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- PDB-5hjd: AF9 YEATS in complex with histone H3 Crotonylation at K18 -

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Basic information

Entry
Database: PDB / ID: 5hjd
TitleAF9 YEATS in complex with histone H3 Crotonylation at K18
Components
  • Protein AF-9
  • peptide of Histone H3.1
KeywordsTRANSCRIPTION/PEPTIDE / AF9 YEATS / histone peptide / crotonyllysine / H3K18 / TRANSCRIPTION-PEPTIDE complex
Function / homology
Function and homology information


modification-dependent protein binding / regulation of stem cell division / segment specification / regulation of chromatin organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / anterior/posterior pattern specification / hematopoietic stem cell differentiation / Chromatin modifying enzymes / epigenetic regulation of gene expression / RNA Polymerase II Transcription Elongation ...modification-dependent protein binding / regulation of stem cell division / segment specification / regulation of chromatin organization / positive regulation of Wnt signaling pathway, planar cell polarity pathway / anterior/posterior pattern specification / hematopoietic stem cell differentiation / Chromatin modifying enzymes / epigenetic regulation of gene expression / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / telomere organization / RNA Polymerase I Promoter Opening / Interleukin-7 signaling / Assembly of the ORC complex at the origin of replication / DNA methylation / transcription elongation factor complex / 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 / PRC2 methylates histones and DNA / Defective pyroptosis / HDACs deacetylate histones / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / negative regulation of canonical Wnt signaling pathway / 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 / B-WICH complex positively regulates rRNA expression / HDMs demethylate histones / 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 / nucleosome / gene expression / chromosome / RUNX1 regulates transcription of genes involved in differentiation of HSCs / chromatin organization / Factors involved in megakaryocyte development and platelet production / HATs acetylate histones / histone binding / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / molecular adaptor activity / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / 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
COPPER (II) ION / Protein AF-9 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.806 Å
AuthorsLi, Y.Y. / Zhao, D. / Guan, H.P. / Li, H.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China91519304 China
CitationJournal: Mol.Cell / Year: 2016
Title: Molecular Coupling of Histone Crotonylation and Active Transcription by AF9 YEATS Domain.
Authors: Li, Y.Y. / Sabari, B.R. / Panchenko, T. / Wen, H. / Zhao, D. / Guan, H.P. / Wan, L. / Huang, H. / Tang, Z. / Zhao, Y. / Roeder, R.G. / Shi, X. / Allis, C.D. / Li, H.T.
History
DepositionJan 13, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _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_conn_type.id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _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
C: Protein AF-9
E: Protein AF-9
G: Protein AF-9
K: Protein AF-9
N: Protein AF-9
Q: Protein AF-9
T: Protein AF-9
L: peptide of Histone H3.1
M: peptide of Histone H3.1
B: peptide of Histone H3.1
D: peptide of Histone H3.1
F: peptide of Histone H3.1
H: peptide of Histone H3.1
I: peptide of Histone H3.1
J: peptide of Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,31334
Polymers139,71416
Non-polymers1,59918
Water73941
1
A: Protein AF-9
C: Protein AF-9
E: Protein AF-9
G: Protein AF-9
L: peptide of Histone H3.1
B: peptide of Histone H3.1
D: peptide of Histone H3.1
F: peptide of Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,81619
Polymers69,8578
Non-polymers95911
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
K: Protein AF-9
N: Protein AF-9
Q: Protein AF-9
T: Protein AF-9
M: peptide of Histone H3.1
H: peptide of Histone H3.1
I: peptide of Histone H3.1
J: peptide of Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,49715
Polymers69,8578
Non-polymers6407
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.264, 101.573, 102.076
Angle α, β, γ (deg.)90.00, 103.06, 90.00
Int Tables number4
Space group name H-MP1211

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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: 16554.107 Da / Num. of mol.: 8 / 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P42568
#2: Protein/peptide
peptide of Histone H3.1


Mass: 910.115 Da / Num. of mol.: 8 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#3: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 3.36 Å3/Da / Density % sol: 63.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20%(w/v) polyethylene glycol 4000, 0.2 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, 0.1 M copper chloride dihydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 - 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 1, 2014
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
211
ReflectionResolution: 2.8→50 Å / Num. obs: 49686 / % possible obs: 98.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 52.63 Å2 / Rmerge(I) obs: 0.116 / Χ2: 1.612 / Net I/av σ(I): 16.207 / Net I/σ(I): 9.8 / Num. measured all: 321423
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.8-2.853.80.88198.1
2.85-2.93.80.689198.2
2.9-2.963.80.632198.1
2.96-3.023.80.522198.4
3.02-3.083.80.455198.3
3.08-3.153.80.351198.4
3.15-3.233.80.277198.3
3.23-3.323.80.222198.2
3.32-3.423.80.204198.4
3.42-3.533.80.158198.3
3.53-3.653.80.14198.7
3.65-3.83.80.123198.5
3.8-3.973.80.109198.2
3.97-4.183.80.095198.4
4.18-4.443.80.085198.5
4.44-4.793.80.075198.4
4.79-5.273.70.071197.8
5.27-6.033.70.077196.6
6.03-7.593.80.071199.7
7.59-503.80.062199.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TMP

4tmp


Resolution: 2.806→48.29 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2734 2233 5.04 %
Rwork0.2417 --
obs0.2433 44285 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.806→48.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9660 0 74 41 9775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410003
X-RAY DIFFRACTIONf_angle_d0.84413473
X-RAY DIFFRACTIONf_dihedral_angle_d16.5993843
X-RAY DIFFRACTIONf_chiral_restr0.0311364
X-RAY DIFFRACTIONf_plane_restr0.0041750
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8059-2.86690.35811290.30652427X-RAY DIFFRACTION93
2.8669-2.93360.37011630.30912609X-RAY DIFFRACTION100
2.9336-3.0070.38841320.31512643X-RAY DIFFRACTION100
3.007-3.08820.3921420.3052634X-RAY DIFFRACTION100
3.0882-3.17910.31721440.29452605X-RAY DIFFRACTION100
3.1791-3.28170.30081190.27252668X-RAY DIFFRACTION100
3.2817-3.3990.30591180.27032642X-RAY DIFFRACTION100
3.399-3.5350.29651470.26282617X-RAY DIFFRACTION100
3.535-3.69580.28241370.26142642X-RAY DIFFRACTION100
3.6958-3.89060.25661420.24972652X-RAY DIFFRACTION100
3.8906-4.13420.27221420.23882630X-RAY DIFFRACTION100
4.1342-4.45320.23261370.22352658X-RAY DIFFRACTION100
4.4532-4.9010.22171430.18412625X-RAY DIFFRACTION100
4.901-5.60930.22341360.19542655X-RAY DIFFRACTION100
5.6093-7.06360.27181610.23922657X-RAY DIFFRACTION100
7.0636-48.29760.24881410.22132688X-RAY DIFFRACTION99

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