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- PDB-5fb1: Crystal Structure of a PHD finger bound to histone H3 K9me3 peptide -

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Basic information

Entry
Database: PDB / ID: 5fb1
TitleCrystal Structure of a PHD finger bound to histone H3 K9me3 peptide
Components
  • Nuclear autoantigen Sp-100
  • Peptide from Histone H3
KeywordsTRANSCRIPTION/STRUCTURAL PROTEIN / zinc finger protein / bromodomain / TRANSCRIPTION-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


regulation of Fas signaling pathway / maintenance of protein location / chromo shadow domain binding / negative regulation of viral transcription / response to type I interferon / negative regulation of protein export from nucleus / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endothelial cell migration / negative regulation of DNA binding / type I interferon-mediated signaling pathway ...regulation of Fas signaling pathway / maintenance of protein location / chromo shadow domain binding / negative regulation of viral transcription / response to type I interferon / negative regulation of protein export from nucleus / regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of endothelial cell migration / negative regulation of DNA binding / type I interferon-mediated signaling pathway / response to type II interferon / type II interferon-mediated signaling pathway / regulation of angiogenesis / response to retinoic acid / SUMOylation of DNA damage response and repair proteins / Chromatin modifying enzymes / retinoic acid receptor signaling pathway / telomere organization / Interleukin-7 signaling / telomere maintenance / RNA Polymerase I Promoter Opening / response to cytokine / Assembly of the ORC complex at the origin of replication / nuclear periphery / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA damage response, signal transduction by p53 class mediator / DNA methylation / Condensation of Prophase Chromosomes / positive regulation of DNA-binding transcription factor activity / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / epigenetic regulation of gene expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / negative regulation of DNA-binding transcription factor activity / RNA Polymerase I Promoter Escape / 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 / HDMs demethylate histones / NoRC negatively regulates rRNA expression / PML body / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / kinase binding / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / Interferon gamma signaling / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / nuclear body / cadherin binding / protein domain specific binding / Amyloid fiber formation / protein heterodimerization activity / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleolus / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / nucleus / membrane / cytoplasm
Similarity search - Function
HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily / HMG-box domain ...HSR domain / Nuclear body protein Sp110/Sp140/Sp140L / HSR domain / HSR domain profile. / SAND domain / SAND domain / SAND domain profile. / SAND domain / SAND-like domain superfamily / HMG-box domain / HMG (high mobility group) box / HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / Bromodomain-like / Histone Acetyltransferase; Chain A / 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 / Up-down Bundle / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
MALONATE ION / Histone H3 / Nuclear autoantigen Sp-100 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsLi, H. / Zhang, X.
Funding support China, 1items
OrganizationGrant numberCountry
Major State Basic Research Development Program2015CB910503 China
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Multifaceted Histone H3 Methylation and Phosphorylation Readout by the Plant Homeodomain Finger of Human Nuclear Antigen Sp100C
Authors: Zhang, X. / Zhao, D. / Xiong, X. / He, Z. / Li, H.
History
DepositionDec 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Oct 4, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear autoantigen Sp-100
C: Peptide from Histone H3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3655
Polymers23,1322
Non-polymers2333
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint1 kcal/mol
Surface area11030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.840, 102.964, 44.955
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Nuclear autoantigen Sp-100 / SP100 nuclear antigen


Mass: 21566.572 Da / Num. of mol.: 1 / Fragment: UNP residues 696-878 / Mutation: M826T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SP100 / Plasmid: pET28b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P23497
#2: Protein/peptide Peptide from Histone H3


Mass: 1565.797 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: chemically synthesized H3 peptide 1-15 with K9me3 modification
Source: (synth.) Homo sapiens (human) / References: UniProt: K7EMV3, UniProt: P68431*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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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: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M sodium citrate/citric acid, pH 5.5, 10% 2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 31, 2014 / Details: mirrors
RadiationMonochromator: double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 14943 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 24.97 Å2 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.047 / Rrim(I) all: 0.125 / Χ2: 1.456 / Net I/av σ(I): 22.3 / Net I/σ(I): 7.4 / Num. measured all: 105585
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.147.20.6657380.8990.2650.7171.159100
2.14-2.187.20.5887220.8980.2350.6341.133100
2.18-2.227.20.5637250.9220.2240.6071.119100
2.22-2.267.20.4527340.9370.1810.4881.143100
2.26-2.317.20.3887410.9650.1540.4181.168100
2.31-2.377.20.3497320.960.1390.3761.17100
2.37-2.427.30.3127220.9660.1240.3361.18299.9
2.42-2.497.30.2817490.9770.1110.3021.162100
2.49-2.567.20.2217230.9840.0880.2381.156100
2.56-2.657.20.2027480.9890.0810.2181.15100
2.65-2.747.20.1767310.9890.070.1891.16100
2.74-2.857.20.1527310.990.0610.1641.214100
2.85-2.987.20.1357520.9920.0540.1451.288100
2.98-3.147.10.1237500.9950.050.1331.712100
3.14-3.3370.1117450.9930.0450.122.03499.9
3.33-3.596.90.0917440.9950.0380.0992.388100
3.59-3.956.70.0767600.9960.0320.0832.706100
3.95-4.526.80.0597780.9980.0240.0642.049100
4.52-5.76.80.0467810.9990.0190.0491.49999.9
5.7-506.50.0388370.9990.0160.0421.63599.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
HKL-2000data reduction
AutoSolphasing
PHENIX1.10_2155: ???refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.1→34.24 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2198 713 4.78 %
Rwork0.1666 14193 -
obs0.1692 14906 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.23 Å2 / Biso mean: 34.1269 Å2 / Biso min: 13.41 Å2
Refinement stepCycle: final / Resolution: 2.1→34.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1508 0 9 155 1672
Biso mean--43.26 41.66 -
Num. residues----182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061550
X-RAY DIFFRACTIONf_angle_d0.8172083
X-RAY DIFFRACTIONf_chiral_restr0.049214
X-RAY DIFFRACTIONf_plane_restr0.005274
X-RAY DIFFRACTIONf_dihedral_angle_d17.214947
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1002-2.26230.2441420.185427732915
2.2623-2.48990.19711400.165528022942
2.4899-2.85010.22971150.165728092924
2.8501-3.59020.23691570.170728312988
3.5902-34.24440.20651590.160429783137
Refinement TLS params.Method: refined / Origin x: 14.3955 Å / Origin y: 17.7576 Å / Origin z: -19.2156 Å
111213212223313233
T0.1608 Å2-0.002 Å20.003 Å2-0.1505 Å20.0137 Å2--0.157 Å2
L1.2823 °20.5393 °2-0.2108 °2-1.158 °2-0.5029 °2--1.0328 °2
S0.0049 Å °-0.0127 Å °-0.286 Å °-0.0123 Å °-0.0949 Å °-0.184 Å °0.0071 Å °0.1026 Å °-0.0044 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA695 - 875
2X-RAY DIFFRACTION1allB1 - 2
3X-RAY DIFFRACTION1allC1 - 8
4X-RAY DIFFRACTION1allD1
5X-RAY DIFFRACTION1allS1 - 155

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