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- PDB-6tyd: Structure of human LDB1 in complex with SSBP2 -

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Basic information

Entry
Database: PDB / ID: 6tyd
TitleStructure of human LDB1 in complex with SSBP2
Components
  • LIM domain-binding protein 1
  • Single-stranded DNA-binding protein 2
KeywordsTRANSCRIPTION / LDB1 / SSBP2 / ChiLS
Function / homology
Function and homology information


Expression and translocation of olfactory receptors / negative regulation of erythrocyte differentiation / regulation of kinase activity / head development / positive regulation of hemoglobin biosynthetic process / beta-catenin-TCF complex / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / LIM domain binding / Cardiogenesis / regulation of focal adhesion assembly ...Expression and translocation of olfactory receptors / negative regulation of erythrocyte differentiation / regulation of kinase activity / head development / positive regulation of hemoglobin biosynthetic process / beta-catenin-TCF complex / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / LIM domain binding / Cardiogenesis / regulation of focal adhesion assembly / cell leading edge / regulation of cell migration / positive regulation of transcription elongation by RNA polymerase II / transcription by RNA polymerase II / transcription coregulator activity / Regulation of expression of SLITs and ROBOs / neuron differentiation / nervous system development / transcription regulator complex / single-stranded DNA binding / RUNX1 regulates transcription of genes involved in differentiation of HSCs / DNA-binding transcription factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Sequence-specific single-strand DNA-binding protein / SSDP conserved region / 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
Similarity search - Domain/homology
Single-stranded DNA-binding protein 2 / LIM domain-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.803 Å
AuthorsWang, H. / Wang, Z. / Xu, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Crystal structure of human LDB1 in complex with SSBP2.
Authors: Wang, H. / Kim, J. / Wang, Z. / Yan, X.X. / Dean, A. / Xu, W.
History
DepositionAug 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 29, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,7083
Polymers49,7083
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6460 Å2
ΔGint-56 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.322, 104.322, 250.419
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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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: 27867.338 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: 10920.196 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
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.44 Å3/Da / Density % sol: 72.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100 mM lithium sulfate monohydrate, 100 mM sodium citrate tribasic dihydrate pH 5.6, 1% v/v PEG400, 10mM DTT

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 37297 / % possible obs: 99.8 % / Redundancy: 6.7 % / CC1/2: 0.991 / Net I/σ(I): 38.73
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.3 % / Num. unique obs: 1989 / CC1/2: 0.513 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.803→43.803 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.15
RfactorNum. reflection% reflection
Rfree0.2812 3633 9.77 %
Rwork0.24 --
obs0.2439 37202 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 371.19 Å2 / Biso mean: 114.6042 Å2 / Biso min: 53.32 Å2
Refinement stepCycle: final / Resolution: 2.803→43.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3079 0 0 0 3079
Num. residues----371
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8033-2.84020.37161320.36118992
2.8402-2.87910.36931400.3306128199
2.8791-2.92020.3861400.34031293100
2.9202-2.96380.49741420.35381304100
2.9638-3.01010.39551400.35841309100
3.0101-3.05940.34811430.32731296100
3.0594-3.11220.36851390.31311287100
3.1122-3.16870.37741420.32021299100
3.1687-3.22970.33451420.30771310100
3.2297-3.29560.32781420.29471278100
3.2956-3.36720.30771450.26841321100
3.3672-3.44550.3741400.27971266100
3.4455-3.53160.3181380.26761300100
3.5316-3.62710.30871370.27081308100
3.6271-3.73370.27451430.24841306100
3.7337-3.85420.29971380.23771292100
3.8542-3.99180.23751360.249128999
3.9918-4.15160.29171400.22991292100
4.1516-4.34030.27121380.21641297100
4.3403-4.56890.24391390.18761282100
4.5689-4.85490.2131380.19011305100
4.8549-5.22920.26961390.21111304100
5.2292-5.75430.26041440.22321284100
5.7543-6.58460.2871380.2537129399
6.5846-8.28670.24741360.22941290100
8.2867-43.8030.2581420.2179129499
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)
12.7013-2.48451.02564.88360.61853.8838-0.05120.077-0.38880.6440.3860.7593-0.5933-0.7883-0.23210.81530.34380.34770.72110.1820.78235.037940.5939106.3144
25.1881.1588-1.9524.955-0.62981.8655-0.057-0.1555-0.2209-0.7503-0.56440.05171.11980.46260.44841.2170.39530.30240.9344-0.00380.738520.012255.2953121.6992
32.7502-0.8031-0.52753.05380.4693.6234-0.1857-0.3379-0.64220.04-0.4680.76121.0873-0.50280.53671.43830.25180.32511.1775-0.12751.172415.866748.587122.6744
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'V' and resid 64 through 282)V64 - 282
2X-RAY DIFFRACTION2(chain 'A' and resid 10 through 94)A10 - 94
3X-RAY DIFFRACTION3(chain 'B' and resid 11 through 77)B11 - 77

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