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- PDB-4tmp: Crystal structure of AF9 YEATS bound to H3K9ac peptide -

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Basic information

Entry
Database: PDB / ID: 4tmp
TitleCrystal structure of AF9 YEATS bound to H3K9ac peptide
Components
  • ALA-ARG-THR-LYS-GLN-THR-ALA-ARG-ALY-SER-THR
  • Protein AF-9
KeywordsTRANSCRIPTION / complex / histone modification / immunoglobin fold
Function / homology
Function and homology information


modification-dependent protein binding / regulation of stem cell division / segment specification / regulation of chromatin organization / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / muscle cell differentiation / pericentric heterochromatin formation ...modification-dependent protein binding / regulation of stem cell division / segment specification / regulation of chromatin organization / negative regulation of chromosome condensation / Barr body / regulation of centromere complex assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / muscle cell differentiation / pericentric heterochromatin formation / inner kinetochore / oocyte maturation / anterior/posterior pattern specification / nucleus organization / spermatid development / single fertilization / subtelomeric heterochromatin formation / hematopoietic stem cell differentiation / RNA polymerase II core promoter sequence-specific DNA binding / nucleosomal DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / Inhibition of DNA recombination at telomere / telomere organization / embryo implantation / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / DNA methylation / Condensation of Prophase Chromosomes / transcription elongation factor complex / 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 / lysine-acetylated histone binding / 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 / negative regulation of canonical Wnt signaling pathway / B-WICH complex positively regulates rRNA expression / multicellular organism growth / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / osteoblast differentiation / Transcriptional regulation of granulopoiesis / structural constituent of chromatin / male gonad development / nucleosome / nucleosome assembly / chromosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / gene expression / histone binding / Senescence-Associated Secretory Phenotype (SASP) / positive regulation of cell growth / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / cell population proliferation / chromosome, telomeric region / molecular adaptor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / Amyloid fiber formation / chromatin binding / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / cytosol
Similarity search - Function
YEATS domain / AF-9, ANC1 homology domain / ANC1 homology domain (AHD) / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 ...YEATS domain / AF-9, ANC1 homology domain / ANC1 homology domain (AHD) / YEATS / YEATS superfamily / YEATS family / YEATS domain profile. / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein AF-9 / Histone H3.3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsLi, H. / Li, Y. / Wang, H. / Ren, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2011CB965300 China
CitationJournal: Cell / Year: 2014
Title: AF9 YEATS Domain Links Histone Acetylation to DOT1L-Mediated H3K79 Methylation.
Authors: Li, Y. / Wen, H. / Xi, Y. / Tanaka, K. / Wang, H. / Peng, D. / Ren, Y. / Jin, Q. / Dent, S.Y. / Li, W. / Li, H. / Shi, X.
History
DepositionJun 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 31, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein AF-9
B: ALA-ARG-THR-LYS-GLN-THR-ALA-ARG-ALY-SER-THR
C: Protein AF-9
D: ALA-ARG-THR-LYS-GLN-THR-ALA-ARG-ALY-SER-THR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0568
Polymers35,8074
Non-polymers2484
Water3,783210
1
A: Protein AF-9
B: ALA-ARG-THR-LYS-GLN-THR-ALA-ARG-ALY-SER-THR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9663
Polymers17,9042
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-3 kcal/mol
Surface area9340 Å2
MethodPISA
2
C: Protein AF-9
D: ALA-ARG-THR-LYS-GLN-THR-ALA-ARG-ALY-SER-THR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0905
Polymers17,9042
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1390 Å2
ΔGint-2 kcal/mol
Surface area9130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.537, 195.704, 106.675
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Protein AF-9 / ALL1-fused gene from chromosome 9 protein / Myeloid/lymphoid or mixed-lineage leukemia translocated ...ALL1-fused gene from chromosome 9 protein / Myeloid/lymphoid or mixed-lineage leukemia translocated to chromosome 3 protein / YEATS domain-containing protein 3


Mass: 16611.160 Da / Num. of mol.: 2 / Fragment: YEATS domain (UNP residues 1-138)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MLLT3, AF9, YEATS3 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P42568
#2: Protein/peptide ALA-ARG-THR-LYS-GLN-THR-ALA-ARG-ALY-SER-THR


Mass: 1292.465 Da / Num. of mol.: 2 / Fragment: UNP residues 2-12 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P84243
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 3.1 Å3/Da / Density % sol: 60.32 % / Description: rod-like
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20% PEG4000, 5% 2-Propanol, 0.1 M Sodium Citrate Tribasic Dihydrate

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21101
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDSep 12, 2013
ADSC QUANTUM 315r2CCDSep 13, 2013
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: 2.3→50 Å / Num. obs: 20468 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.7 % / Biso Wilson estimate: 36.39 Å2 / Rmerge(I) obs: 0.121 / Χ2: 2.367 / Net I/av σ(I): 42.475 / Net I/σ(I): 10.3 / Num. measured all: 219747
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.3-2.3410.70.7656.3210151.497100
2.34-2.3811.30.66410031.486100
2.38-2.4311.30.5669831.486100
2.43-2.4811.30.50510161.557100
2.48-2.5311.40.49310101.581100
2.53-2.5911.30.429941.62100
2.59-2.6611.30.36310321.679100
2.66-2.7311.30.3169971.731100
2.73-2.8111.30.27310141.787100
2.81-2.911.30.20410011.927100
2.9-311.30.17510222.128100
3-3.1211.20.14610022.345100
3.12-3.2611.10.11810362.521100
3.26-3.44110.10310112.889100
3.44-3.659.80.09910243.44299.9
3.65-3.938.90.09410324.082100
3.93-4.339.60.0810394.126100
4.33-4.959.70.07310404.248100
4.95-6.2410.20.06410613.13199.9
6.24-509.80.05611363.12999.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
MOLREP11.2.05phasing
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.4_1496)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FK3

3fk3


Resolution: 2.3→48.926 Å / FOM work R set: 0.8495 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2288 1046 5.12 %Random selection
Rwork0.1623 19396 --
obs0.1656 20442 99.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 127.12 Å2 / Biso mean: 38.97 Å2 / Biso min: 17.49 Å2
Refinement stepCycle: final / Resolution: 2.3→48.926 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2450 0 40 210 2700
Biso mean--54.52 42.03 -
Num. residues----295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132533
X-RAY DIFFRACTIONf_angle_d1.2713405
X-RAY DIFFRACTIONf_chiral_restr0.057349
X-RAY DIFFRACTIONf_plane_restr0.008444
X-RAY DIFFRACTIONf_dihedral_angle_d13.896971
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2959-2.41690.25651490.19252694X-RAY DIFFRACTION99
2.4169-2.56830.27081520.19062728X-RAY DIFFRACTION100
2.5683-2.76660.22921540.19822728X-RAY DIFFRACTION100
2.7666-3.0450.25011470.1832772X-RAY DIFFRACTION100
3.045-3.48550.23991480.16642738X-RAY DIFFRACTION100
3.4855-4.39090.20291360.14052815X-RAY DIFFRACTION100
4.3909-500.2181600.14852921X-RAY DIFFRACTION100

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