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- PDB-3qlc: Complex structure of ATRX ADD domain bound to unmodified H3 1-15 ... -

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Basic information

Entry
Database: PDB / ID: 3qlc
TitleComplex structure of ATRX ADD domain bound to unmodified H3 1-15 peptide
Components
  • Transcriptional regulator ATRX
  • peptide of Histone H3.3
KeywordsTRANSCRIPTION/STRUCTURAL PROTEIN / Zinc Finger / ATP-dependent chromatin remodeller / chromatin binding / lysine methylation / 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, subtelomeric region / chromosome organization involved in meiotic cell cycle / negative regulation of chromosome condensation / Sertoli cell development / 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, subtelomeric region / chromosome organization involved in meiotic cell cycle / negative regulation of chromosome condensation / Sertoli cell development / Barr body / regulation of centromere complex assembly / cellular response to hydroxyurea / meiotic spindle organization / chromo shadow domain binding / DNA translocase activity / condensed chromosome, centromeric region / pericentric heterochromatin formation / inner kinetochore / muscle cell differentiation / oocyte maturation / protein localization to chromosome, telomeric region / nucleosomal DNA binding / nuclear chromosome / seminiferous tubule development / nucleus organization / spermatid development / positive regulation of telomere maintenance / replication fork processing / single fertilization / subtelomeric heterochromatin formation / heterochromatin / pericentric heterochromatin / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / forebrain development / : / embryo implantation / telomere organization / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / 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 / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA 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) / 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 / NoRC negatively regulates rRNA expression / PML body / multicellular organism growth / B-WICH complex positively regulates rRNA expression / Meiotic recombination / chromatin DNA binding / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / male gonad development / osteoblast differentiation / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / 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 / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / spermatogenesis / DNA helicase / Estrogen-dependent gene expression / histone binding / transcription by RNA polymerase II / forked DNA-dependent helicase activity / single-stranded 3'-5' DNA helicase activity / four-way junction helicase activity / double-stranded DNA helicase activity / chromosome, telomeric region / cell population proliferation / nuclear body / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / Amyloid fiber formation / protein heterodimerization activity / DNA repair / chromatin binding / regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / protein-containing complex / ATP hydrolysis activity
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 / 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 / Helicase conserved C-terminal domain / Zinc finger, FYVE/PHD-type / 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 / 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 / molecular replacement / Resolution: 2.5 Å
AuthorsLi, H. / Patel, D.J.
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_sheet / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _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
B: Transcriptional regulator ATRX
C: peptide of Histone H3.3
D: peptide of Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,11210
Polymers32,7194
Non-polymers3926
Water2,054114
1
A: Transcriptional regulator ATRX
C: peptide of Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5565
Polymers16,3602
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-3 kcal/mol
Surface area7930 Å2
MethodPISA
2
B: Transcriptional regulator ATRX
D: peptide of Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5565
Polymers16,3602
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint-1 kcal/mol
Surface area7800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.607, 80.607, 136.173
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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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: 1565.797 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.9 Å3/Da / Density % sol: 68.49 % / Mosaicity: 0.25 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 24% PEG 3350, 0.1M HEPES-NaOH, 0.2M KCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 20, 2010 / Details: mirrors
RadiationMonochromator: Kohzu HLD8-24 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 18318 / % possible obs: 99.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 12.4 % / Rmerge(I) obs: 0.063 / Χ2: 1.219 / Net I/σ(I): 14.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.567.70.53211760.8481100
2.56-2.627.70.44112000.8741100
2.62-2.697.80.34212240.9371100
2.69-2.778.10.25811961199.9
2.77-2.868.20.22511780.9821100
2.86-2.9612.20.22812101.0091100
2.96-3.0814.70.212131.0491100
3.08-3.22150.13212071.1051100
3.22-3.3915.20.10711951.221100
3.39-3.6115.30.07312131.2691100
3.61-3.8815.30.0612241.2931100
3.88-4.2715.40.05612271.2911100
4.27-4.8915.30.06112201.781100
4.89-6.1614.90.05312731.331100
6.16-5012.90.04412911.505196.6

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3qln


Resolution: 2.5→38.054 Å / Occupancy max: 1 / Occupancy min: 0.73 / FOM work R set: 0.812 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 1437 7.87 %random
Rwork0.1944 ---
all0.198 18308 --
obs0.198 18264 99.76 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.487 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso max: 94.99 Å2 / Biso mean: 51.2267 Å2 / Biso min: 28.9 Å2
Baniso -1Baniso -2Baniso -3
1-1.8779 Å2-0 Å2-0 Å2
2--1.8779 Å20 Å2
3----3.7557 Å2
Refinement stepCycle: LAST / Resolution: 2.5→38.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2116 0 6 114 2236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092156
X-RAY DIFFRACTIONf_angle_d1.2062906
X-RAY DIFFRACTIONf_chiral_restr0.08310
X-RAY DIFFRACTIONf_plane_restr0.005380
X-RAY DIFFRACTIONf_dihedral_angle_d17.078798
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 (%)
2.5002-2.58950.36111590.313616671826100
2.5895-2.69320.34211420.295116501792100
2.6932-2.81570.31871490.249816241773100
2.8157-2.96410.2861450.24921652179799
2.9641-3.14970.34841120.23231682179499
3.1497-3.39280.28181350.210216801815100
3.3928-3.73390.20511450.185916821827100
3.7339-4.27360.21291370.1617111848100
4.2736-5.38190.19231480.150817081856100
5.3819-38.05820.19951650.16891771193699

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