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- PDB-3iuf: Crystal structure of the C2H2-type zinc finger domain of human ubi-d4 -

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Basic information

Entry
Database: PDB / ID: 3iuf
TitleCrystal structure of the C2H2-type zinc finger domain of human ubi-d4
ComponentsZinc finger protein ubi-d4
KeywordsPROTEIN BINDING / Structural Genomics Consortium (SGC) / zinc finger / C2H2 / Apoptosis / Metal-binding / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Zinc-finger
Function / homology
Function and homology information


negative regulation of myeloid progenitor cell differentiation / histone H3K14ac reader activity / histone H4K16ac reader activity / histone H3K9me2/3 reader activity / nBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair ...negative regulation of myeloid progenitor cell differentiation / histone H3K14ac reader activity / histone H4K16ac reader activity / histone H3K9me2/3 reader activity / nBAF complex / regulation of G0 to G1 transition / regulation of nucleotide-excision repair / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / positive regulation of double-strand break repair / positive regulation of stem cell population maintenance / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / : / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / apoptotic signaling pathway / transcription corepressor activity / nervous system development / chromatin remodeling / intracellular membrane-bounded organelle / apoptotic process / centrosome / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
DPF1-3, N-terminal domain / DPF1-3, N-terminal / zinc finger / PHD-finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger PHD-type signature. / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / Zinc finger PHD-type profile. ...DPF1-3, N-terminal domain / DPF1-3, N-terminal / zinc finger / PHD-finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / 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 / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Zinc finger protein ubi-d4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / mad / Resolution: 1.8 Å
AuthorsTempel, W. / Xu, C. / Bian, C. / Adams-Cioaba, M. / Eryilmaz, J. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. ...Tempel, W. / Xu, C. / Bian, C. / Adams-Cioaba, M. / Eryilmaz, J. / Bountra, C. / Weigelt, J. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC)
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Crystal structure of the Cys2His2-type zinc finger domain of human DPF2.
Authors: Zhang, W. / Xu, C. / Bian, C. / Tempel, W. / Crombet, L. / MacKenzie, F. / Min, J. / Liu, Z. / Qi, C.
History
DepositionAug 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 2, 2012Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Zinc finger protein ubi-d4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,5662
Polymers5,5011
Non-polymers651
Water32418
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.714, 57.657, 22.585
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-13-

HOH

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Components

#1: Protein/peptide Zinc finger protein ubi-d4 / Requiem / Apoptosis response zinc finger protein / D4 / zinc and double PHD fingers family 2


Mass: 5500.914 Da / Num. of mol.: 1 / Fragment: UNP residues 203-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPF2, REQ, UBID4 / Plasmid: pET28-MHL / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: Q92785
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 1.45 Å3/Da / Density % sol: 15.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 9.5
Details: 30% PEG 3000, 0.1M CHES, protein concentration 5mg/mL., pH 9.5, vapor diffusion, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID11.26514
SYNCHROTRONAPS 19-ID21.28335
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDAug 6, 2009
ADSC QUANTUM 3152CCDAug 6, 2009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.265141
21.283351
ReflectionRedundancy: 4.6 % / Av σ(I) over netI: 7.8 / Number: 22760 / Rmerge(I) obs: 0.102 / Χ2: 2.16 / D res high: 1.9 Å / D res low: 40 Å / Num. obs: 4911 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.154010010.0461.4684.9
4.095.1510010.0521.6894.9
3.584.0910010.0531.8134.8
3.253.5810010.0671.6334.9
3.023.2510010.081.6934.9
2.843.0210010.0931.3154.9
2.72.8410010.0991.5064.8
2.582.710010.1211.4684.8
2.482.5899.610.1311.3864.8
2.392.4810010.161.4684.7
2.322.3910010.1611.3414.9
2.252.3210010.2351.6174.7
2.192.2599.210.2031.3574.5
2.142.1910010.2563.0024.8
2.092.1410010.2756.014.7
2.052.0910010.331.8794.4
2.012.0599.610.3241.514.3
1.972.0110010.4366.5474.1
1.931.9799.210.53.5054.1
1.91.9399.610.552.5433.7
ReflectionResolution: 1.8→40 Å / Num. obs: 3263 / % possible obs: 99.9 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.8-1.8360.5221,298.7
1.83-1.866.60.4781,299.4
1.86-1.96.90.4611,2100
1.9-1.947.40.4951,2100
1.94-1.987.80.3911,2100
1.98-2.038.60.371,2100
2.03-2.088.40.2941,2100
2.08-2.138.90.3031,2100
2.13-2.290.2451,2100
2.2-2.278.70.2251,2100
2.27-2.358.90.221,2100
2.35-2.448.90.1771,2100
2.44-2.558.60.1741,2100
2.55-2.698.90.1541,2100
2.69-2.868.60.1311,2100
2.86-3.088.60.1241,2100
3.08-3.398.50.0971,2100
3.39-3.888.10.0721,2100
3.88-4.888.30.0651,2100
4.88-407.50.0681,2100

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Phasing

PhasingMethod: mad

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→22.72 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.906 / SU B: 2.653 / SU ML: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.237 140 4.321 %
Rwork0.193 --
obs0.195 3240 99.5 %
Solvent computationSolvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.71 Å2
Baniso -1Baniso -2Baniso -3
1--0.502 Å20 Å20 Å2
2--0.442 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.8→22.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms258 0 1 18 277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021272
X-RAY DIFFRACTIONr_bond_other_d0.0010.02192
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.931368
X-RAY DIFFRACTIONr_angle_other_deg0.9343459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.026533
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.55521.33315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.4821541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.467153
X-RAY DIFFRACTIONr_chiral_restr0.0940.234
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021311
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0264
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9781.5162
X-RAY DIFFRACTIONr_mcbond_other0.1951.564
X-RAY DIFFRACTIONr_mcangle_it1.7642256
X-RAY DIFFRACTIONr_scbond_it2.8053110
X-RAY DIFFRACTIONr_scangle_it4.6054.5111
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å
RfactorNum. reflection% reflection
Rfree0.273 10 -
Rwork0.24 213 -
obs--94.09 %

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