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- PDB-6wau: Complex structure of PHF19 -

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Basic information

Entry
Database: PDB / ID: 6wau
TitleComplex structure of PHF19
Components
  • Histone H3.1t peptide
  • PHD finger protein 19
KeywordsGENE REGULATION / PHF19 / Tudor / histone variant / complex / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


histone H3K36me3 reader activity / spermatogonial cell division / DNA replication-dependent chromatin assembly / ESC/E(Z) complex / histone H3K4me3 reader activity / stem cell population maintenance / negative regulation of gene expression, epigenetic / : / regulation of cell differentiation / heterochromatin ...histone H3K36me3 reader activity / spermatogonial cell division / DNA replication-dependent chromatin assembly / ESC/E(Z) complex / histone H3K4me3 reader activity / stem cell population maintenance / negative regulation of gene expression, epigenetic / : / regulation of cell differentiation / heterochromatin / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / Condensation of Prophase Chromosomes / condensed nuclear chromosome / PRC2 methylates histones and DNA / stem cell differentiation / Nonhomologous End-Joining (NHEJ) / Formation of the beta-catenin:TCF transactivating complex / G2/M DNA damage checkpoint / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / structural constituent of chromatin / nucleosome / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / Processing of DNA double-strand break ends / chromosome, telomeric region / protein heterodimerization activity / chromatin binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
PHF19, PHD domain 2 / : / 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 ...PHF19, PHD domain 2 / : / 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-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Histone H3 signature 1. / 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
Histone H3.1t / PHD finger protein 19
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 1.2Jun 30, 2021Group: Data collection / Category: pdbx_reflns_twin
Item: _pdbx_reflns_twin.crystal_id / _pdbx_reflns_twin.diffrn_id
Revision 1.3Oct 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

Downloads & links

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Assembly

Deposited unit
A: PHD finger protein 19
B: PHD finger protein 19
C: PHD finger protein 19
D: PHD finger protein 19
E: PHD finger protein 19
F: PHD finger protein 19
G: Histone H3.1t peptide
H: Histone H3.1t peptide
I: Histone H3.1t peptide
J: Histone H3.1t peptide
K: Histone H3.1t peptide
L: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)48,92023
Polymers48,92012
Non-polymers011
Water64936
1
A: PHD finger protein 19
G: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)8,1533
Polymers8,1532
Non-polymers01
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-7 kcal/mol
Surface area4630 Å2
MethodPISA
2
B: PHD finger protein 19
H: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)8,1536
Polymers8,1532
Non-polymers04
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-7 kcal/mol
Surface area4600 Å2
MethodPISA
3
C: PHD finger protein 19
I: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)8,1534
Polymers8,1532
Non-polymers02
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-7 kcal/mol
Surface area4610 Å2
MethodPISA
4
D: PHD finger protein 19
J: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)8,1536
Polymers8,1532
Non-polymers04
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-8 kcal/mol
Surface area4510 Å2
MethodPISA
5
E: PHD finger protein 19
K: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)8,1532
Polymers8,1532
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-7 kcal/mol
Surface area4310 Å2
MethodPISA
6
F: PHD finger protein 19
L: Histone H3.1t peptide


Theoretical massNumber of molelcules
Total (without water)8,1532
Polymers8,1532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-8 kcal/mol
Surface area4380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.477, 111.477, 34.409
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
PHD finger protein 19 / Polycomb-like protein 3 / hPCL3


Mass: 6907.817 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHF19, PCL3 / Plasmid: pET28-MHL / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -V3R / References: UniProt: Q5T6S3
#2: Protein/peptide
Histone H3.1t peptide / H3t / H3/g


Mass: 1245.491 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q16695
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 11 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.52 Å3/Da / Density % sol: 51.25 % / Mosaicity: 0.16 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.3M ammonium phosphate dibasic and 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.97951 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.5033
pseudo-merohedral11-h,-k,l20.4967
ReflectionResolution: 1.71→55.74 Å / Num. obs: 51838 / % possible obs: 99.4 % / Redundancy: 5.4 % / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.023 / Rrim(I) all: 0.054 / Net I/σ(I): 21.6 / Num. measured all: 279619
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
1.71-1.742.91.314741825470.190.9061.6080.792.1
9.02-55.745.70.015199435210.0070.01795.899.6

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Processing

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

4hcz


Resolution: 1.75→48.271 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.728 / SU ML: 0.06 / Cross valid method: FREE R-VALUE / ESU R: 0.024 / ESU R Free: 0.024
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2497 2242 4.652 %
Rwork0.213 --
all0.215 --
obs-48195 99.921 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.856 Å2
Baniso -1Baniso -2Baniso -3
1-3.308 Å20 Å20 Å2
2--3.308 Å20 Å2
3----6.615 Å2
Refinement stepCycle: LAST / Resolution: 1.75→48.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3031 0 11 36 3078
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0133110
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172859
X-RAY DIFFRACTIONr_angle_refined_deg1.9941.6324222
X-RAY DIFFRACTIONr_angle_other_deg1.2891.5826568
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5265379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.66721.408142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72115494
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1281518
X-RAY DIFFRACTIONr_chiral_restr0.0850.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023413
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02702
X-RAY DIFFRACTIONr_nbd_refined0.1930.2504
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.22636
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21347
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21659
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.281
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0460.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1950.242
X-RAY DIFFRACTIONr_nbd_other0.2020.2138
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1330.211
X-RAY DIFFRACTIONr_mcbond_it3.2162.8591528
X-RAY DIFFRACTIONr_mcbond_other3.2162.8581527
X-RAY DIFFRACTIONr_mcangle_it4.1314.2751895
X-RAY DIFFRACTIONr_mcangle_other4.134.2761896
X-RAY DIFFRACTIONr_scbond_it3.3843.0231582
X-RAY DIFFRACTIONr_scbond_other3.3833.0241583
X-RAY DIFFRACTIONr_scangle_it4.4634.4642325
X-RAY DIFFRACTIONr_scangle_other4.4634.4642325
X-RAY DIFFRACTIONr_lrange_it5.6131.0493294
X-RAY DIFFRACTIONr_lrange_other5.61131.0533292
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 allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.75-1.7950.4481260.58934300.58435900.9760.98599.05290.327
1.795-1.8440.4241980.35732540.36134520.9830.9931000.219
1.844-1.8980.3921660.3632270.36233930.9690.9791000.23
1.898-1.9560.5781360.48731110.49132470.9010.9341000.318
1.956-2.020.251500.19130750.19332250.9720.9871000.15
2.02-2.0910.2061340.17829180.17930520.9760.9851000.149
2.091-2.170.2061600.16628310.16829910.9780.9851000.148
2.17-2.2580.3111480.27426830.27628310.9380.9591000.217
2.258-2.3580.2991340.20625960.2127300.9650.9821000.152
2.358-2.4730.2781560.19325040.19826600.9680.9811000.166
2.473-2.6070.2811090.19523640.19924730.9580.9791000.173
2.607-2.7640.25670.18422790.18623460.9660.9781000.168
2.764-2.9540.255940.18120910.18421850.960.9771000.171
2.954-3.190.24960.19220050.19421010.9580.9731000.187
3.19-3.4930.206910.19117940.19118850.9730.9771000.189
3.493-3.9030.215920.18316330.18517250.9740.9821000.186
3.903-4.5010.134680.14414390.14415090.9880.98799.86750.152
4.501-5.5010.219540.17112360.17312900.9750.9841000.186
5.501-7.7290.308340.2459470.2479830.9610.96499.79650.252
7.729-48.0090.209290.2415360.2395650.9710.9661000.29

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