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- PDB-5kl4: Wilms Tumor Protein (WT1) ZnF2-4 Q369H in complex with formylated DNA -

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Basic information

Entry
Database: PDB / ID: 5kl4
TitleWilms Tumor Protein (WT1) ZnF2-4 Q369H in complex with formylated DNA
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(5FC)P*GP*T)-3')
  • DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*CP*GP*C)-3')
  • Wilms tumor protein
KeywordsTRANSCRIPTION/DNA / Wilms Tumor Protein / WT1 / zinc finger / 5-formyl cytosine / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


posterior mesonephric tubule development / negative regulation of metanephric glomerular mesangial cell proliferation / positive regulation of metanephric ureteric bud development / thorax and anterior abdomen determination / metanephric epithelium development / regulation of animal organ formation / adrenal cortex formation / : / negative regulation of female gonad development / positive regulation of heart growth ...posterior mesonephric tubule development / negative regulation of metanephric glomerular mesangial cell proliferation / positive regulation of metanephric ureteric bud development / thorax and anterior abdomen determination / metanephric epithelium development / regulation of animal organ formation / adrenal cortex formation / : / negative regulation of female gonad development / positive regulation of heart growth / visceral serous pericardium development / glomerular basement membrane development / diaphragm development / sex determination / mesenchymal to epithelial transition / metanephric mesenchyme development / metanephric S-shaped body morphogenesis / positive regulation of male gonad development / cellular response to gonadotropin stimulus / Transcriptional regulation of testis differentiation / gonad development / podocyte differentiation / cardiac muscle cell fate commitment / double-stranded methylated DNA binding / hemi-methylated DNA-binding / tissue development / male genitalia development / glomerulus development / camera-type eye development / C2H2 zinc finger domain binding / ureteric bud development / branching involved in ureteric bud morphogenesis / adrenal gland development / germ cell development / vasculogenesis / cellular response to cAMP / epithelial cell differentiation / RNA splicing / kidney development / negative regulation of cell growth / positive regulation of miRNA transcription / male gonad development / heart development / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / negative regulation of translation / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of gene expression / nucleolus / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Wilm's tumour protein, N-terminal / Wilm's tumour protein / 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 ...Wilm's tumour protein, N-terminal / Wilm's tumour protein / 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) / Wilms tumor protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.783 Å
AuthorsHashimoto, H. / Cheng, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM049245 United States
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Denys-Drash syndrome associated WT1 glutamine 369 mutants have altered sequence-preferences and altered responses to epigenetic modifications.
Authors: Hashimoto, H. / Zhang, X. / Zheng, Y. / Wilson, G.G. / Cheng, X.
History
DepositionJun 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Database references
Revision 1.2Dec 14, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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_conn_type
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Wilms tumor protein
B: DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(5FC)P*GP*T)-3')
C: DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*CP*GP*C)-3')
D: Wilms tumor protein
E: DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(5FC)P*GP*T)-3')
F: DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,70817
Polymers36,0896
Non-polymers62011
Water3,153175
1
A: Wilms tumor protein
B: DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(5FC)P*GP*T)-3')
C: DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3438
Polymers18,0443
Non-polymers2985
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-9 kcal/mol
Surface area8560 Å2
2
D: Wilms tumor protein
E: DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(5FC)P*GP*T)-3')
F: DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3669
Polymers18,0443
Non-polymers3216
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-22 kcal/mol
Surface area8040 Å2
Unit cell
Length a, b, c (Å)35.766, 43.853, 54.808
Angle α, β, γ (deg.)81.95, 88.57, 88.51
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein Wilms tumor protein / / WT33


Mass: 11292.900 Da / Num. of mol.: 2 / Fragment: UNP residues 333-420 / Mutation: Q369H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WT1 / Variant: -KTS / Plasmid: pXC1305 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL codon plus / References: UniProt: P19544

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DNA chain , 2 types, 4 molecules BECF

#2: DNA chain DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(5FC)P*GP*T)-3')


Mass: 3458.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*CP*GP*C)-3')


Mass: 3293.178 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 186 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2 M CaCl2, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Jul 20, 2015
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.783→30 Å / Num. obs: 29040 / % possible obs: 92.9 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.7
Reflection shellResolution: 1.783→1.85 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.7 / % possible all: 69.6

