[English] 日本語
Yorodumi
- PDB-8hib: The crystal structure of Pygo2-LDB1-SSBP2 triple complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hib
TitleThe crystal structure of Pygo2-LDB1-SSBP2 triple complex
Components
  • LIM domain-binding protein 1
  • Pygopus homolog 2
  • Single-stranded DNA-binding protein 2
KeywordsTRANSCRIPTION / Protein binding / Complex
Function / homology
Function and homology information


histone acetyltransferase regulator activity / Expression and translocation of olfactory receptors / regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / spermatid nucleus differentiation / regulation of mammary gland epithelial cell proliferation / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery ...histone acetyltransferase regulator activity / Expression and translocation of olfactory receptors / regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / spermatid nucleus differentiation / regulation of mammary gland epithelial cell proliferation / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / beta-catenin-TCF complex / epithelial structure maintenance / LIM domain binding / mammary gland development / gastrulation with mouth forming second / Cardiogenesis / anterior/posterior axis specification / lens development in camera-type eye / regulation of focal adhesion assembly / roof of mouth development / cell leading edge / somatic stem cell population maintenance / developmental growth / hair follicle development / canonical Wnt signaling pathway / regulation of cell migration / positive regulation of cell adhesion / kidney development / Deactivation of the beta-catenin transactivating complex / positive regulation of transcription elongation by RNA polymerase II / Formation of the beta-catenin:TCF transactivating complex / brain development / neuron differentiation / Wnt signaling pathway / Regulation of expression of SLITs and ROBOs / single-stranded DNA binding / RUNX1 regulates transcription of genes involved in differentiation of HSCs / nervous system development / histone binding / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / transcription by RNA polymerase II / transcription coactivator activity / cell adhesion / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / 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 / DNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
Sequence-specific single-strand DNA-binding protein / Single-stranded DNA binding protein, SSDP / : / LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain profile. / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. ...Sequence-specific single-strand DNA-binding protein / Single-stranded DNA binding protein, SSDP / : / LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain profile. / Lissencephaly type-1-like homology motif / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
Single-stranded DNA-binding protein 2 / LIM domain-binding protein 1 / Pygopus homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsWang, H.Y. / Yan, X.X. / Xu, W.Q.
Funding support China, 5items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB37030302 China
Chinese Academy of Sciences2021kf01 China
National Natural Science Foundation of China (NSFC)32000862 China
National Natural Science Foundation of China (NSFC)32171218 China
Other governmentBX20200351
CitationJournal: To Be Published
Title: The crystal structure of Pygo2-LDB1-SSBP2 triple complex
Authors: Wang, H.Y. / Yan, X.X. / Xu, W.Q.
History
DepositionNov 19, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
V: LIM domain-binding protein 1
A: Single-stranded DNA-binding protein 2
B: Single-stranded DNA-binding protein 2
D: Pygopus homolog 2


Theoretical massNumber of molelcules
Total (without water)51,9874
Polymers51,9874
Non-polymers00
Water1,20767
1
V: LIM domain-binding protein 1
A: Single-stranded DNA-binding protein 2
B: Single-stranded DNA-binding protein 2
D: Pygopus homolog 2

V: LIM domain-binding protein 1
A: Single-stranded DNA-binding protein 2
B: Single-stranded DNA-binding protein 2
D: Pygopus homolog 2


Theoretical massNumber of molelcules
Total (without water)103,9748
Polymers103,9748
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+5/61
Buried area20160 Å2
ΔGint-144 kcal/mol
Surface area37100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.499, 104.499, 252.274
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11V-345-

HOH

-
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 / hLdb1 / Nuclear LIM interactor


Mass: 27294.443 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LDB1, CLIM2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86U70
#2: Protein Single-stranded DNA-binding protein 2 / Sequence-specific single-stranded-DNA-binding protein 2


Mass: 10863.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SSBP2, SSDP2 / Production host: Escherichia coli (E. coli) / References: UniProt: P81877
#3: Protein/peptide Pygopus homolog 2


Mass: 2966.210 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: mutant 58Y was generated for monitoring UV280 to know where proteins are during purification
Source: (gene. exp.) Homo sapiens (human) / Gene: PYGO2, PP7910 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BRQ0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 3.82 Å3/Da / Density % sol: 67.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 100 mM Li2SO4, 100 mM sodium citrate tribasic dihydrate pH 5.6, 1% v/v PEG400, and 10 mM DTT

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. obs: 30828 / % possible obs: 100 % / Redundancy: 12.7 % / CC1/2: 0.998 / Net I/σ(I): 44.86
Reflection shellResolution: 2.45→2.52 Å / Num. unique obs: 2491 / CC1/2: 0.614

-
Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIX1.19.2-4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TYD

6tyd


Resolution: 2.45→19.92 Å / SU ML: 0.36 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 25.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2462 1513 4.92 %
Rwork0.213 --
obs0.2146 30755 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3231 0 0 67 3298
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013334
X-RAY DIFFRACTIONf_angle_d1.114524
X-RAY DIFFRACTIONf_dihedral_angle_d5.988426
X-RAY DIFFRACTIONf_chiral_restr0.058472
X-RAY DIFFRACTIONf_plane_restr0.01578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.530.37891310.34542600X-RAY DIFFRACTION100
2.53-2.620.32471400.29372586X-RAY DIFFRACTION100
2.62-2.720.29641420.27682581X-RAY DIFFRACTION100
2.72-2.850.26881390.25992620X-RAY DIFFRACTION100
2.85-30.30521270.27222624X-RAY DIFFRACTION100
3-3.180.30221420.25752620X-RAY DIFFRACTION100
3.18-3.430.27371290.24512644X-RAY DIFFRACTION100
3.43-3.770.31741250.22182680X-RAY DIFFRACTION100
3.77-4.310.24431380.20662683X-RAY DIFFRACTION100
4.31-5.420.19031580.17672701X-RAY DIFFRACTION100
5.42-19.920.21641420.18652903X-RAY DIFFRACTION100
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)
13.3473-1.8951-1.35514.89470.62143.61930.20720.253-0.0344-0.0707-0.11550.1462-0.4744-0.42440.02970.52160.14170.10680.4088-0.03130.473734.772240.25107.1095
23.8795-0.8003-0.68232.62031.73040.97940.8129-0.11480.0443-0.4678-0.80620.1112-0.384-0.1654-0.04620.91570.31260.12160.7193-0.12670.542519.584255.4716123.1422
31.5462-1.2989-0.14151.78351.20891.64250.39660.1531-0.3580.1374-0.50240.3381-0.1085-0.81660.00060.82090.12330.11720.7669-0.15780.717715.818649.1556123.8102
40.34220.0310.01250.0412-0.19450.43320.29170.54370.2528-0.2971-0.57270.4299-0.3201-0.72390.00040.89930.10170.02431.1638-0.35211.12227.582348.9726118.9724
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain V and resseq 65:280)
2X-RAY DIFFRACTION2(chain A and resseq 11:93)
3X-RAY DIFFRACTION3(chain B and resseq 10:77)
4X-RAY DIFFRACTION4(chain D and resseq 58:81)

+
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