[English] 日本語
Yorodumi
- PDB-2if5: Structure of the POZ domain of human LRF, a master regulator of o... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2if5
TitleStructure of the POZ domain of human LRF, a master regulator of oncogenesis
ComponentsZinc finger and BTB domain-containing protein 7A
KeywordsTRANSCRIPTION / POZ domain / BTB domain / POK / proto oncogene / transcription factor
Function / homology
Function and homology information


regulation of transcription regulatory region DNA binding / negative regulation of androgen receptor signaling pathway / DNA-dependent protein kinase complex / double-strand break repair via classical nonhomologous end joining / regulation of DNA-binding transcription factor activity / regulation of glycolytic process / nuclear androgen receptor binding / histone acetyltransferase binding / regulation of alternative mRNA splicing, via spliceosome / negative regulation of Notch signaling pathway ...regulation of transcription regulatory region DNA binding / negative regulation of androgen receptor signaling pathway / DNA-dependent protein kinase complex / double-strand break repair via classical nonhomologous end joining / regulation of DNA-binding transcription factor activity / regulation of glycolytic process / nuclear androgen receptor binding / histone acetyltransferase binding / regulation of alternative mRNA splicing, via spliceosome / negative regulation of Notch signaling pathway / fat cell differentiation / erythrocyte maturation / SMAD binding / protein localization to nucleus / B cell differentiation / transcription corepressor binding / negative regulation of transforming growth factor beta receptor signaling pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / chromatin organization / positive regulation of NF-kappaB transcription factor activity / site of double-strand break / DNA-binding transcription factor binding / regulation of apoptotic process / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA-templated transcription / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding / cytoplasm
Similarity search - Function
: / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / 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. ...: / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / 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 / SKP1/BTB/POZ domain superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PRASEODYMIUM ION / Zinc finger and BTB domain-containing protein 7A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSchubot, F.D. / Waugh, D.S. / Tropea, J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2006
Title: Structure of the POZ domain of human LRF, a master regulator of oncogenesis.
Authors: Schubot, F.D. / Tropea, J.E. / Waugh, D.S.
History
DepositionSep 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Aug 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Zinc finger and BTB domain-containing protein 7A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3624
Polymers12,9401
Non-polymers4233
Water2,108117
1
A: Zinc finger and BTB domain-containing protein 7A
hetero molecules

A: Zinc finger and BTB domain-containing protein 7A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7258
Polymers25,8792
Non-polymers8456
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_545-x,-y-1,z1
Buried area4050 Å2
ΔGint-63 kcal/mol
Surface area11630 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)65.850, 65.850, 162.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-131-

HOH

21A-139-

HOH

DetailsThe second part of the biological assembly is generated by the symmetry operation (-X, -Y, Z)

-
Components

#1: Protein Zinc finger and BTB domain-containing protein 7A / Leukemia/lymphoma- related factor / Factor that binds to inducer of short transcripts protein 1 / ...Leukemia/lymphoma- related factor / Factor that binds to inducer of short transcripts protein 1 / Factor binding IST protein 1 / FBI-1 / HIV-1 1st-binding protein 1 / TTF-I-interacting peptide 21 / TIP21


Mass: 12939.632 Da / Num. of mol.: 1 / Fragment: BTB/POZ-domain, residues 9-128
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB7A, FBI1, LRF, ZBTB7 / Plasmid: pJT18 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O95365
#2: Chemical ChemComp-PR / PRASEODYMIUM ION


Mass: 140.908 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Pr
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.87 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein at 24 mg/ml in 25 mM Tris, 150 mM NaCl, 2mM DTT, 0.18 M Calcium acetate hydrate, 18% w/v Polyethylene glycol 3350, 0.01 M Praseodymium (III) Acetate, pH 7.5, VAPOR DIFFUSION, SITTING ...Details: Protein at 24 mg/ml in 25 mM Tris, 150 mM NaCl, 2mM DTT, 0.18 M Calcium acetate hydrate, 18% w/v Polyethylene glycol 3350, 0.01 M Praseodymium (III) Acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 12540 / % possible obs: 98.2 % / Observed criterion σ(I): -1 / Redundancy: 13 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 25.9
Reflection shellResolution: 2.03→2.13 Å / Redundancy: 13 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 9 / Rsym value: 0.259 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BUO

1buo


Resolution: 2→40.08 Å / Cor.coef. Fo:Fc: 0.908 / Cor.coef. Fo:Fc free: 0.87 / SU B: 5.932 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29096 620 5 %RANDOM
Rwork0.22933 ---
obs0.23245 11695 98.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.928 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20 Å2
2--0.2 Å20 Å2
3----0.41 Å2
Refine analyzeLuzzati coordinate error obs: 0.113 Å / Luzzati d res low obs: 40 Å / Luzzati sigma a obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2→40.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms877 0 3 117 997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022892
X-RAY DIFFRACTIONr_angle_refined_deg1.581.971215
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2855113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.3424.73738
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92115143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.641154
X-RAY DIFFRACTIONr_chiral_restr0.1110.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02664
X-RAY DIFFRACTIONr_nbd_refined0.2360.2425
X-RAY DIFFRACTIONr_nbtor_refined0.3140.2629
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.297
X-RAY DIFFRACTIONr_metal_ion_refined0.0950.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.219
X-RAY DIFFRACTIONr_mcbond_it1.1981.5591
X-RAY DIFFRACTIONr_mcangle_it1.8912926
X-RAY DIFFRACTIONr_scbond_it2.8573338
X-RAY DIFFRACTIONr_scangle_it3.9664.5289
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 47 -
Rwork0.194 843 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -11.481 Å / Origin y: -32.481 Å / Origin z: -4.221 Å
111213212223313233
T-0.0832 Å20.003 Å20.0035 Å2-0.0259 Å2-0.0051 Å2---0.0479 Å2
L1.816 °20.2185 °2-0.7356 °2-0.3995 °20.163 °2--0.4674 °2
S0.002 Å °-0.2032 Å °0.0372 Å °0.0346 Å °-0.0384 Å °0.0537 Å °0.0442 Å °0.165 Å °0.0364 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 641 - 57
2X-RAY DIFFRACTION1AA70 - 12763 - 120

+
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://pdbjlc1.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