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- PDB-9uth: DPF3b in complex with H3K14cr peptide -

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Basic information

Entry
Database: PDB / ID: 9uth
TitleDPF3b in complex with H3K14cr peptide
Components
  • Histone H3.3
  • Zinc finger protein DPF3
KeywordsPEPTIDE BINDING PROTEIN / DPF3b / H3K14 crotonylation
Function / homology
Function and homology information


Barr body / brahma complex / nBAF complex / Formation of the canonical BAF (cBAF) complex / negative regulation of chromosome condensation / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / pericentric heterochromatin formation / inner kinetochore / regulation of G0 to G1 transition / muscle cell differentiation ...Barr body / brahma complex / nBAF complex / Formation of the canonical BAF (cBAF) complex / negative regulation of chromosome condensation / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / pericentric heterochromatin formation / inner kinetochore / regulation of G0 to G1 transition / muscle cell differentiation / regulation of nucleotide-excision repair / oocyte maturation / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / muscle organ development / nucleosomal DNA binding / nucleus organization / positive regulation of double-strand break repair / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / spermatid development / positive regulation of myoblast differentiation / single fertilization / subtelomeric heterochromatin formation / RNA polymerase II core promoter sequence-specific DNA binding / Replacement of protamines by nucleosomes in the male pronucleus / embryo implantation / telomere organization / RNA Polymerase I Promoter Opening / Inhibition of DNA recombination at telomere / 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 / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / positive regulation of cell differentiation / 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 / NoRC negatively regulates rRNA expression / Negative Regulation of CDH1 Gene Transcription / B-WICH complex positively regulates rRNA expression / male gonad development / Meiotic recombination / Pre-NOTCH Transcription and Translation / multicellular organism growth / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / osteoblast differentiation / structural constituent of chromatin / nucleosome / nervous system development / nucleosome assembly / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of cell growth / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / chromosome, telomeric region / cell population proliferation / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / Amyloid fiber formation / protein heterodimerization activity / regulation of transcription by RNA polymerase II / chromatin / protein-containing complex / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
DPF1-3, N-terminal domain / DPF1-3, N-terminal / zinc finger / PHD-finger / Zinc finger C2H2 type domain profile. / Zinc finger PHD-type signature. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type profile. / Zinc finger C2H2-type ...DPF1-3, N-terminal domain / DPF1-3, N-terminal / zinc finger / PHD-finger / Zinc finger C2H2 type domain profile. / Zinc finger PHD-type signature. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type profile. / Zinc finger C2H2-type / 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
Histone H3.3 / Zinc finger protein DPF3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsFeng, F. / Huang, J. / Xiang, B. / Li, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: DPF3b in complex with H3K14cr peptide
Authors: Feng, F. / Huang, J. / Xiang, B. / Li, H.
History
DepositionMay 3, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 6, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger protein DPF3
B: Histone H3.3
C: Zinc finger protein DPF3
D: Histone H3.3
E: Zinc finger protein DPF3
F: Histone H3.3
G: Zinc finger protein DPF3
H: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,37824
Polymers62,3318
Non-polymers1,04716
Water2,612145
1
A: Zinc finger protein DPF3
B: Histone H3.3
C: Zinc finger protein DPF3
D: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,68912
Polymers31,1664
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-39 kcal/mol
Surface area14890 Å2
MethodPISA
2
E: Zinc finger protein DPF3
F: Histone H3.3
G: Zinc finger protein DPF3
H: Histone H3.3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,68912
Polymers31,1664
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-24 kcal/mol
Surface area15150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.088, 84.253, 111.123
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Zinc finger protein DPF3 / BRG1-associated factor 45C / BAF45C / Zinc finger protein cer-d4


Mass: 12810.580 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPF3, BAF45C, CERD4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92784
#2: Protein/peptide
Histone H3.3


Mass: 2772.234 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H3-3A, H3.3A, H3F3, H3F3A, PP781, H3-3B, H3.3B, H3F3B / Production host: Homo sapiens (human) / References: UniProt: P84243
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 4 M Sodium Formate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: May 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. obs: 18737 / % possible obs: 99.7 % / Redundancy: 6.7 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.064 / Rrim(I) all: 0.168 / Χ2: 0.881 / Net I/σ(I): 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.7-2.756.80.6749200.8610.9620.2760.730.47999.7
2.75-2.86.70.6119230.8750.9660.2510.6620.50999.9
2.8-2.856.60.5369100.8940.9720.2230.5820.5199.6
2.85-2.916.50.4369230.9330.9820.1830.4740.59399.4
2.91-2.976.30.439180.9330.9820.1830.4690.568100
2.97-3.045.50.3469210.9540.9880.1610.3830.59299.7
3.04-3.125.50.2989080.9590.990.1370.3290.62999.7
3.12-3.270.2769410.9740.9930.1110.2980.65599.7
3.2-3.37.30.2589040.9740.9930.1010.2780.75899.9
3.3-3.47.40.2149340.9850.9960.0830.230.81599.9
3.4-3.527.20.2229300.9830.9960.0890.241.16299.9
3.52-3.667.30.1559430.9850.9960.0620.1670.989100
3.66-3.837.20.159260.9910.9980.060.1621.16499.9
3.83-4.0370.1339330.9840.9960.0540.1441.353100
4.03-4.297.10.19380.9960.9990.040.1081.125100
4.29-4.6270.0919460.9950.9990.0370.0991.07999.9
4.62-5.086.70.0829550.9970.9990.0330.0881.0499.9
5.08-5.815.90.0899530.9970.9990.0390.0970.86498.8
5.81-7.326.30.0779720.9960.9990.0330.0840.9499.5
7.32-506.30.05810390.99810.0260.0641.52299.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
SCALEPACKdata scaling
DENZOdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.69→36.11 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 2.01 / Phase error: 22.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 1318 7.06 %
Rwork0.181 --
obs0.1844 18674 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.69→36.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4270 0 16 145 4431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034358
X-RAY DIFFRACTIONf_angle_d0.5565882
X-RAY DIFFRACTIONf_dihedral_angle_d14.3651634
X-RAY DIFFRACTIONf_chiral_restr0.039625
X-RAY DIFFRACTIONf_plane_restr0.004775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.80.29961450.24591824X-RAY DIFFRACTION96
2.8-2.930.32361610.2271889X-RAY DIFFRACTION100
2.93-3.080.28091430.22241885X-RAY DIFFRACTION100
3.08-3.270.27391590.22061911X-RAY DIFFRACTION100
3.28-3.530.25581210.20091946X-RAY DIFFRACTION100
3.53-3.880.20651400.16821952X-RAY DIFFRACTION100
3.88-4.440.18891590.14911929X-RAY DIFFRACTION100
4.44-5.590.21231380.14611969X-RAY DIFFRACTION100
5.59-36.110.18161520.15912051X-RAY DIFFRACTION99

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