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- PDB-2x4y: Molecular basis of Histone H3K36me3 recognition by the PWWP domai... -

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Basic information

Entry
Database: PDB / ID: 2x4y
TitleMolecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
Components
  • HISTONE H3.2
  • PEREGRIN
KeywordsTRANSCRIPTION / METAL-BINDING / ZINC-FINGER / CHROMATIN REGULATOR / TRANSCRIPTION REGULATION / NUCLEOSOME
Function / homology
Function and homology information


acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / Chromatin modifying enzymes / Regulation of TP53 Activity through Acetylation / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication ...acetyltransferase activator activity / MOZ/MORF histone acetyltransferase complex / regulation of developmental process / regulation of hemopoiesis / histone acetyltransferase complex / Chromatin modifying enzymes / Regulation of TP53 Activity through Acetylation / Interleukin-7 signaling / 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 methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / 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 / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / 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 / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
BRPF1, PHD domain / Peregrin, ePHD domain / : / SH3 type barrels. - #140 / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain ...BRPF1, PHD domain / Peregrin, ePHD domain / : / SH3 type barrels. - #140 / : / Enhancer of polycomb-like, N-terminal / Enhancer of polycomb-like / PHD-finger / PHD-zinc-finger like domain / Extended PHD (ePHD) domain / Extended PHD (ePHD) domain profile. / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / Zinc finger, PHD-type, conserved site / Zinc finger C2H2 type domain profile. / Zinc finger PHD-type signature. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / SH3 type barrels. / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Bromodomain, conserved site / Bromodomain signature. / Bromodomain / Histone-fold / bromo domain / Bromodomain / Bromodomain (BrD) profile. / Bromodomain-like superfamily / Zinc finger, RING/FYVE/PHD-type / Roll / Mainly Beta
Similarity search - Domain/homology
Peregrin / Histone H3.2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVezzoli, A. / Bonadies, N. / Allen, M.D. / Freund, S.M.V. / Santiveri, C.M. / Kvinlaug, B. / Huntly, B.J.P. / Gottgens, B. / Bycroft, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Molecular Basis of Histone H3K36Me3 Recognition by the Pwwp Domain of Brpf1.
Authors: Vezzoli, A. / Bonadies, N. / Allen, M.D. / Freund, S.M.V. / Santiveri, C.M. / Kvinlaug, B. / Huntly, B.J.P. / Gottgens, B. / Bycroft, M.
History
DepositionFeb 2, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jun 9, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: PEREGRIN
B: HISTONE H3.2
C: PEREGRIN
D: HISTONE H3.2
E: PEREGRIN
F: HISTONE H3.2
G: PEREGRIN
H: HISTONE H3.2
I: PEREGRIN
J: HISTONE H3.2
K: PEREGRIN
L: HISTONE H3.2
M: PEREGRIN
N: HISTONE H3.2
O: PEREGRIN
P: HISTONE H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,31523
Polymers140,64316
Non-polymers6727
Water19,4201078
1
O: PEREGRIN
P: HISTONE H3.2


Theoretical massNumber of molelcules
Total (without water)17,5802
Polymers17,5802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-11.4 kcal/mol
Surface area8050 Å2
MethodPISA
2
E: PEREGRIN
F: HISTONE H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6763
Polymers17,5802
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-11.6 kcal/mol
Surface area8540 Å2
MethodPISA
3
C: PEREGRIN
D: HISTONE H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7724
Polymers17,5802
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-41.2 kcal/mol
Surface area8270 Å2
MethodPISA
4
G: PEREGRIN
H: HISTONE H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,6763
Polymers17,5802
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-27.3 kcal/mol
Surface area8210 Å2
MethodPISA
5
K: PEREGRIN
L: HISTONE H3.2


Theoretical massNumber of molelcules
Total (without water)17,5802
Polymers17,5802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-10.6 kcal/mol
Surface area8310 Å2
MethodPISA
6
M: PEREGRIN
N: HISTONE H3.2


Theoretical massNumber of molelcules
Total (without water)17,5802
Polymers17,5802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-9.1 kcal/mol
Surface area8510 Å2
MethodPISA
7
I: PEREGRIN
J: HISTONE H3.2


Theoretical massNumber of molelcules
Total (without water)17,5802
Polymers17,5802
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-20 kcal/mol
Surface area8360 Å2
MethodPISA
8
A: PEREGRIN
B: HISTONE H3.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8695
Polymers17,5802
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-51.3 kcal/mol
Surface area8860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.757, 97.906, 102.524
Angle α, β, γ (deg.)86.80, 80.96, 87.24
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PEREGRIN / BROMODOMAIN AND PHD FINGER-CONTAINING PROTEIN 1 / PROTEIN BR140