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Processing

Software
NameVersionClassification
PHENIX(dev_2257: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R2R

4r2r


Resolution: 1.783→29.558 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2462 1453 5.01 %Random
Rwork0.2165 ---
obs0.218 28982 92.22 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.783→29.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 896 17 175 2598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152628
X-RAY DIFFRACTIONf_angle_d1.3673683
X-RAY DIFFRACTIONf_dihedral_angle_d21.4731430
X-RAY DIFFRACTIONf_chiral_restr0.068373
X-RAY DIFFRACTIONf_plane_restr0.009319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.783-1.84680.30021010.28061937X-RAY DIFFRACTION65
1.8468-1.92070.31631350.27132518X-RAY DIFFRACTION85
1.9207-2.00810.32141420.2572818X-RAY DIFFRACTION94
2.0081-2.11390.30181550.23442897X-RAY DIFFRACTION97
2.1139-2.24630.25951460.22232903X-RAY DIFFRACTION97
2.2463-2.41970.27441540.2192907X-RAY DIFFRACTION97
2.4197-2.66310.25971530.21852902X-RAY DIFFRACTION98
2.6631-3.04810.26911530.22562926X-RAY DIFFRACTION98
3.0481-3.83890.23591550.20742866X-RAY DIFFRACTION96
3.8389-29.56180.19791590.19542855X-RAY DIFFRACTION95
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)
16.87480.5386-0.92216.6561-0.39567.1642-0.09250.4655-0.176-0.49670.0131-0.0660.43830.17470.02180.2090.031-0.01240.2356-0.01270.246293.434126.9232-145.6934
22.5307-0.91980.67294.5506-0.64523.88310.0947-0.15780.01530.2282-0.2158-0.3773-0.05790.2380.12410.1725-0.0405-0.02320.1634-0.00060.165283.4124141.1401-130.3545
37.2557-2.7168-0.47175.42-1.71082.6017-0.09730.02930.33930.16550.04450.2092-0.3625-0.89780.02490.26730.042-0.00330.27850.00120.237572.0576153.6633-145.3389
41.3767-0.74110.31111.01050.61092.9304-0.01790.41930.1530.1153-0.0991-0.12740.00190.03770.0970.2065-0.0308-0.01350.2510.04880.264483.4629139.3199-142.6845
57.9421.0106-1.23072.8858-1.61171.0914-0.54610.16740.6634-0.13240.2790.03540.04090.10810.24440.21360.00870.00180.3030.05630.237885.1447140.1404-142.2209
66.0849-0.15683.97945.59891.69628.6367-0.5952-0.13440.6914-0.3676-0.0343-0.101-1.959-0.53220.54180.48930.0565-0.02590.3601-0.07020.369969.7303131.39-104.9204
71.468-0.4656-0.6931.74851.13373.7058-0.0118-0.2158-0.08170.068-0.0110.11470.1774-0.13740.0480.1812-0.02520.00050.22390.03010.197877.921112.7927-110.6252
85.1416-0.3174-2.16718.6184-0.72286.4727-0.03920.11250.0339-0.3699-0.0942-0.66470.15510.23990.17530.18360.0203-0.00960.19440.02740.199791.3209117.2574-129.8828
92.1570.7535-0.30012.69380.31241.0098-0.10270.30460.17960.02410.01120.0914-0.0356-0.01490.07220.1973-0.0156-0.0070.2810.0230.160280.1975120.686-115.9081
108.98030.18662.12120.56810.34634.5109-0.59860.508-0.044-0.07690.26740.0113-0.23790.07140.31980.23370.0351-0.01330.25040.03090.225278.855120.3556-116.651
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 348 through 378 )
2X-RAY DIFFRACTION2chain 'A' and (resid 379 through 411 )
3X-RAY DIFFRACTION3chain 'A' and (resid 412 through 437 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 11 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 11 )
6X-RAY DIFFRACTION6chain 'D' and (resid 351 through 366 )
7X-RAY DIFFRACTION7chain 'D' and (resid 367 through 411 )
8X-RAY DIFFRACTION8chain 'D' and (resid 412 through 436 )
9X-RAY DIFFRACTION9chain 'E' and (resid 1 through 11 )
10X-RAY DIFFRACTION10chain 'F' and (resid 1 through 11 )

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