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- PDB-4f2j: Crystal structure of ZNF217 bound to DNA, P6522 crystal form -

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Basic information

Entry
Database: PDB / ID: 4f2j
TitleCrystal structure of ZNF217 bound to DNA, P6522 crystal form
Components
  • 5'-D(*TP*TP*TP*GP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*TP*CP*TP*GP*CP*A)-3'
  • Zinc finger protein 217
KeywordsMETAL BINDING PROTEIN/DNA / Zinc Finger / Transcription Factor / DNA Binding / Nucleus / METAL BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


histone deacetylase complex / Negative Regulation of CDH1 Gene Transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription ...histone deacetylase complex / Negative Regulation of CDH1 Gene Transcription / DNA-binding transcription repressor activity, RNA polymerase II-specific / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / Classic Zinc Finger / Double Stranded RNA Binding Domain / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Zinc finger protein 217
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 2.64 Å
AuthorsVandevenne, M.S. / Jacques, D.A. / Guss, J.M. / Mackay, J.P.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: New insights into DNA recognition by zinc fingers revealed by structural analysis of the oncoprotein ZNF217
Authors: Vandevenne, M.S. / Jacques, D.A. / Artuz, C. / Nguyen, C.D. / Kwan, A.H. / Segal, D.J. / Matthews, J.M. / Crossley, M. / Guss, J.M. / Mackay, J.P.
History
DepositionMay 8, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: 5'-D(*TP*TP*TP*GP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*TP*CP*TP*GP*CP*A)-3'
C: Zinc finger protein 217
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1044
Polymers12,9732
Non-polymers1312
Water00
1
A: 5'-D(*TP*TP*TP*GP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*TP*CP*TP*GP*CP*A)-3'
C: Zinc finger protein 217
hetero molecules

A: 5'-D(*TP*TP*TP*GP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*TP*CP*TP*GP*CP*A)-3'
C: Zinc finger protein 217
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2078
Polymers25,9454
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+1/31
Buried area5120 Å2
ΔGint-35 kcal/mol
Surface area13010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.928, 56.928, 242.542
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: DNA chain 5'-D(*TP*TP*TP*GP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*TP*CP*TP*GP*CP*A)-3'


Mass: 6123.977 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein Zinc finger protein 217 / transcription factor ZnF217


Mass: 6848.725 Da / Num. of mol.: 1 / Fragment: Zinc fingers 6 and 7 (UNP RESIDUES 469-523)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZNF217, ZABC1 / Plasmid: pMAL / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2 / References: UniProt: O75362
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Mosaicity (°)
14.3771.870.834
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop720% PEG 3350, 0.2M Sodium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, hanging drop720% PEG 3350, 0.2M Sodium sulfate, 10mM Trimethyllead acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
Detector
TypeIDDetectorDate
MAR scanner 345 mm plate1IMAGE PLATESep 6, 2011
MAR scanner 345 mm plate2IMAGE PLATESep 15, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1OSMIC VARIMAXSINGLE WAVELENGTHMx-ray1
2OSMIC VARIMAXSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionRedundancy: 10.4 % / Av σ(I) over netI: 28.64 / Number: 79317 / Rmerge(I) obs: 0.097 / Χ2: 1.06 / D res high: 2.63 Å / D res low: 50 Å / Num. obs: 7637 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
7.135099.810.0470.91313.6
5.667.1310010.0761.09814.8
4.955.6610010.1071.05715.3
4.54.9510010.1321.16515.2
4.174.510010.1461.01715.6
3.934.1710010.1741.06615.4
3.733.9310010.2271.08115.9
3.573.7310010.2421.02816
3.433.5710010.371.08115.3
3.313.4399.210.2291.0927.2
3.213.3198.110.1311.046.1
3.123.2198.910.1941.0776
3.043.1298.110.3811.0595.9
2.963.0499.210.5281.0925.9
2.892.9699.210.6281.0836.1
2.832.8999.210.6291.075.8
2.782.8399.210.6621.0946
2.722.7810010.7361.0845.7
2.682.7299.710.5411.0755.9
2.632.6899.510.4471.0335.9
ReflectionResolution: 2.64→99 Å / Num. all: 7517 / Num. obs: 7517 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.091 / Χ2: 3.235 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.64-2.681.80.1883440.9231,295
2.68-2.731.80.2483680.8831,299.5
2.73-2.791.80.3053480.841,299.4
2.79-2.841.80.2323790.9191,299
2.84-2.91.70.2813490.9131,299.1
2.9-2.971.80.2653700.9681,298.9
2.97-3.051.80.2083520.9921,299.2
3.05-3.131.70.1493690.8871,298.9
3.13-3.221.80.0683640.9571,298.6
3.22-3.321.70.0433680.9751,298.7
3.32-3.441.70.0353570.7951,298.1
3.44-3.583.30.2343873.2211,299.2
3.58-3.743.50.0943641.381,299.5
3.74-3.943.40.0923771.3751,299.2
3.94-4.193.30.083841.721,299
4.19-4.513.30.0683781.8841,299.2
4.51-4.973.30.0653932.3981,298.7
4.97-5.683.20.0593982.9431,298.8
5.68-7.163.10.0514123.7711,298.3
7.16-992.80.10845620.0351,294

