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- PDB-4is1: Crystal structure of ZNF217 bound to DNA -

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Basic information

Entry
Database: PDB / ID: 4is1
TitleCrystal structure of ZNF217 bound to DNA
Components
  • 5'-D(*AP*AP*TP*GP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*TP*CP*TP*GP*CP*A)-3'
  • 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 / METAL BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


histone deacetylase complex / DNA-binding transcription repressor activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 ...histone deacetylase complex / DNA-binding transcription repressor activity, RNA polymerase II-specific / Estrogen-dependent gene expression / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / 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 / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
Classic Zinc Finger / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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. / 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
DepositionJan 16, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Data collection
Revision 1.2Dec 18, 2019Group: Database references / Source and taxonomy
Category: citation / citation_author ...citation / citation_author / pdbx_entity_src_syn / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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_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'
B: 5'-D(*AP*AP*TP*GP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*TP*CP*TP*GP*CP*A)-3'
C: Zinc finger protein 217
D: Zinc finger protein 217
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,52213
Polymers25,9634
Non-polymers5599
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-138 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.670, 40.980, 52.040
Angle α, β, γ (deg.)90.00, 97.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

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DNA chain , 2 types, 2 molecules AB

#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 / Source: (synth.) synthetic construct (others)
#2: DNA chain 5'-D(*AP*AP*TP*GP*CP*AP*GP*AP*AP*TP*CP*GP*AP*TP*TP*CP*TP*GP*CP*A)-3'


Mass: 6142.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein , 1 types, 2 molecules CD

#3: Protein Zinc finger protein 217 / transcription factor ZnF217


Mass: 6848.725 Da / Num. of mol.: 2 / 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

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Non-polymers , 3 types, 66 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.01M ZINC CHLORIDE, 0.1M MES, 20% PEG 6000 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 7, 2011 / Details: OSMIC MIRRORS
RadiationMonochromator: OSMIC VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→61.84 Å / Num. all: 15360 / Num. obs: 15360 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.086
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.898 / Num. unique all: 741 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.7.0029refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F2J

4f2j


Resolution: 2.1→15 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.94 / SU B: 16.982 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26214 769 5 %RANDOM
Rwork0.23741 ---
all0.23873 15360 --
obs0.23873 14519 98.32 %-
Displacement parametersBiso mean: 53.39 Å2
Baniso -1Baniso -2Baniso -3
1--7.91 Å2-0 Å20.33 Å2
2--0.92 Å2-0 Å2
3---6.73 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms909 814 9 57 1789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0151858
X-RAY DIFFRACTIONr_bond_other_d0.0030.021294
X-RAY DIFFRACTIONr_angle_refined_deg1.381.5252673
X-RAY DIFFRACTIONr_angle_other_deg1.53433005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3645106
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.58221.09155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.75215160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6461510
X-RAY DIFFRACTIONr_chiral_restr0.1030.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021541
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02467
LS refinement shellResolution: 2.098→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.567 60 -
Rwork0.435 970 -
obs--89.02 %
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)
15.30623.54750.19063.30650.97091.3073-0.03170.266-0.64130.05550.0052-0.2822-0.031-0.01160.02650.5738-0.00530.01470.3196-0.0030.136519.2549-1.651641.9305
25.473.72210.78672.82710.44470.25250.0682-0.04640.09260.0787-0.0649-0.1133-0.01840.0959-0.00330.5923-0.03110.02750.40160.00940.160226.65230.657241.9564
36.58160.78452.13657.13033.94437.34950.10340.63520.1695-0.1792-0.4025-0.2161-0.1606-0.65580.29910.6185-0.01760.05980.56220.00810.048334.89728.540333.5797
44.13010.14030.4655.9675-0.05553.1234-0.14450.3910.7191-0.1532-0.0370.2462-0.2634-0.07980.18140.5988-0.01610.00020.28010.10060.19078.0054-1.812832.2973
516.62112.6835-1.719116.497-0.63693.5789-0.01950.23820.07470.1399-0.0903-0.58570.00950.0510.10970.3497-0.00050.02430.40190.19850.580522.0628-0.48436.8457
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 20
2X-RAY DIFFRACTION2B1 - 20
3X-RAY DIFFRACTION3C471 - 522
4X-RAY DIFFRACTION3C601 - 602
5X-RAY DIFFRACTION4D470 - 523
6X-RAY DIFFRACTION4D601 - 602
7X-RAY DIFFRACTION5B101
8X-RAY DIFFRACTION5C603

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