Mass: 15249.579 Da / Num. of mol.: 8 / Fragment: BRPF1 PWWP DOMAIN, RESIDUES 1076-1205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P55201
#2: Protein/peptide
HISTONE H3.2 / HUMAN H3 HISTONE / H3/M / H3/O


Mass: 2330.777 Da / Num. of mol.: 8 / Fragment: RESIDUES 23-43 / Source method: obtained synthetically / Details: TRIMETHYLATED AT POSITION 36 / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q71DI3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1078 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsLYSINE 36 IS TRIMETHYLATED

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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: 2.51 Å3/Da / Density % sol: 51.08 % / Description: NONE
Crystal growpH: 8.5
Details: 30% PEG4K, 0.2M LITHIUM SULPHATE, 0.1M TRIS (PH 8.5), 0.01M NACL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.7→48.85 Å / Num. obs: 1418928 / % possible obs: 94.2 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Biso Wilson estimate: 23.91 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 2 / % possible all: 90.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→24.771 Å / SU ML: 0.26 / σ(F): 1.35 / Phase error: 22.94 / Stereochemistry target values: ML / Details: DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY.
RfactorNum. reflection% reflection
Rfree0.2267 6576 5 %
Rwork0.1904 --
obs0.1922 141892 87.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.898 Å2 / ksol: 0.397 e/Å3
Displacement parametersBiso mean: 30.37 Å2
Baniso -1Baniso -2Baniso -3
1-1.8708 Å21.401 Å2-0.3066 Å2
2---0.9367 Å2-0.6258 Å2
3----0.9341 Å2
Refinement stepCycle: LAST / Resolution: 1.7→24.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8993 0 35 1078 10106
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0169295
X-RAY DIFFRACTIONf_angle_d1.59812592
X-RAY DIFFRACTIONf_dihedral_angle_d16.6683628
X-RAY DIFFRACTIONf_chiral_restr0.1191320
X-RAY DIFFRACTIONf_plane_restr0.0091609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.29134550.25947621X-RAY DIFFRACTION82
1.7193-1.73950.30454740.25437733X-RAY DIFFRACTION82
1.7395-1.76070.28424620.24617726X-RAY DIFFRACTION82
1.7607-1.7830.27514430.23977867X-RAY DIFFRACTION81
1.783-1.80650.28883670.2327854X-RAY DIFFRACTION82
1.8065-1.83120.26343900.21977909X-RAY DIFFRACTION83
1.8312-1.85740.27694070.22058094X-RAY DIFFRACTION84
1.8574-1.88510.24134110.20468105X-RAY DIFFRACTION84
1.8851-1.91450.2373760.19887904X-RAY DIFFRACTION84
1.9145-1.94590.24884210.20398186X-RAY DIFFRACTION85
1.9459-1.97950.21334620.20088259X-RAY DIFFRACTION86
1.9795-2.01540.26953760.20798211X-RAY DIFFRACTION86
2.0154-2.05420.25884510.20268290X-RAY DIFFRACTION87
2.0542-2.09610.23984140.20448499X-RAY DIFFRACTION88
2.0961-2.14160.23884350.28323X-RAY DIFFRACTION88
2.1416-2.19140.24084560.18598413X-RAY DIFFRACTION88
2.1914-2.24620.21533910.17998631X-RAY DIFFRACTION89
2.2462-2.30690.21364310.1778370X-RAY DIFFRACTION89
2.3069-2.37470.22514330.18918787X-RAY DIFFRACTION90
2.3747-2.45130.24394420.19648499X-RAY DIFFRACTION90
2.4513-2.53880.25744590.19928697X-RAY DIFFRACTION91
2.5388-2.64040.24794690.19858602X-RAY DIFFRACTION90
2.6404-2.76040.2224660.18678740X-RAY DIFFRACTION91
2.7604-2.90570.23164810.19798617X-RAY DIFFRACTION91
2.9057-3.08740.2554430.20268867X-RAY DIFFRACTION92
3.0874-3.32530.214430.18889091X-RAY DIFFRACTION95
3.3253-3.6590.20244400.16939132X-RAY DIFFRACTION95
3.659-4.18630.17825130.15489065X-RAY DIFFRACTION96
4.1863-5.26590.18285020.14849168X-RAY DIFFRACTION96
5.2659-24.77380.24224390.20428642X-RAY DIFFRACTION90

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