[English] 日本語
Yorodumi
- PDB-5vmv: Kaiso (ZBTB33) zinc finger DNA binding domain in complex with its... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vmv
TitleKaiso (ZBTB33) zinc finger DNA binding domain in complex with its double CpG-methylated DNA consensus binding site
Components
  • DNA (5'-D(*TP*GP*CP*TP*TP*CP*TP*(5CM)P*GP*(5CM)P*GP*AP*GP*AP*AP*GP*CP*A)-3')
  • Transcriptional regulator Kaiso
KeywordsTRANSCRIPTION/DNA / DNA methylation / Zinc finger / Transcriptional regulator / TRANSCRIPTION-DNA complex
Function / homology
Function and homology information


regulation of immune system process / methyl-CpG binding / regulation of cytokine production / Wnt signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / 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 ...regulation of immune system process / methyl-CpG binding / regulation of cytokine production / Wnt signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / 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 / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
BTB/POZ domain / BTB domain profile. / 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
Similarity search - Domain/homology
DNA / DNA (> 10) / Transcriptional regulator Kaiso
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.313 Å
AuthorsNikolova, E.N. / Stanfield, R.L. / Martinez-Yamout, M.A. / 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: 2018
Title: CH···O Hydrogen Bonds Mediate Highly Specific Recognition of Methylated CpG Sites by the Zinc Finger Protein Kaiso.
Authors: Nikolova, E.N. / Stanfield, R.L. / Dyson, H.J. / Wright, P.E.
History
DepositionApr 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / 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_audit_support.funding_organization / _pdbx_audit_support.grant_number / _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
Revision 1.3Oct 4, 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*TP*(5CM)P*GP*(5CM)P*GP*AP*GP*AP*AP*GP*CP*A)-3')
E: DNA (5'-D(*TP*GP*CP*TP*TP*CP*TP*(5CM)P*GP*(5CM)P*GP*AP*GP*AP*AP*GP*CP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5397
Polymers27,3073
Non-polymers2324
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, complex formation also monitored by NMR and biolayer interferometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-15 kcal/mol
Surface area11470 Å2
Unit cell
Length a, b, c (Å)44.219, 183.792, 104.566
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-846-

HOH

-
Components

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


Mass: 16217.771 Da / Num. of mol.: 1 / Fragment: residues 471-604
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB33, KAISO, ZNF348 / Plasmid: PET21D / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) [DNAY] / References: UniProt: Q86T24
#2: DNA chain DNA (5'-D(*TP*GP*CP*TP*TP*CP*TP*(5CM)P*GP*(5CM)P*GP*AP*GP*AP*AP*GP*CP*A)-3')


Mass: 5544.634 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.89 Å3/Da / Density % sol: 68.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris pH 8.5, 0.2 M Ammonium Acetate, 30 % (v/v) 2-propanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.313→45.443 Å / Num. obs: 17383 / % possible obs: 90.81 % / Redundancy: 6 % / Biso Wilson estimate: 35.35 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.08636 / Net I/σ(I): 13.11
Reflection shellResolution: 2.313→2.396 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.2765 / Mean I/σ(I) obs: 4.29 / Num. unique obs: 946 / CC1/2: 0.945 / % possible all: 51.16

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.9_1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F6N