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Phasing

PhasingMethod: SIRAS
Phasing dmFOM : 0.57 / FOM acentric: 0.55 / FOM centric: 0.62 / Reflection: 7411 / Reflection acentric: 5383 / Reflection centric: 2028
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
4.7-7.50.880.90.851026653373
3.8-4.70.80.810.781237882355
3.3-3.80.670.680.651245938307
2.8-3.30.380.370.3921831680503
2.6-2.80.250.250.2413481076272

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVE2.15phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: SIRAS / Resolution: 2.64→48.31 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.2778 / WRfactor Rwork: 0.2563 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7219 / SU B: 32.121 / SU ML: 0.285 / SU R Cruickshank DPI: 0.3269 / SU Rfree: 0.2467 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.327 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2643 344 4.6 %RANDOM
Rwork0.2523 ---
obs0.2529 7467 99.04 %-
all-7467 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 68.69 Å2 / Biso mean: 96.517 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-5.31 Å22.66 Å20 Å2
2--5.31 Å20 Å2
3----7.97 Å2
Refinement stepCycle: LAST / Resolution: 2.64→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms449 406 2 0 857
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.021917
X-RAY DIFFRACTIONr_bond_other_d0.0020.02515
X-RAY DIFFRACTIONr_angle_refined_deg2.3182.4891319
X-RAY DIFFRACTIONr_angle_other_deg1.12531253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.45551
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.74721.11127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0561579
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.995155
X-RAY DIFFRACTIONr_chiral_restr0.0830.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02723
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02159
X-RAY DIFFRACTIONr_mcbond_it2.2632258
X-RAY DIFFRACTIONr_mcbond_other0.5692104
X-RAY DIFFRACTIONr_mcangle_it3.8193411
X-RAY DIFFRACTIONr_scbond_it8.1224659
X-RAY DIFFRACTIONr_scangle_it10.1856908
LS refinement shellResolution: 2.64→2.709 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 22 -
Rwork0.422 508 -
all-530 -
obs--99.07 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
18.14615.13179.12874.69985.332114.58240.05140.1885-0.3932-0.03940.05190.03581.21670.1555-0.10340.49270.20840.00150.3269-0.08220.53531.225638.213338.23
27.42510.0596-2.55389.3964.346827.8988-0.3465-0.50840.0928-0.1847-0.42590.7424-0.2368-2.07780.77230.4751-0.1111-0.16240.6739-0.17640.563418.155742.250730.4185
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 19
2X-RAY DIFFRACTION2C471 - 522
3X-RAY DIFFRACTION2C601 - 602

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