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- PDB-6e94: Crystal Structure of ZBTB38 C-terminal Zinc Fingers 6-9 K1055R in... -

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Basic information

Entry
Database: PDB / ID: 6.0E+94
TitleCrystal Structure of ZBTB38 C-terminal Zinc Fingers 6-9 K1055R in complex with methylated DNA
Components
  • DNA (5'-D(*GP*CP*AP*CP*TP*CP*AP*TP*(DCM)P*GP*GP*(DCM)P*GP*CP*AP*GP*AP*C)-3')
  • DNA (5'-D(*GP*TP*CP*TP*GP*(DCM)P*GP*CP*(DCM)P*GP*AP*TP*GP*AP*GP*TP*GP*C)-3')
  • Zinc finger and BTB domain-containing protein 38
KeywordsDNA BINDING PROTEIN/DNA / ZBTB38 methylated DNA Zinc Finger / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


methyl-CpG binding / regulation of DNA replication / chromosome / blood microparticle / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA damage response / regulation of DNA-templated transcription ...methyl-CpG binding / regulation of DNA replication / chromosome / blood microparticle / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA damage response / regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Classic Zinc Finger / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily ...Classic Zinc Finger / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / Double Stranded RNA Binding Domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / SKP1/BTB/POZ domain 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 and BTB domain-containing protein 38
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.594 Å
AuthorsHudson, N.O. / Whitby, F.G. / Buck-Koehntop, B.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1715379 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural insights into methylated DNA recognition by the C-terminal zinc fingers of the DNA reader protein ZBTB38.
Authors: Hudson, N.O. / Whitby, F.G. / Buck-Koehntop, B.A.
History
DepositionJul 31, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 13, 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_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc finger and BTB domain-containing protein 38
C: DNA (5'-D(*GP*TP*CP*TP*GP*(DCM)P*GP*CP*(DCM)P*GP*AP*TP*GP*AP*GP*TP*GP*C)-3')
D: DNA (5'-D(*GP*CP*AP*CP*TP*CP*AP*TP*(DCM)P*GP*GP*(DCM)P*GP*CP*AP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6167
Polymers25,3553
Non-polymers2624
Water3,639202
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7560 Å2
ΔGint-23 kcal/mol
Surface area11130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.804, 77.270, 103.756
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-130-

HOH

21D-138-

HOH

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Components

#1: Protein Zinc finger and BTB domain-containing protein 38


Mass: 14263.491 Da / Num. of mol.: 1 / Mutation: K1055R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB38 / Plasmid: pET-21d / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q8NAP3
#2: DNA chain DNA (5'-D(*GP*TP*CP*TP*GP*(DCM)P*GP*CP*(DCM)P*GP*AP*TP*GP*AP*GP*TP*GP*C)-3')


Mass: 5576.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*GP*CP*AP*CP*TP*CP*AP*TP*(DCM)P*GP*GP*(DCM)P*GP*CP*AP*GP*AP*C)-3')


Mass: 5514.611 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.25M ammonium Chloride MES (pH:6.0) 19% PEG 6000

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Data collection

DiffractionMean temperature: 277.15 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.59→38.8 Å / Num. obs: 37856 / % possible obs: 99.3 % / Redundancy: 12.9 % / CC1/2: 0.61 / Net I/σ(I): 9.4
Reflection shellResolution: 1.59→1.62 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementResolution: 1.594→35.402 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.76
RfactorNum. reflection% reflection
Rfree0.2183 7161 9.98 %
Rwork0.1939 --
obs0.1963 37492 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.594→35.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms935 736 4 202 1877
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071782
X-RAY DIFFRACTIONf_angle_d1.0162549
X-RAY DIFFRACTIONf_dihedral_angle_d21.209909
X-RAY DIFFRACTIONf_chiral_restr0.049266
X-RAY DIFFRACTIONf_plane_restr0.005201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5941-1.61230.40971490.38031321X-RAY DIFFRACTION61
1.6123-1.63120.32592410.31442188X-RAY DIFFRACTION99
1.6312-1.65110.28442370.25962165X-RAY DIFFRACTION99
1.6511-1.6720.27632430.25162182X-RAY DIFFRACTION99
1.672-1.6940.24462510.22992228X-RAY DIFFRACTION99
1.694-1.71720.28532400.24442169X-RAY DIFFRACTION100
1.7172-1.74180.28162400.24762197X-RAY DIFFRACTION99
1.7418-1.76780.2432430.20912160X-RAY DIFFRACTION100
1.7678-1.79540.21572490.20462225X-RAY DIFFRACTION99
1.7954-1.82480.20272410.21832175X-RAY DIFFRACTION100
1.8248-1.85630.22362370.20922203X-RAY DIFFRACTION100
1.8563-1.890.2692440.25412187X-RAY DIFFRACTION99
1.89-1.92640.32762270.32092089X-RAY DIFFRACTION94
1.9264-1.96570.26072490.23772160X-RAY DIFFRACTION98
1.9657-2.00840.24552460.21172172X-RAY DIFFRACTION100
2.0084-2.05520.25512400.21972208X-RAY DIFFRACTION100
2.0552-2.10650.29772260.24112086X-RAY DIFFRACTION94
2.1065-2.16350.25242430.19942200X-RAY DIFFRACTION100
2.1635-2.22710.2372470.19882161X-RAY DIFFRACTION100
2.2271-2.2990.27662280.22522118X-RAY DIFFRACTION96
2.299-2.38120.22822490.19052221X-RAY DIFFRACTION100
2.3812-2.47650.21172420.19322186X-RAY DIFFRACTION100
2.4765-2.58920.22852480.18812198X-RAY DIFFRACTION100
2.5892-2.72560.2182430.20282178X-RAY DIFFRACTION99
2.7256-2.89630.24552490.19742210X-RAY DIFFRACTION100
2.8963-3.11980.27822470.19782189X-RAY DIFFRACTION100
3.1198-3.43360.19842380.18372191X-RAY DIFFRACTION99
3.4336-3.92980.17142400.15952205X-RAY DIFFRACTION100
3.9298-4.9490.13982440.14052191X-RAY DIFFRACTION100
4.949-35.41070.15992400.13912210X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -12.6447 Å / Origin y: -20.0975 Å / Origin z: -14.0457 Å
111213212223313233
T0.1387 Å2-0.0295 Å20.0034 Å2-0.1381 Å20.0105 Å2--0.1397 Å2
L0.408 °2-0.0589 °20.4373 °2-0.3427 °20.1759 °2--0.8392 °2
S-0.0762 Å °0.0464 Å °0.0203 Å °-0.0232 Å °0.0024 Å °0.0075 Å °-0.0452 Å °0.1044 Å °-0.002 Å °
Refinement TLS groupSelection details: all

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