4f6n


Resolution: 2.313→45.443 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 1738 10.01 %
Rwork0.203 --
obs0.2075 17361 90.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.313→45.443 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 736 4 76 1799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112116
X-RAY DIFFRACTIONf_angle_d1.2033012
X-RAY DIFFRACTIONf_dihedral_angle_d27.666822
X-RAY DIFFRACTIONf_chiral_restr0.05315
X-RAY DIFFRACTIONf_plane_restr0.005221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3135-2.38160.2967770.2229692X-RAY DIFFRACTION50
2.3816-2.45840.2331970.2323863X-RAY DIFFRACTION61
2.4584-2.54630.3081310.23441175X-RAY DIFFRACTION84
2.5463-2.64820.26281490.23531341X-RAY DIFFRACTION95
2.6482-2.76870.26881570.2321412X-RAY DIFFRACTION98
2.7687-2.91470.26851570.21331409X-RAY DIFFRACTION100
2.9147-3.09720.25651560.22071410X-RAY DIFFRACTION100
3.0972-3.33630.28231590.21981437X-RAY DIFFRACTION100
3.3363-3.67190.24861610.18891439X-RAY DIFFRACTION100
3.6719-4.20290.22361590.17361432X-RAY DIFFRACTION100
4.2029-5.2940.21151630.17541471X-RAY DIFFRACTION100
5.294-45.45180.24941720.21831542X-RAY DIFFRACTION99
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)
10.7296-1.792-0.66775.49210.40511.9339-0.1111-0.2972-0.6070.34740.0726-0.09770.43790.1881-0.30060.88130.0558-0.02040.1874-0.12951.289820.6944.886527.6925
23.85942.68362.43784.04731.8574.79640.08720.2245-0.4898-0.11870.20120.2610.50840.2725-0.20640.72430.04430.00360.0781-0.16341.053217.03179.4921.9111
30.5135-0.53240.64682.53730.14481.36880.1431-0.2746-0.7745-0.0790.28941.42170.863-0.29820.09510.4353-0.1216-0.03460.19090.02321.44475.525818.742223.5479
41.08531.23840.46691.57580.12421.28080.18210.0191-0.332-0.5424-0.00750.89310.3983-0.2259-0.25820.53650.0207-0.28110.0277-0.14321.31262.125424.762818.0569
51.5341-1.19440.49772.214-2.29134.7098-0.1007-0.1025-0.4803-0.03480.37760.32130.0726-0.3137-0.28030.38770.028-0.0380.2296-0.08150.65986.82331.649621.0907
67.65570.8547-2.0680.71970.6411.76310.00770.3741-0.0117-0.1465-0.02740.37590.070.0418-0.02930.20660.0481-0.05070.15610.00460.401621.243841.528919.3166
76.2006-3.1204-5.53455.08375.15416.5144-0.5048-1.2796-1.08461.41990.4116-0.88431.03350.83630.23010.44160.0223-0.07480.40160.00610.701431.092338.542524.4438
83.9535-3.81020.54773.99850.54163.3327-0.1462-0.7279-0.8330.58910.08810.39240.3563-0.0884-0.13490.40630.06020.03350.17690.03010.532212.274638.865329.9899
92.8524-0.64783.09564.3756-4.80637.39310.42150.77040.237-0.29780.19060.756-0.54670.3205-0.49080.70330.1370.18310.4702-0.00030.491919.719929.61610.6758
106.3471.55581.19350.9323-0.89375.56910.1177-1.75960.39352.46780.38060.89390.7411-1.067-0.41081.3790.16950.43240.80660.08650.934711.426722.111439.3357
115.4242-1.3399-1.85081.00790.79590.8049-0.4082-2.5111-0.7051.98040.03780.23731.98770.36530.96461.706-0.01940.5121.13680.37011.06649.404919.956843.7955
128.1278-3.4594-1.33326.02682.11462.6601-0.26481.8078-0.3831-1.57270.1095-0.01650.2552-0.29650.20690.9167-0.21950.09590.566-0.06390.485620.346425.712913.8652
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 481 through 496 )
2X-RAY DIFFRACTION2chain 'A' and (resid 497 through 505 )
3X-RAY DIFFRACTION3chain 'A' and (resid 506 through 527 )
4X-RAY DIFFRACTION4chain 'A' and (resid 528 through 533 )
5X-RAY DIFFRACTION5chain 'A' and (resid 534 through 545 )
6X-RAY DIFFRACTION6chain 'A' and (resid 546 through 573 )
7X-RAY DIFFRACTION7chain 'A' and (resid 574 through 583 )
8X-RAY DIFFRACTION8chain 'A' and (resid 584 through 596 )
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 8 )
10X-RAY DIFFRACTION10chain 'D' and (resid 9 through 18 )
11X-RAY DIFFRACTION11chain 'E' and (resid 19 through 26 )
12X-RAY DIFFRACTION12chain 'E' and (resid 27 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