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- PDB-5l81: Crystal structure of the PH domain of murine kindlin-3 -

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Basic information

Entry
Database: PDB / ID: 5l81
TitleCrystal structure of the PH domain of murine kindlin-3
ComponentsFermitin family homolog 3
KeywordsSIGNALING PROTEIN / Pleckstrin homology domain / Membrane binding / Integrin activation
Function / homology
Function and homology information


cell-substrate junction / regulation of cell-cell adhesion mediated by integrin / Platelet degranulation / integrin activation / podosome / leukocyte cell-cell adhesion / substrate adhesion-dependent cell spreading / cell-matrix adhesion / cell projection / integrin-mediated signaling pathway ...cell-substrate junction / regulation of cell-cell adhesion mediated by integrin / Platelet degranulation / integrin activation / podosome / leukocyte cell-cell adhesion / substrate adhesion-dependent cell spreading / cell-matrix adhesion / cell projection / integrin-mediated signaling pathway / platelet aggregation / integrin binding / positive regulation of cell migration
Similarity search - Function
Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / FERM central domain ...Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / FERM central domain / FERM superfamily, second domain / Band 4.1 domain / Band 4.1 homologues / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Fermitin family homolog 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsNi, T. / Harlos, K. / Gilbert, R.J.C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MR/N000331/1 United Kingdom
CitationJournal: Biochem. J. / Year: 2017
Title: Structure and lipid-binding properties of the kindlin-3 pleckstrin homology domain.
Authors: Ni, T. / Kalli, A.C. / Naughton, F.B. / Yates, L.A. / Naneh, O. / Kozorog, M. / Anderluh, G. / Sansom, M.S. / Gilbert, R.J.
History
DepositionJun 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Advisory / Author supporting evidence
Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_residues
Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.4Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fermitin family homolog 3
B: Fermitin family homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8113
Polymers33,7882
Non-polymers231
Water23413
1
A: Fermitin family homolog 3


Theoretical massNumber of molelcules
Total (without water)16,8941
Polymers16,8941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fermitin family homolog 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9172
Polymers16,8941
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.040, 36.190, 52.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Fermitin family homolog 3 / Kindlin-3 / Unc-112-related protein 2


Mass: 16894.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fermt3, Kind3, Urp2 / Production host: Escherichia coli B (bacteria) / Variant (production host): B834 / References: UniProt: Q8K1B8
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

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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: 33.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 4M sodium nitrate, 0.1M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 2.1→31.73 Å / Num. obs: 12441 / % possible obs: 96 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 13.68

