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- PDB-6wav: Crystal structure of PHF1 in complex with H3K36me3 substitution -

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Basic information

Entry
Database: PDB / ID: 6wav
TitleCrystal structure of PHF1 in complex with H3K36me3 substitution
Components
  • Histone H3.1
  • PHD finger protein 1
KeywordsGENE REGULATION / PHF1 / Tudor / H3K36me3-H39V / complex / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H3K36me3 reader activity / histone methyltransferase binding / ESC/E(Z) complex / histone H3K4me3 reader activity / DNA repair-dependent chromatin remodeling / negative regulation of gene expression, epigenetic / : / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling ...histone H3K36me3 reader activity / histone methyltransferase binding / ESC/E(Z) complex / histone H3K4me3 reader activity / DNA repair-dependent chromatin remodeling / negative regulation of gene expression, epigenetic / : / Chromatin modifying enzymes / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / epigenetic regulation of gene expression / 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 / transcription corepressor binding / 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 / Pre-NOTCH Transcription and Translation / Meiotic recombination / Activation of anterior HOX genes in hindbrain development during early embryogenesis / RMTs methylate histone arginines / Transcriptional regulation of granulopoiesis / HCMV Early Events / structural constituent of chromatin / nucleosome / nucleosome assembly / site of double-strand break / HATs acetylate histones / 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 / chromatin organization / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / gene expression / Estrogen-dependent gene expression / cadherin binding / Amyloid fiber formation / protein heterodimerization activity / centrosome / chromatin binding / protein-containing complex / DNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / identical protein binding / nucleus / membrane / cytosol
Similarity search - Function
PHD finger protein 1 / : / : / Polycomb-like MTF2 factor 2, C-terminal domain / Polycomb-like MTF2 factor 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / Zinc finger, PHD-type, conserved site ...PHD finger protein 1 / : / : / Polycomb-like MTF2 factor 2, C-terminal domain / Polycomb-like MTF2 factor 2 / Lysine-specific demethylase 4, Tudor domain / Jumonji domain-containing protein 2A Tudor domain / Tudor domain / Tudor domain / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / 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 domain / Histone-fold / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
PHD finger protein 1 / Histone H3.1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDong, C. / Bountra, C. / Edwards, A.M. / Arrowsmith, C.H. / Min, J.R. / Structural Genomics Consortium (SGC)
CitationJournal: Elife / Year: 2020
Title: Structural basis for histone variant H3tK27me3 recognition by PHF1 and PHF19.
Authors: Dong, C. / Nakagawa, R. / Oyama, K. / Yamamoto, Y. / Zhang, W. / Dong, A. / Li, Y. / Yoshimura, Y. / Kamiya, H. / Nakayama, J.I. / Ueda, J. / Min, J.
History
DepositionMar 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHD finger protein 1
B: PHD finger protein 1
C: PHD finger protein 1
D: PHD finger protein 1
E: Histone H3.1
F: Histone H3.1
G: Histone H3.1
H: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,36253
Polymers33,2668
Non-polymers9645
Water2,054114
1
A: PHD finger protein 1
E: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,41320
Polymers8,3172
Non-polymers9618
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PHD finger protein 1
F: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)8,31713
Polymers8,3172
Non-polymers011
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PHD finger protein 1
G: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)8,31710
Polymers8,3172
Non-polymers08
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-8 kcal/mol
Surface area4750 Å2
MethodPISA
4
D: PHD finger protein 1
H: Histone H3.1


Theoretical massNumber of molelcules
Total (without water)8,31710
Polymers8,3172
Non-polymers08
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-9 kcal/mol
Surface area4640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.003, 65.616, 29.026
Angle α, β, γ (deg.)90.000, 97.122, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
PHD finger protein 1 / hPHF1 / Polycomb-like protein 1 / hPCl1


Mass: 6938.849 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF1, PCL1 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -V3R / References: UniProt: O43189
#2: Protein/peptide
Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 1377.678 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: SO4
#4: Chemical...
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 44 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.17 Å3/Da / Density % sol: 43.4 % / Mosaicity: 0.33 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.2 M ammonium sulfate and 0.1 M sodium acetate 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→40.07 Å / Num. obs: 29381 / % possible obs: 93.8 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.029 / Rrim(I) all: 0.056 / Net I/σ(I): 16.4 / Num. measured all: 107846 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.733.60.416541015010.810.2510.4873.190.9
8.99-40.073.20.0317062190.9980.0210.03834.394.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HCZ

4hcz


Resolution: 1.7→32.802 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.342 / SU ML: 0.078 / Cross valid method: FREE R-VALUE / ESU R: 0.124 / ESU R Free: 0.124
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2407 1455 4.956 %
Rwork0.197 --
all0.199 --
obs-29359 93.42 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.886 Å2
Baniso -1Baniso -2Baniso -3
1-0.098 Å20 Å20.025 Å2
2--0.766 Å20 Å2
3----0.844 Å2
Refinement stepCycle: LAST / Resolution: 1.7→32.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2152 0 49 114 2315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132250
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172142
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.6373081
X-RAY DIFFRACTIONr_angle_other_deg1.3051.584923
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1475284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.63821.504113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4815341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4491517
X-RAY DIFFRACTIONr_chiral_restr0.0640.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022486
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02487
X-RAY DIFFRACTIONr_nbd_refined0.2280.2414
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.21998
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21027
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.21185
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.283
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3050.226
X-RAY DIFFRACTIONr_nbd_other0.2010.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1490.25
X-RAY DIFFRACTIONr_mcbond_it1.7081.9131109
X-RAY DIFFRACTIONr_mcbond_other1.7031.9111108
X-RAY DIFFRACTIONr_mcangle_it2.5842.8391377
X-RAY DIFFRACTIONr_mcangle_other2.5852.8421378
X-RAY DIFFRACTIONr_scbond_it2.1062.111140
X-RAY DIFFRACTIONr_scbond_other2.0922.1071137
X-RAY DIFFRACTIONr_scangle_it3.1663.0971696
X-RAY DIFFRACTIONr_scangle_other3.173.0911690
X-RAY DIFFRACTIONr_lrange_it4.53322.0172432
X-RAY DIFFRACTIONr_lrange_other4.42321.7992396
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)WRfactor Rwork
1.7-1.7440.2991180.23919660.242228391.28340.214
1.744-1.7920.253960.20719940.209224793.01290.182
1.792-1.8430.216900.20319570.203219393.34250.175
1.843-1.90.312910.21918830.223211693.28920.188
1.9-1.9620.241910.21518520.216206394.18320.195
1.962-2.0310.27920.19217860.196199993.9470.169
2.031-2.1070.268910.19417110.198191993.90310.176
2.107-2.1930.254910.20216590.205186493.88410.183
2.193-2.290.229700.2116050.211175895.27870.2
2.29-2.4010.255830.19615700.199173295.43880.183
2.401-2.530.256540.19214830.194160995.52520.181
2.53-2.6830.214780.19613900.197153895.44860.189
2.683-2.8660.229760.19112840.193145093.79310.189
2.866-3.0940.214720.1911780.192133793.49290.198
3.094-3.3860.264620.19210750.196124191.61970.2
3.386-3.7810.181530.18710000.187114292.20670.197
3.781-4.3560.204470.1738380.17599289.21370.191
4.356-5.3120.242450.1697290.17385390.73860.192
5.312-7.4160.287400.2425880.24467692.89940.274
7.416-32.8020.359150.2433560.24639593.9240.306

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