[English] 日本語
Yorodumi
- PDB-8rir: S103A mutant of the BTB domain of ZBTB8A from Xenopus laevis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rir
TitleS103A mutant of the BTB domain of ZBTB8A from Xenopus laevis
ComponentsZinc finger and BTB domain-containing protein 8A.1-A
KeywordsTRANSCRIPTION / Transcription regulation / BTB domain / polymerisation
Function / homology
Function and homology information


DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
: / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / 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. ...: / BTB/POZ domain / BTB domain profile. / Zinc finger, C2H2 type / 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
Similarity search - Domain/homology
Zinc finger and BTB domain-containing protein 8A.1-A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.72 Å
AuthorsCoste, F. / Suskiewicz, M.J.
Funding support France, 1items
OrganizationGrant numberCountry
Centre National de la Recherche Scientifique (CNRS) France
CitationJournal: Mol.Cell / Year: 2024
Title: Dynamic BTB-domain filaments promote clustering of ZBTB proteins.
Authors: Mance, L. / Bigot, N. / Zhamungui Sanchez, E. / Coste, F. / Martin-Gonzalez, N. / Zentout, S. / Biliskov, M. / Pukalo, Z. / Mishra, A. / Chapuis, C. / Arteni, A.A. / Lateur, A. / Goffinont, ...Authors: Mance, L. / Bigot, N. / Zhamungui Sanchez, E. / Coste, F. / Martin-Gonzalez, N. / Zentout, S. / Biliskov, M. / Pukalo, Z. / Mishra, A. / Chapuis, C. / Arteni, A.A. / Lateur, A. / Goffinont, S. / Gaudon, V. / Talhaoui, I. / Casuso, I. / Beaufour, M. / Garnier, N. / Artzner, F. / Cadene, M. / Huet, S. / Castaing, B. / Suskiewicz, M.J.
History
DepositionDec 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Zinc finger and BTB domain-containing protein 8A.1-A
B: Zinc finger and BTB domain-containing protein 8A.1-A


Theoretical massNumber of molelcules
Total (without water)35,1482
Polymers35,1482
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-23 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.149, 154.149, 154.149
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Space group name HallP4bd2ab3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+3/4,z+1/4,-y+1/4
#4: z+3/4,y+1/4,-x+1/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+3/4,x+1/4,-z+1/4
#20: -y+3/4,-x+3/4,-z+3/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+3/4,-y+3/4,-x+3/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+3/4,-z+3/4,-y+3/4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 5 through 57 or (resid 58...
d_2ens_1(chain "B" and (resid 5 through 32 or (resid 33...

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 5 - 126 / Label seq-ID: 7 - 128

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.999414292803, 0.0184922497936, 0.0287942362145), (-0.0228296235373, -0.987102730016, -0.158451912842), (0.0254927368235, -0.159016467989, 0.986946747944)Vector: -32. ...NCS oper: (Code: given
Matrix: (-0.999414292803, 0.0184922497936, 0.0287942362145), (-0.0228296235373, -0.987102730016, -0.158451912842), (0.0254927368235, -0.159016467989, 0.986946747944)
Vector: -32.912499973, 75.2463619957, 6.41520092125)

-
Components

#1: Protein Zinc finger and BTB domain-containing protein 8A.1-A


Mass: 17573.959 Da / Num. of mol.: 2 / Mutation: S103A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: zbtb8a.1-a, zbtb8, zbtb8.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q0IH98
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.52 Å3/Da / Density % sol: 77.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: caesium chloride, MES, Jeffamine M-600

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98012 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98012 Å / Relative weight: 1
ReflectionResolution: 3.72→48.75 Å / Num. obs: 7053 / % possible obs: 99.9 % / Redundancy: 19.1 % / Biso Wilson estimate: 144.79 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.047 / Net I/σ(I): 10.4
Reflection shellResolution: 3.72→4.16 Å / Redundancy: 20.1 % / Mean I/σ(I) obs: 2 / Num. unique obs: 1944 / CC1/2: 0.786 / Rpim(I) all: 0.411 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.72→44.5 Å / SU ML: 0.5196 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.3131
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2897 730 10.4 %
Rwork0.2605 6289 -
obs0.2634 7019 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 142.01 Å2
Refinement stepCycle: LAST / Resolution: 3.72→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1793 0 0 0 1793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00141827
X-RAY DIFFRACTIONf_angle_d0.31812484
X-RAY DIFFRACTIONf_chiral_restr0.0342297
X-RAY DIFFRACTIONf_plane_restr0.0019320
X-RAY DIFFRACTIONf_dihedral_angle_d10.5082602
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.502810144336 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.72-4.010.34621340.35851233X-RAY DIFFRACTION99.93
4.01-4.410.27951480.30311216X-RAY DIFFRACTION100
4.41-5.040.31450.2681229X-RAY DIFFRACTION99.93
5.05-6.350.33011460.29211260X-RAY DIFFRACTION100
6.36-44.50.26551570.21971351X-RAY DIFFRACTION99.34
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)
10.9258238232811.06065855709-0.6535723733921.63421787595-0.2613769673520.785555808349-0.1726394684450.4770223917790.0177229190939-0.07172800082150.134258904867-0.276597958387-0.18343172507-0.173433754319-0.0007760974787960.672210809524-0.04257796882840.09359991846861.15310802191-0.0992429902181.27805037171-23.077670244827.6887863748-14.6582370397
20.786209792142-0.7606171790280.07090546283722.52062295857-0.5805005611920.3066379894870.007217778991850.6546399042530.4908260437760.225568233746-0.207108065235-0.188961606927-0.5501931455720.137673231909-8.26887527204E-50.797957931714-0.078337229289-0.1329200660661.30779618470.12374389051.19647655346-9.7566956650750.9813595631-12.9533738639
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'A' and resid 4 through 126)AA4 - 1261 - 123
22(chain 'B' and resid 5 through 126)BB5 - 1261 - 122

+
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