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4bbk

4bbk


Resolution: 2.23→31.73 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.75
RfactorNum. reflection% reflection
Rfree0.2709 617 4.96 %
Rwork0.2193 --
obs0.2221 12441 96.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.23→31.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2123 0 1 13 2137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072165
X-RAY DIFFRACTIONf_angle_d1.1052925
X-RAY DIFFRACTIONf_dihedral_angle_d12.2191834
X-RAY DIFFRACTIONf_chiral_restr0.062323
X-RAY DIFFRACTIONf_plane_restr0.008373
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.45430.35741530.30382805X-RAY DIFFRACTION94
2.4543-2.80930.34011460.28572954X-RAY DIFFRACTION97
2.8093-3.53870.32651600.26212988X-RAY DIFFRACTION98
3.5387-31.7380.23351580.18383077X-RAY DIFFRACTION96
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)
12.87170.45780.12928.32514.80635.10340.01260.21530.256-0.555-0.91180.40922.14460.49160.04831.0565-0.20930.15020.9053-0.06071.0844142.3992-37.2938-75.7365
28.28841.42775.16835.48383.14158.926-1.61561.77440.4072-1.26840.85721.1884-0.644-1.21010.22770.7388-0.31280.0860.61530.05440.5872145.5556-19.7874-61.9123
33.1023.5412-0.84978.26814.77398.7051-0.1162-0.90190.08060.5117-0.0604-1.4443-1.09950.4059-0.17170.88350.03830.10650.5188-0.04730.801158.6657-13.0238-54.9763
44.62620.85710.23589.02352.38337.4785-0.81031.6158-0.0177-1.38480.3313-0.39420.2689-0.57840.06050.6634-0.1940.0310.76160.00250.5965149.7573-21.8338-64.9084
56.82641.4577-0.02347.8528-1.06616.8357-0.64292.27580.1723-2.00651.60180.52060.4934-0.32520.3361.0211-0.44220.18051.10950.16140.6485153.6652-21.6173-67.4509
63.5722-0.4145-1.70052.22150.02717.5161-0.4248-1.18550.58950.31410.4368-0.04590.1740.13350.0710.5762-0.03480.20840.3804-0.07860.7995148.4432-23.8928-49.4895
72.1396-0.9259-0.25149.4198-0.03985.71920.1568-0.0418-0.61780.6464-0.06350.20520.34190.01130.17180.7333-0.05370.09630.289-0.02480.9263153.941-21.5899-54.6384
88.23833.01080.84083.0346-0.91365.3397-0.55310.6089-0.8865-0.20430.53930.57671.0927-0.31690.00260.723-0.22620.23580.5117-0.05720.7736144.3221-32.604-57.9683
95.951.2552-0.5337.75530.45074.2165-0.16470.64520.9485-0.27291.20040.9854-0.0626-0.1920.48670.5595-0.14620.35920.6136-0.01730.7858136.428-31.6756-50.5162
108.5898-4.9739-6.03638.75575.6556.8856-0.2329-0.721-0.12271.3558-0.5711-0.83451.2322-0.1270.2730.80570.0940.04041.07430.12880.6343149.3283-37.8039-28.4951
113.4227-1.9789-0.63231.2718-0.16412.44270.04750.1783-0.70450.97540.9910.8404-0.685-0.75212.8250.29390.99121.01140.5748-0.21560.8203165.5305-44.5273-40.2414
124.72411.63152.3241.77520.90338.65190.2924-1.8247-1.29081.7546-0.79780.19991.0853-0.64980.37651.02150.01170.08630.98720.25090.7061155.0616-37.9835-29.3569
133.85441.5862.24087.24383.77492.52971.1203-3.4888-1.6412.9432-0.5692-2.16960.2327-1.2122-0.08931.24920.0215-0.18271.72120.40651.2233159.6954-42.2696-22.6302
149.08151.7644-0.11524.86872.57498.7116-0.1374-0.441-0.735-1.0509-0.5557-0.87740.14360.29040.23440.63880.08950.14430.50960.11850.5623152.9345-35.2222-41.658
153.5321-0.7932-1.82579.32893.40443.29360.22761.0855-0.62470.180.0666-2.47191.08322.08190.44631.00130.3211-0.36071.03420.33831.4779164.2168-26.3023-41.5856
168.10510.49722.16626.6470.15496.4178-0.03970.0881-0.51250.86370.04560.49810.9056-0.08050.44760.79670.10440.19250.49450.06160.5529148.8599-36.695-38.637
173.4807-0.02090.49274.8939-1.12055.83840.3713-0.84990.355-0.1206-0.13240.69740.78280.05251.24530.6563-0.07250.61720.7982-0.20270.3766139.1071-33.6059-39.7502
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 345 through 350 )
2X-RAY DIFFRACTION2chain 'A' and (resid 351 through 359 )
3X-RAY DIFFRACTION3chain 'A' and (resid 360 through 369 )
4X-RAY DIFFRACTION4chain 'A' and (resid 370 through 384 )
5X-RAY DIFFRACTION5chain 'A' and (resid 385 through 403 )
6X-RAY DIFFRACTION6chain 'A' and (resid 404 through 424 )
7X-RAY DIFFRACTION7chain 'A' and (resid 425 through 437 )
8X-RAY DIFFRACTION8chain 'A' and (resid 438 through 461 )
9X-RAY DIFFRACTION9chain 'A' and (resid 462 through 477 )
10X-RAY DIFFRACTION10chain 'B' and (resid 345 through 360 )
11X-RAY DIFFRACTION11chain 'B' and (resid 361 through 369 )
12X-RAY DIFFRACTION12chain 'B' and (resid 370 through 384 )
13X-RAY DIFFRACTION13chain 'B' and (resid 385 through 395 )
14X-RAY DIFFRACTION14chain 'B' and (resid 396 through 422 )
15X-RAY DIFFRACTION15chain 'B' and (resid 423 through 428 )
16X-RAY DIFFRACTION16chain 'B' and (resid 429 through 453 )
17X-RAY DIFFRACTION17chain 'B' and (resid 454 through 478 )

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