[English] 日本語
Yorodumi
- PDB-1gxr: WD40 Region of Human Groucho/TLE1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gxr
TitleWD40 Region of Human Groucho/TLE1
ComponentsTRANSDUCIN-LIKE ENHANCER PROTEIN 1
KeywordsTRANSCRIPTION / TRANSCRIPTIONAL CO-REPRESSOR / WD40 / TRANSCRIPTION REPRESSOR / WD REPEAT
Function / homology
Function and homology information


Repression of WNT target genes / beta-catenin-TCF complex / negative regulation of Wnt signaling pathway / negative regulation of anoikis / negative regulation of canonical NF-kappaB signal transduction / animal organ morphogenesis / Deactivation of the beta-catenin transactivating complex / negative regulation of canonical Wnt signaling pathway / Formation of the beta-catenin:TCF transactivating complex / NOTCH1 Intracellular Domain Regulates Transcription ...Repression of WNT target genes / beta-catenin-TCF complex / negative regulation of Wnt signaling pathway / negative regulation of anoikis / negative regulation of canonical NF-kappaB signal transduction / animal organ morphogenesis / Deactivation of the beta-catenin transactivating complex / negative regulation of canonical Wnt signaling pathway / Formation of the beta-catenin:TCF transactivating complex / NOTCH1 Intracellular Domain Regulates Transcription / Wnt signaling pathway / transcription corepressor activity / transcription regulator complex / DNA-binding transcription factor binding / negative regulation of DNA-templated transcription / positive regulation of gene expression / signal transduction / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Groucho/TLE, N-terminal Q-rich domain / Groucho/TLE N-terminal Q-rich domain / Groucho/transducin-like enhancer / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. ...Groucho/TLE, N-terminal Q-rich domain / Groucho/TLE N-terminal Q-rich domain / Groucho/transducin-like enhancer / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Transducin-like enhancer protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPearl, L.H. / Roe, S.M. / Pickles, L.M.
CitationJournal: Structure / Year: 2002
Title: Crystal Structure of the C-Terminal Wd40 Repeat Domain of the Human Groucho/Tle1 Transcriptional Corepressor
Authors: Pickles, L.M. / Roe, S.M. / Hemingway, E.J. / Stifani, S. / Pearl, L.H.
History
DepositionApr 10, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2002Provider: repository / Type: Initial release
Revision 1.1Feb 6, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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: TRANSDUCIN-LIKE ENHANCER PROTEIN 1
B: TRANSDUCIN-LIKE ENHANCER PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7473
Polymers73,7072
Non-polymers401
Water10,160564
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)62.407, 56.656, 102.034
Angle α, β, γ (deg.)90.00, 102.29, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein TRANSDUCIN-LIKE ENHANCER PROTEIN 1 / ESG1


Mass: 36853.469 Da / Num. of mol.: 2
Fragment: RESIDUES 443-770 (END OF SP-REGION 443-473 AND WD40 REPEAT DOMAIN 474-770)
Source method: isolated from a genetically manipulated source
Details: THIS CONSTRUCT CONTAINS ALL THE SEVEN WD REPEATS / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q04724
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B RESIDUES 475-511 WD REPEAT 1 CHAIN A, B RESIDUES 522-558 WD REPEAT 2 CHAIN A, B RESIDUES ...CHAIN A, B RESIDUES 475-511 WD REPEAT 1 CHAIN A, B RESIDUES 522-558 WD REPEAT 2 CHAIN A, B RESIDUES 565-602 WD REPEAT 3 CHAIN A, B RESIDUES 607-644 WD REPEAT 4 CHAIN A, B RESIDUES 649-685 WD REPEAT 5 CHAIN A, B RESIDUES 791-726 WD REPEAT 6 CHAIN A, B RESIDUES 732-768 WD REPEAT 7
Sequence detailsTHE CONFLICT IS CONFIRMED BY RESEQUENCING THE GENE AND THE RESIDUES 464 AND 465 ARE CONFIRMED TO BE ...THE CONFLICT IS CONFIRMED BY RESEQUENCING THE GENE AND THE RESIDUES 464 AND 465 ARE CONFIRMED TO BE ASP AND ALA RESPECTIVELY.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 287 K / Method: microbatch / pH: 7
Details: CRYSTALS WERE GROWN BY MICROBATCH METHODS AT 14C. PROTEIN AT 6MG/ML, WAS MIXED WITH AN EQUAL VOLUME O PRECIPITANT (22% PEG8000, 100MM, NACACODYLATE, 100MM CAACETATE)., pH 7.00
Crystal grow
*PLUS
Temperature: 14 ℃ / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein11
222 %PEG800011
3100 mMsodium cacodylate11
4100 mMcalcium acetate11

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. obs: 92007 / % possible obs: 100 % / Redundancy: 5.2 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 5.4
Reflection shellResolution: 1.6→1.67 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 2.6 / % possible all: 100
Reflection
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 50 Å / Num. obs: 83990 / % possible obs: 100 %
Reflection shell
*PLUS
Highest resolution: 1.6 Å / Lowest resolution: 1.7 Å / % possible obs: 100 %

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ERJ

1erj


Resolution: 1.65→40.45 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1439675.18 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3977 4.7 %RANDOM
Rwork0.229 ---
obs0.229 83957 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.0585 Å2 / ksol: 0.348345 e/Å3
Displacement parametersBiso mean: 32.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.44 Å20 Å20.39 Å2
2---0.69 Å20 Å2
3----4.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.65→40.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5029 0 1 564 5594
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.3 596 4.3 %
Rwork0.268 13329 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.23 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
LS refinement shell
*PLUS
Rfactor obs: 0.268

+
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