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- PDB-5vdc: Crystal structure of the human DPF2 tandem PHD finger domain -

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Basic information

Entry
Database: PDB / ID: 5vdc
TitleCrystal structure of the human DPF2 tandem PHD finger domain
ComponentsZinc finger protein ubi-d4
KeywordsGENE REGULATION / Histone Reader / Tandem PHD Finger / AML / Myeloid Differentiation
Function / homology
Function and homology information


negative regulation of myeloid progenitor cell differentiation / H3K9me3 modified histone binding / nBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / positive regulation of stem cell population maintenance / regulation of G1/S transition of mitotic cell cycle ...negative regulation of myeloid progenitor cell differentiation / H3K9me3 modified histone binding / nBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / regulation of mitotic metaphase/anaphase transition / SWI/SNF complex / positive regulation of double-strand break repair / positive regulation of stem cell population maintenance / regulation of G1/S transition of mitotic cell cycle / apoptotic signaling pathway / lysine-acetylated histone binding / transcription corepressor activity / nervous system development / chromatin remodeling / intracellular membrane-bounded organelle / centrosome / apoptotic process / chromatin / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
DPF1-3, N-terminal domain / DPF1-3, N-terminal / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / PHD-finger / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type signature. ...DPF1-3, N-terminal domain / DPF1-3, N-terminal / Zinc/RING finger domain, C3HC4 (zinc finger) / Herpes Virus-1 / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / PHD-finger / Zinc finger C2H2 type domain signature. / Zinc finger PHD-type 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 / Zinc finger, RING/FYVE/PHD-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Zinc finger protein ubi-d4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsHuber, F.M. / Davenport, A.M. / Hoelz, A.
Funding support United States, 2items
OrganizationGrant numberCountry
Heritage Medical Research Institute United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Histone-binding of DPF2 mediates its repressive role in myeloid differentiation.
Authors: Huber, F.M. / Greenblatt, S.M. / Davenport, A.M. / Martinez, C. / Xu, Y. / Vu, L.P. / Nimer, S.D. / Hoelz, A.
History
DepositionApr 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2Jun 21, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Zinc finger protein ubi-d4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,69610
Polymers14,0641
Non-polymers6329
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.500, 107.500, 53.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Zinc finger protein ubi-d4 / Apoptosis response zinc finger protein / BRG1-associated factor 45D / BAF45D / D4 / zinc and double ...Apoptosis response zinc finger protein / BRG1-associated factor 45D / BAF45D / D4 / zinc and double PHD fingers family 2 / Protein requiem


Mass: 14063.899 Da / Num. of mol.: 1
Fragment: DPF2 tandem PHD finger domain (UNP residues 270-391)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPF2, BAF45D, REQ, UBID4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q92785
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 2.2 M Ammonium sulfate, 0.15 M Ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.2818, 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.28181
20.97951
ReflectionResolution: 1.6→50 Å / Num. obs: 20713 / % possible obs: 99 % / Redundancy: 26.1 % / CC1/2: 1 / Net I/σ(I): 28.9
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 26.9 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3249 / CC1/2: 0.78 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XSCALEdata scaling
AutoSolphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.6→47.753 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.56
RfactorNum. reflection% reflection
Rfree0.1906 1035 5 %
Rwork0.1406 --
obs0.1431 20701 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→47.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms908 0 28 117 1053
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121024
X-RAY DIFFRACTIONf_angle_d1.2851386
X-RAY DIFFRACTIONf_dihedral_angle_d14.418389
X-RAY DIFFRACTIONf_chiral_restr0.08140
X-RAY DIFFRACTIONf_plane_restr0.006187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.68440.26591460.18242733X-RAY DIFFRACTION98
1.6844-1.78990.23491460.14112759X-RAY DIFFRACTION99
1.7899-1.92810.16431440.11572761X-RAY DIFFRACTION99
1.9281-2.12220.14981450.11132803X-RAY DIFFRACTION99
2.1222-2.42920.16631480.11572795X-RAY DIFFRACTION99
2.4292-3.06050.20771490.1542845X-RAY DIFFRACTION99
3.0605-47.77390.19431570.14722970X-RAY DIFFRACTION99

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