[English] 日本語
Yorodumi
- PDB-6ptl: Structure of the self-association domain of the chromatin looping... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ptl
TitleStructure of the self-association domain of the chromatin looping factor LDB1
ComponentsLIM domain-binding protein 1
KeywordsGENE REGULATION / Dimer / Chromatin looping factor / nuclear protein / transcriptional regulator
Function / homology
Function and homology information


regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / epithelial structure maintenance / head development / primitive erythrocyte differentiation / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / beta-catenin-TCF complex ...regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / epithelial structure maintenance / head development / primitive erythrocyte differentiation / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / beta-catenin-TCF complex / RUNX1 regulates transcription of genes involved in differentiation of HSCs / LIM domain binding / gastrulation with mouth forming second / anterior/posterior axis specification / regulation of focal adhesion assembly / cell leading edge / somatic stem cell population maintenance / hair follicle development / positive regulation of cell adhesion / regulation of cell migration / cerebellum development / positive regulation of transcription elongation by RNA polymerase II / neuron differentiation / Wnt signaling pathway / RNA polymerase II transcription regulator complex / : / nervous system development / DNA-binding transcription factor binding / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / transcription coactivator activity / cell adhesion / negative regulation of DNA-templated transcription / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain profile.
Similarity search - Domain/homology
LIM domain-binding protein 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMacindoe, I. / Silva, A. / Guss, J.M. / Mackay, J.P. / Matthews, J.M.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP1064442 Australia
Australian Research Council (ARC)DP190102543 Australia
CitationJournal: To Be Published
Title: Structure of the self-association domain of the chromatin looping factor LDB1
Authors: Macindoe, I. / Silva, A. / Guss, J.M. / Mackay, J.P. / Matthews, J.M.
History
DepositionJul 16, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LIM domain-binding protein 1


Theoretical massNumber of molelcules
Total (without water)22,6081
Polymers22,6081
Non-polymers00
Water1629
1
A: LIM domain-binding protein 1

A: LIM domain-binding protein 1


  • defined by author&software
  • Evidence: light scattering, Under concentrations tested, MALLS analysis indicates a dimer is the main species in solution, SAXS, Supports major species being dimer. Crysol modelling indicates that a ...Evidence: light scattering, Under concentrations tested, MALLS analysis indicates a dimer is the main species in solution, SAXS, Supports major species being dimer. Crysol modelling indicates that a dimer with the major interface is the most likely species in solution. Some evidence of concentration dependent higher order association at higher concentrations., cross-linking, Analysed by mass spectrometry supports the main interface, mass spectrometry, Native mass spectrometry indicates that dimer is the most prevalent multimeric species
  • 45.2 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)45,2152
Polymers45,2152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2280 Å2
ΔGint-10 kcal/mol
Surface area15280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.869, 81.869, 66.828
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein LIM domain-binding protein 1 / LDB-1 / Carboxyl-terminal LIM domain-binding protein 2 / CLIM-2 / LIM domain-binding factor CLIM2 / ...LDB-1 / Carboxyl-terminal LIM domain-binding protein 2 / CLIM-2 / LIM domain-binding factor CLIM2 / mLdb1 / Nuclear LIM interactor


Mass: 22607.703 Da / Num. of mol.: 1 / Fragment: UNP residues 50-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ldb1, Nli / Plasmid: pHIS-GB1
Details (production host): T7 regulated expression with a His tag for purification and a GB1 tag to enhance soluble expression
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P70662
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.8656.99
22.8656.99
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2931vapor diffusion, sitting drop18.6% PEG3350, 140 mM sodium phosphate dibasic
2932vapor diffusion, sitting drop18.6% PEG3350, 140 mM sodium phosphate dibasic, crystal soaked overnight in mother liquor containing 10 mM ethylmercury thiosalicylic acid

-
Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001N
21002N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAustralian Synchrotron MX210.9537
SYNCHROTRONAustralian Synchrotron MX120.9537
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDSep 27, 2014
ADSC QUANTUM 210r2CCDFeb 28, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-IDMonochromator
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2double crystal Si(111)
Radiation wavelength
IDWavelength (Å)Relative weight
10.95371
21
Reflection

Entry-ID: 6PTL

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Biso Wilson estimate (Å2)CC1/2Rmerge(I) obsRpim(I) allRrim(I) allΧ2Diffraction-IDNet I/σ(I)
2.5-35.5921299.710.775.20.9980.0830.0270.0871.01114.7
2.8-501252399.911.697.60.9940.0950.0320.1071.3215.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.6111.2132.510150.9290.3811.2711.07100
2.8-2.8511.61.4741.46680.60.6632.2561.354100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-20002.3.12data reduction
SCALEPACKdata scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→35.48 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.939 / SU B: 11.32 / SU ML: 0.234 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.357 / ESU R Free: 0.26
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2708 496 5.4 %RANDOM
Rwork0.2448 ---
obs0.2463 8696 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 163.85 Å2 / Biso mean: 87.291 Å2 / Biso min: 64.86 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å21.14 Å20 Å2
2--2.28 Å2-0 Å2
3----7.41 Å2
Refinement stepCycle: final / Resolution: 2.5→35.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1213 0 0 9 1222
Biso mean---81.32 -
Num. residues----142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0010.0131257
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171118
X-RAY DIFFRACTIONr_angle_refined_deg1.141.6561696
X-RAY DIFFRACTIONr_angle_other_deg1.0131.5772583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.465142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.68520.84383
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75215218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2341512
X-RAY DIFFRACTIONr_chiral_restr0.0320.2157
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021396
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02320
LS refinement shellResolution: 2.502→2.567 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 20 -
Rwork0.347 669 -
all-689 -
obs--100 %

+
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