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- PDB-8iw5: Crystal structure of liprin-beta H2H3 dimer -

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Basic information

Entry
Database: PDB / ID: 8iw5
TitleCrystal structure of liprin-beta H2H3 dimer
ComponentsLiprin-beta-1
KeywordsPROTEIN BINDING / Focal adhesion / Cortical microtubule stabilizing complex
Function / homology
Function and homology information


Receptor-type tyrosine-protein phosphatases / cortical microtubule organization / cell cortex / plasma membrane
Similarity search - Function
Liprin-beta, SAM domain repeat 1 / Liprin-beta, SAM domain repeat 2 / Liprin-beta, SAM domain repeat 3 / LAR-interacting protein, Liprin / SAM domain (Sterile alpha motif) / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZhang, J. / Chen, S. / Wei, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971131 China
National Natural Science Foundation of China (NSFC)32170697 China
CitationJournal: Cell Rep / Year: 2023
Title: KANK1 shapes focal adhesions by orchestrating protein binding, mechanical force sensing, and phase separation.
Authors: Guo, K. / Zhang, J. / Huang, P. / Xu, Y. / Pan, W. / Li, K. / Chen, L. / Luo, L. / Yu, W. / Chen, S. / He, S. / Wei, Z. / Yu, C.
History
DepositionMar 29, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Liprin-beta-1
B: Liprin-beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4713
Polymers11,4312
Non-polymers401
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-37 kcal/mol
Surface area5610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.793, 50.637, 30.780
Angle α, β, γ (deg.)90.00, 113.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Liprin-beta-1 / Protein tyrosine phosphatase receptor type f polypeptide-interacting protein-binding protein 1 / ...Protein tyrosine phosphatase receptor type f polypeptide-interacting protein-binding protein 1 / PTPRF-interacting protein-binding protein 1


Mass: 5715.494 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ppfibp1, Kiaa1230 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8C8U0
#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.: 39 / Source method: isolated from a natural source / Formula: H2O
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: 1.86 Å3/Da / Density % sol: 34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Calcium acetate, 0.1 M Sodium cacodylate pH 6.0 and 25% v/v MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 1, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 8724 / % possible obs: 93.3 % / Redundancy: 5.7 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.051 / Rrim(I) all: 0.116 / Χ2: 1.32 / Net I/σ(I): 8.4 / Num. measured all: 49910
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.7-1.734.30.7244310.7040.9090.3960.8320.67292.7
1.73-1.764.90.6994410.8310.9530.3430.7820.6896.1
1.76-1.795.60.5224570.9120.9770.2390.5750.821100
1.79-1.836.10.4474770.9310.9820.1960.4890.896100
1.83-1.876.60.3864630.9620.990.1590.4180.9199.8
1.87-1.916.70.3244610.9650.9910.1340.3511.008100
1.91-1.966.60.2764740.9620.990.1180.3011.21299.8
1.96-2.026.20.234510.9610.990.1010.2521.274100
2.02-2.076.60.1914590.980.9950.0810.2081.51199.6
2.07-2.146.20.1694660.9760.9940.0760.1861.63999.6
2.14-2.226.40.1454720.9780.9940.0630.1591.73299.2
2.22-2.316.20.1374580.9820.9950.0620.151.80898.9
2.31-2.415.80.1224610.9830.9960.0570.1351.76198.9
2.41-2.545.70.1114580.9810.9950.0520.1231.68497.2
2.54-2.75.50.0964370.9870.9970.0450.1071.5594.6
2.7-2.915.70.0894220.9920.9980.0420.0991.51991.3
2.91-3.24.80.0814100.990.9970.0420.0921.59486.5
3.2-3.664.70.0793690.9880.9970.0410.0891.42178.2
3.66-4.614.30.0753080.9860.9970.040.0861.24164.3
4.61-504.30.0763490.990.9970.0410.0871.20171.5

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→27.33 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 37.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2717 445 5.13 %
Rwork0.221 --
obs0.2236 8679 93.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→27.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms713 0 1 39 753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005739
X-RAY DIFFRACTIONf_angle_d0.7741000
X-RAY DIFFRACTIONf_dihedral_angle_d14.763288
X-RAY DIFFRACTIONf_chiral_restr0.043118
X-RAY DIFFRACTIONf_plane_restr0.005130
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.950.32841520.2232883X-RAY DIFFRACTION98
1.95-2.450.2911600.24392896X-RAY DIFFRACTION99
2.45-27.330.25481330.21082455X-RAY DIFFRACTION82
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)
12.3239-0.0430.50380.64170.46760.8002-0.03560.1545-0.0352-0.36150.07270.13460.3537-0.02290.00030.24850.00910.00920.2537-0.03980.263713.84527.6567-1.4342
22.17881.2869-0.70891.57770.89082.8055-0.1672-0.4019-0.11990.25730.2222-0.1138-0.1034-0.167-0.00020.3325-0.0243-0.0250.2578-0.00030.23579.511610.191611.8484
32.27831.1813-1.87832.3122-0.67242.7271-0.16540.25420.1345-0.12710.0818-0.0562-0.35320.28930.00040.29950.0256-0.01420.2615-0.01930.27399.952215.92770.3155
40.73710.5361.29451.45422.69275.16620.2674-0.1543-0.20860.2590.0217-0.0110.731-1.15130.12690.2248-0.01610.02190.25580.01860.32664.46974.37266.8192
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 41 through 61 )
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 88 )
3X-RAY DIFFRACTION3chain 'B' and (resid 45 through 73 )
4X-RAY DIFFRACTION4chain 'B' and (resid 74 through 88 )

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