, HIST1H2AB, H2AC8, H2AFA, HIST1H2AE / Production host: Escherichia coli (E. coli) / References: UniProt: P04908
#5: Protein Histone H2B type 1-K / H2B K / HIRA-interacting protein 1


Mass: 10607.174 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2BC12, H2BFT, HIRIP1, HIST1H2BK / Production host: Escherichia coli (E. coli) / References: UniProt: O60814

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DNA chain , 2 types, 2 molecules IIIJJJ

#6: DNA chain DNA (145-MER)


Mass: 44749.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#7: DNA chain DNA (145-MER)


Mass: 44740.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Protein/peptide / Non-polymers , 2 types, 2 molecules MMM

#1: Protein/peptide GLY-GLY-TYR-ASN-LEU-ARG-PRO-ARG-THR-TYR-GLN-PRO-GLN-ARG-TYR-GLY-GLY-GLY


Mass: 2043.228 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide is connected at the N-terminus to a long polyethylene glycol linker, which is in turn connected to a gold(I)-based compound [Au(4-diphenylphosphanyl-benzoic acid)Cl]. Only the ...Details: The peptide is connected at the N-terminus to a long polyethylene glycol linker, which is in turn connected to a gold(I)-based compound [Au(4-diphenylphosphanyl-benzoic acid)Cl]. Only the peptide, GGYNLRPRTYQPQRYGG (C-terminal G has an amide group in place of the carboxylate group), is incorporated into the model.
Source: (synth.) Human spumaretrovirus
#8: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Details

Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.27 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Buffers containing MnCl2, KCl and K-cacodylate [pH 6.0]

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Data collection

DiffractionMean temperature: 98 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.04 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.17→48.852 Å / Num. obs: 112248 / % possible obs: 98.2 % / Redundancy: 12.2 % / CC1/2: 1 / Net I/σ(I): 20.3
Reflection shellResolution: 2.17→2.29 Å / Num. unique obs: 14533 / CC1/2: 0.573

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.174→48.852 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.264 / WRfactor Rwork: 0.228 / SU B: 8.266 / SU ML: 0.195 / Average fsc free: 0.8283 / Average fsc work: 0.8343 / Cross valid method: FREE R-VALUE / ESU R: 0.231 / ESU R Free: 0.198
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2697 2303 2.056 %3
Rwork0.2343 109713 --
all0.235 ---
obs-112016 98.108 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 80.065 Å2
Baniso -1Baniso -2Baniso -3
1-1.289 Å2-0 Å2-0 Å2
2---3.34 Å20 Å2
3---2.051 Å2
Refinement stepCycle: LAST / Resolution: 2.174→48.852 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6257 5939 1 0 12197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01213004
X-RAY DIFFRACTIONr_bond_other_d0.0020.0189652
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.39918797
X-RAY DIFFRACTIONr_angle_other_deg1.492.07722429
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.285777
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.45418.418373
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.019151211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8971591
X-RAY DIFFRACTIONr_chiral_restr0.0840.21697
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0210496
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022856
X-RAY DIFFRACTIONr_nbd_refined0.2060.22770
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2140.29972
X-RAY DIFFRACTIONr_nbtor_refined0.2060.25635
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.24835
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2178
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0930.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1850.214
X-RAY DIFFRACTIONr_nbd_other0.2340.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2980.21
X-RAY DIFFRACTIONr_mcbond_it5.2775.6073136
X-RAY DIFFRACTIONr_mcbond_other5.2655.6053135
X-RAY DIFFRACTIONr_mcangle_it7.3318.3813905
X-RAY DIFFRACTIONr_mcangle_other7.338.3843906
X-RAY DIFFRACTIONr_scbond_it7.2639.9889868
X-RAY DIFFRACTIONr_scbond_other7.2619.9889867
X-RAY DIFFRACTIONr_scangle_it10.62214.96914892
X-RAY DIFFRACTIONr_scangle_other10.62114.96914893
X-RAY DIFFRACTIONr_lrange_it13.67495.96816715
X-RAY DIFFRACTIONr_lrange_other13.67495.96916714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.174-2.230.4441240.4226128X-RAY DIFFRACTION74.74
2.23-2.2920.3941560.3887985X-RAY DIFFRACTION99.9632
2.292-2.3580.3521790.3447707X-RAY DIFFRACTION99.9873
2.358-2.430.3441690.3317568X-RAY DIFFRACTION99.9871
2.43-2.510.3421450.3017297X-RAY DIFFRACTION99.9866
2.51-2.5980.3321410.2947093X-RAY DIFFRACTION100
2.598-2.6960.3461390.2856837X-RAY DIFFRACTION99.9857
2.696-2.8060.331360.2666579X-RAY DIFFRACTION99.9851
2.806-2.9310.2351160.2286334X-RAY DIFFRACTION100
2.931-3.0740.311160.2446085X-RAY DIFFRACTION100
3.074-3.240.361260.2755770X-RAY DIFFRACTION99.9661
3.24-3.4360.2781160.2745469X-RAY DIFFRACTION99.9821
3.436-3.6730.3131330.2745128X-RAY DIFFRACTION99.981
3.673-3.9670.278890.244816X-RAY DIFFRACTION99.9592
3.967-4.3450.232880.2044436X-RAY DIFFRACTION99.9779
4.345-4.8560.241840.1794044X-RAY DIFFRACTION100
4.856-5.6050.228880.2013577X-RAY DIFFRACTION100
5.605-6.8580.266710.2033055X-RAY DIFFRACTION100
6.858-9.6730.172390.1572417X-RAY DIFFRACTION100
9.673-48.8520.18480.171387X-RAY DIFFRACTION99.0338

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