[English] 日本語
Yorodumi
- PDB-6dfb: Kaiso (ZBTB33) K539A zinc finger DNA binding domain in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6dfb
TitleKaiso (ZBTB33) K539A zinc finger DNA binding domain in complex with the specific Kaiso binding sequence (KBS)
Components
  • DNA (5'-D(*CP*GP*TP*TP*AP*TP*TP*GP*GP*CP*AP*GP*GP*AP*AP*GP*CP*A)-3')
  • DNA (5'-D(*TP*GP*CP*TP*TP*CP*CP*TP*GP*CP*CP*AP*AP*TP*AP*AP*CP*G)-3')
  • Transcriptional regulator Kaiso
KeywordsDNA BINDING PROTEIN/DNA / DNA methylation / Zinc finger / Transcriptional regulator / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


methyl-CpG binding / regulation of immune system process / regulation of cytokine production / DNA-binding transcription repressor activity, RNA polymerase II-specific / Wnt signaling pathway / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding ...methyl-CpG binding / regulation of immune system process / regulation of cytokine production / DNA-binding transcription repressor activity, RNA polymerase II-specific / Wnt signaling pathway / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin / nucleolus / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
: / Classic Zinc Finger / BTB/POZ domain / BTB domain profile. / 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. / 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 / Zinc finger C2H2 type domain signature. / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional regulator Kaiso
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsNikolova, E.N. / Stanfield, R.L. / Dyson, H.J. / Wright, P.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM36643 United States
CitationJournal: Biochemistry / Year: 2020
Title: A conformational switch in the zinc finger protein Kaiso mediates differential readout of specific and methylated DNA sequences.
Authors: Nikolova, E.N. / Stanfield, R.L. / Dyson, H.J. / Wright, P.E.
History
DepositionMay 14, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1May 13, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.3Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transcriptional regulator Kaiso
D: DNA (5'-D(*TP*GP*CP*TP*TP*CP*CP*TP*GP*CP*CP*AP*AP*TP*AP*AP*CP*G)-3')
E: DNA (5'-D(*CP*GP*TP*TP*AP*TP*TP*GP*GP*CP*AP*GP*GP*AP*AP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4247
Polymers27,1923
Non-polymers2324
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, NMR spectroscopy, biolayer interferometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-34 kcal/mol
Surface area12150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.467, 184.271, 105.188
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-704-

CL

21A-869-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Transcriptional regulator Kaiso / Zinc finger and BTB domain-containing protein 33


Mass: 16159.668 Da / Num. of mol.: 1 / Fragment: residues 471-604 / Mutation: K539A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB33, KAISO, ZNF348 / Plasmid: PLASMID / Details (production host): PET21D / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) [DNAY] / References: UniProt: Q86T24

-
DNA chain , 2 types, 2 molecules DE

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


Mass: 5451.542 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*GP*TP*TP*AP*TP*TP*GP*GP*CP*AP*GP*GP*AP*AP*GP*CP*A)-3')


Mass: 5580.628 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 3 types, 196 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / 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.: 192 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 0.2 M Disodium Tartrate, 20 % PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.66→42.198 Å / Num. obs: 50786 / % possible obs: 98.34 % / Redundancy: 11.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.0738 / Rrim(I) all: 0.0772 / Net I/σ(I): 14.89
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 7.9 % / Mean I/σ(I) obs: 2.83 / Num. unique obs: 4731 / CC1/2: 0.945 / % possible all: 92.65

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F6M

4f6m


Resolution: 1.66→42.198 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.11
RfactorNum. reflection% reflection
Rfree0.2016 5075 10 %
Rwork0.1788 --
obs0.1811 50730 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.66→42.198 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms991 732 4 192 1919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091902
X-RAY DIFFRACTIONf_angle_d1.0892700
X-RAY DIFFRACTIONf_dihedral_angle_d24.671748
X-RAY DIFFRACTIONf_chiral_restr0.044284
X-RAY DIFFRACTIONf_plane_restr0.006217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.69870.30283060.27272743X-RAY DIFFRACTION90
1.6987-1.74110.26133300.23942987X-RAY DIFFRACTION98
1.7411-1.78820.23693370.21733036X-RAY DIFFRACTION99
1.7882-1.84080.23923370.20493029X-RAY DIFFRACTION99
1.8408-1.90020.22153360.2013025X-RAY DIFFRACTION99
1.9002-1.96820.2383360.20723019X-RAY DIFFRACTION98
1.9682-2.0470.22773380.21243033X-RAY DIFFRACTION99
2.047-2.14010.23723400.1943055X-RAY DIFFRACTION100
2.1401-2.25290.23913410.19693072X-RAY DIFFRACTION99
2.2529-2.39410.22133400.19833051X-RAY DIFFRACTION99
2.3941-2.57890.253410.19193074X-RAY DIFFRACTION98
2.5789-2.83840.21983440.20493100X-RAY DIFFRACTION100
2.8384-3.2490.20763430.18463081X-RAY DIFFRACTION99
3.249-4.09280.16243450.15993102X-RAY DIFFRACTION98
4.0928-42.21190.17573610.14753248X-RAY DIFFRACTION98
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)
13.91253.1754-2.29998.8824-1.43295.50860.1396-0.15220.9841-0.25640.08540.595-0.89810.038-0.26650.549-0.0399-0.02950.2184-0.02670.5968-5.82-8.831227.4092
25.52670.9599-1.35136.1168-0.14784.0625-0.06030.1070.62990.3460.23711.43-0.2743-0.2909-0.23440.25670.01350.01570.2882-0.05180.5416-18.8394-27.724231.9741
33.2676-1.36282.65135.62440.15824.08140.04940.1105-0.0146-0.09570.0161-0.491-0.15340.3074-0.04980.1388-0.04440.04310.2207-0.00050.22062.3387-40.581531.5609
44.60620.7899-0.20097.19391.45172.2397-0.2930.82990.5431-1.04680.21520.6684-0.5207-0.08230.03250.3795-0.0529-0.06650.35470.06840.2757-9.6852-38.502622.4199
55.4292-0.1326-0.8035.66483.92295.7884-0.06620.43420.2822-0.02070.15540.82620.5677-0.285-0.2590.3873-0.118-0.09560.23130.04790.2543-8.2436-24.714925.0464
66.51090.0117-1.13076.67860.37061.4657-0.25050.6380.3286-0.13150.1450.5579-0.70120.06060.05840.4381-0.0569-0.09490.25370.04190.2036-7.5213-23.617924.5184
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 481 through 517 )
2X-RAY DIFFRACTION2chain 'A' and (resid 518 through 545 )
3X-RAY DIFFRACTION3chain 'A' and (resid 546 through 583 )
4X-RAY DIFFRACTION4chain 'A' and (resid 584 through 597 )
5X-RAY DIFFRACTION5chain 'D' and (resid 1 through 18 )
6X-RAY DIFFRACTION6chain 'E' and (resid 19 through 36 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more