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- PDB-3qla: Hexagonal complex structure of ATRX ADD bound to H3K9me3 peptide -

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Basic information

Entry
Database: PDB / ID: 3qla
TitleHexagonal complex structure of ATRX ADD bound to H3K9me3 peptide
Components
  • Transcriptional regulator ATRX
  • peptide of Histone H3.3
KeywordsTRANSCRIPTION/STRUCTURAL PROTEIN / zinc finger / transcription / histone / lysine trimethylation / nuclear protein / HISTONE-BINDING PROTEIN / TRANSCRIPTION-STRUCTURAL PROTEIN complex
Function / homology
Function and homology information


post-embryonic forelimb morphogenesis / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / positive regulation of nuclear cell cycle DNA replication / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / chromosome organization involved in meiotic cell cycle / chromosome, subtelomeric region / Sertoli cell development / negative regulation of chromosome condensation / Barr body ...post-embryonic forelimb morphogenesis / Defective Inhibition of DNA Recombination at Telomere Due to DAXX Mutations / Defective Inhibition of DNA Recombination at Telomere Due to ATRX Mutations / positive regulation of nuclear cell cycle DNA replication / negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric / chromosome organization involved in meiotic cell cycle / chromosome, subtelomeric region / Sertoli cell development / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / meiotic spindle organization / cellular response to hydroxyurea / DNA translocase activity / muscle cell differentiation / chromo shadow domain binding / pericentric heterochromatin formation / positive regulation of telomere maintenance / inner kinetochore / condensed chromosome, centromeric region / ATP-dependent chromatin remodeler activity / oocyte maturation / protein localization to chromosome, telomeric region / nuclear chromosome / nucleus organization / seminiferous tubule development / replication fork processing / DNA damage response, signal transduction by p53 class mediator / spermatid development / subtelomeric heterochromatin formation / single fertilization / RNA polymerase II core promoter sequence-specific DNA binding / heterochromatin / pericentric heterochromatin / Replacement of protamines by nucleosomes in the male pronucleus / nucleosomal DNA binding / forebrain development / Inhibition of DNA recombination at telomere / methylated histone binding / telomere organization / RNA Polymerase I Promoter Opening / embryo implantation / Assembly of the ORC complex at the origin of replication / DNA methylation / helicase activity / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / PRC2 methylates histones and DNA / Defective pyroptosis / 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 / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / B-WICH complex positively regulates rRNA expression / multicellular organism growth / chromatin DNA binding / PML body / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / osteoblast differentiation / structural constituent of chromatin / male gonad development / nucleosome / nucleosome assembly / chromatin organization / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / histone binding / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / spermatogenesis / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / DNA helicase / cell population proliferation / transcription by RNA polymerase II / chromosome, telomeric region / nuclear body / chromatin remodeling / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / DNA repair / chromatin binding / regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / metal ion binding
Similarity search - Function
ATRX, ADD domain / Cysteine Rich ADD domain / ADD domain / ADD domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Histone H3 signature 1. / Helicase conserved C-terminal domain ...ATRX, ADD domain / Cysteine Rich ADD domain / ADD domain / ADD domain profile. / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Histone H3 signature 1. / Helicase conserved C-terminal domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Zinc finger, FYVE/PHD-type / Histone-fold / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / Transcriptional regulator ATRX / Histone H3.3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsXiang, B. / Li, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: ATRX ADD domain links an atypical histone methylation recognition mechanism to human mental-retardation syndrome
Authors: Iwase, S. / Xiang, B. / Ghosh, S. / Ren, T. / Lewis, P.W. / Cochrane, J.C. / Allis, C.D. / Picketts, D.J. / Patel, D.J. / Li, H. / Shi, Y.
History
DepositionFeb 2, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator ATRX
C: peptide of Histone H3.3
D: Transcriptional regulator ATRX
F: peptide of Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,23511
Polymers32,8034
Non-polymers4327
Water8,485471
1
A: Transcriptional regulator ATRX
C: peptide of Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,6376
Polymers16,4022
Non-polymers2354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-5 kcal/mol
Surface area7670 Å2
MethodPISA
2
D: Transcriptional regulator ATRX
F: peptide of Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5985
Polymers16,4022
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-4 kcal/mol
Surface area7270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.709, 66.709, 131.641
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Transcriptional regulator ATRX / ATP-dependent helicase ATRX / X-linked helicase II / X-linked nuclear protein / XNP / Znf-HX


Mass: 14793.869 Da / Num. of mol.: 2 / Fragment: N-terminal ADD domain, UNP residues 167-289 / Mutation: K251R, F284Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATRX, RAD54L, XH2 / Plasmid: pGEX6p / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: P46100, DNA helicase
#2: Protein/peptide peptide of Histone H3.3


Mass: 1607.877 Da / Num. of mol.: 2 / Fragment: N-terminal tail, UNP residues 2-16 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.58 Å3/Da / Density % sol: 52.28 % / Mosaicity: 0.171 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: 14% PEG 4000, 0.1M MES, 0.2M KCL, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.97924 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 2, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 43055 / % possible obs: 98.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.7 % / Rmerge(I) obs: 0.083 / Χ2: 0.619 / Net I/σ(I): 5.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.639.30.56621410.471197.3
1.63-1.669.70.47221050.494197.5
1.66-1.699.70.4321100.489197.5
1.69-1.729.70.37821400.477197.8
1.72-1.769.70.31921420.475197.9
1.76-1.89.70.27421520.477198
1.8-1.859.70.24321130.497198.2
1.85-1.99.70.20221510.522198.1
1.9-1.959.70.18221240.531198.3
1.95-2.029.70.1521600.557198.6
2.02-2.099.70.12321390.593198.6
2.09-2.179.70.11421620.603198.9
2.17-2.279.70.10521620.63198.7
2.27-2.399.80.09421570.644199.1
2.39-2.549.80.08521710.663199.1
2.54-2.749.70.07221630.693199.3
2.74-3.019.80.06221850.739199.4
3.01-3.459.80.04721700.81199.5
3.45-4.349.80.03821930.86199.5
4.34-509.60.04222151.105198.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
DENZOdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3QLN

3qln


Resolution: 1.6→28.596 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.9151 / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1786 2093 5.03 %random
Rwork0.1572 ---
all0.1583 43639 --
obs0.1583 41649 95.44 %-
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 58.19 Å2 / Biso mean: 21.3995 Å2 / Biso min: 7.16 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2125 0 7 471 2603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152220
X-RAY DIFFRACTIONf_angle_d1.3653003
X-RAY DIFFRACTIONf_chiral_restr0.08315
X-RAY DIFFRACTIONf_plane_restr0.007386
X-RAY DIFFRACTIONf_dihedral_angle_d14.422841
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5998-1.6570.22351800.21283710389089
1.657-1.72340.20172040.17543775397991
1.7234-1.80180.1891870.16273895408293
1.8018-1.89680.18232150.16413858407394
1.8968-2.01560.17662170.15993935415295
2.0156-2.17110.18762530.15643950420397
2.1711-2.38950.17722350.15854006424197
2.3895-2.73510.16542120.15094093430599
2.7351-3.4450.17622040.14674126433099
3.445-28.60040.16821860.15242084394100

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