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- PDB-4bbk: Structural and functional characterisation of the kindlin-1 pleck... -

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Basic information

Entry
Database: PDB / ID: 4bbk
TitleStructural and functional characterisation of the kindlin-1 pleckstrin homology domain
ComponentsFERMITIN FAMILY HOMOLOG 1
KeywordsCELL ADHESION / PH DOMAIN
Function / homology
Function and homology information


negative regulation of timing of anagen / keratinocyte migration / positive regulation of wound healing, spreading of epidermal cells / basement membrane organization / positive regulation of transforming growth factor beta production / establishment of epithelial cell polarity / positive regulation of integrin activation / positive regulation of cell adhesion mediated by integrin / positive regulation of cell-matrix adhesion / negative regulation of protein import into nucleus ...negative regulation of timing of anagen / keratinocyte migration / positive regulation of wound healing, spreading of epidermal cells / basement membrane organization / positive regulation of transforming growth factor beta production / establishment of epithelial cell polarity / positive regulation of integrin activation / positive regulation of cell adhesion mediated by integrin / positive regulation of cell-matrix adhesion / negative regulation of protein import into nucleus / positive regulation of transforming growth factor beta receptor signaling pathway / keratinocyte proliferation / negative regulation of stem cell proliferation / cell-matrix adhesion / cell periphery / integrin-mediated signaling pathway / negative regulation of canonical Wnt signaling pathway / ruffle membrane / actin filament binding / integrin binding / cell junction / cytoskeleton / cell adhesion / negative regulation of gene expression / focal adhesion / cytosol / cytoplasm
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 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / PH-domain like / FERM superfamily, second domain ...Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / FERM domain signature 2. / FERM central domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / FERM central domain / PH-domain like / 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 1
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYates, L.A. / Lumb, C.N. / Brahme, N.N. / Zalyte, R. / Bird, L.E. / De Colibus, L. / Owens, R.J. / Calderwood, D.A. / Sansom, M.S.P. / Gilbert, R.J.C.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural and Functional Characterisation of the Kindlin-1 Pleckstrin Homology Domain
Authors: Yates, L.A. / Lumb, C.N. / Brahme, N.N. / Zalyte, R. / Bird, L.E. / De Colibus, L. / Owens, R.J. / Calderwood, D.A. / Sansom, M.S.P. / Gilbert, R.J.C.
History
DepositionSep 25, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2012Group: Database references
Revision 1.2Jan 16, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FERMITIN FAMILY HOMOLOG 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9612
Polymers18,8691
Non-polymers921
Water88349
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.290, 82.780, 95.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2005-

HOH

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Components

#1: Protein FERMITIN FAMILY HOMOLOG 1 / KINDLIN-1


Mass: 18868.938 Da / Num. of mol.: 1 / Fragment: PLECKSTRIN HOMOLOGY DOMAIN, RESIDUES 178-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA (PLYSS/RARE) / References: UniProt: E9Q7J9, UniProt: P59113*PLUS
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE IS A FRAGMENT - THE PH DOMAIN - AND INCLUDES THE CLONING ARTEFACT HIS6 TAG

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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: 2.5 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growpH: 7.5
Details: 5MG/ML - 12MG/ML IN 20MM TRIS-HCL, PH 7.5, 200MM NACL, 0.5MM TCEP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9745
DetectorType: ADSC CCD / Detector: CCD
Details: SI (111) DOUBLE CRYSTAL MONOCHROMATOR. KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9745 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 10324 / % possible obs: 95.4 % / Observed criterion σ(I): 3.5 / Redundancy: 7 % / Biso Wilson estimate: 32.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.7
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 3.5 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YS3

2ys3


Resolution: 2.1→39.732 Å / SU ML: 0.3 / σ(F): 1.35 / Phase error: 20.02 / Stereochemistry target values: ML
Details: A LOOP FROM RESIDUES 381-387 WAS DISORDERED IN THE STRUCTURE AND WAS THEREFORE NOT MODELLED.
RfactorNum. reflection% reflection
Rfree0.2131 483 4.7 %
Rwork0.1821 --
obs0.1835 10323 94.83 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.389 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso mean: 42.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.6955 Å20 Å20 Å2
2--14.2707 Å20 Å2
3----11.5752 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 0 6 49 1032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081011
X-RAY DIFFRACTIONf_angle_d1.0111356
X-RAY DIFFRACTIONf_dihedral_angle_d14.77388
X-RAY DIFFRACTIONf_chiral_restr0.068145
X-RAY DIFFRACTIONf_plane_restr0.005169
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1003-2.40410.22661690.19883213X-RAY DIFFRACTION95
2.4041-3.02880.22841610.18283256X-RAY DIFFRACTION95
3.0288-39.73930.2031530.1783371X-RAY DIFFRACTION95
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)
14.10691.39250.04240.69371.0476.5276-0.4317-0.31510.36910.11440.0230.2141-0.6568-1.0810.51090.24920.0844-0.0460.2654-0.06710.3207-5.8275-13.4135-16.6145
28.1204-4.07781.45525.9013-3.89212.88240.3538-0.2295-1.8316-0.3716-0.92640.06642.111-0.53370.33660.6782-0.21880.16630.45430.0750.7415-6.3319-27.4055-15.4295
34.88520.71740.06811.46960.23474.3218-0.0039-0.13150.25460.2094-0.24030.4932-0.1494-1.93240.10170.22930.05680.07660.6514-0.05410.3734-12.8374-14.5609-14.2879
46.33391.6919-3.1571.9312-0.56748.17020.0343-0.6403-0.06060.3374-0.1453-0.01290.81450.27640.37650.3187-0.00570.03310.21050.03850.23080.9335-21.2398-6.4586
54.65431.2119-0.9652.5593-2.43123.0411-0.6402-0.3547-1.10040.1143-0.4228-0.56511.3049-0.44510.70140.4501-0.0780.08880.28770.00640.442-2.9206-24.5193-8.2451
63.41240.3504-0.12935.37191.84727.7126-0.0267-0.09230.37990.1798-0.1944-0.0575-0.64740.09380.14370.23190.0174-0.0320.14910.00590.24742.8426-9.3157-9.2299
76.01790.5997-5.02475.3181.4944.93060.25950.36090.2085-0.44090.4111-1.16150.30152.29990.05510.1468-0.0140.04491.1089-0.2110.859715.4018-12.9522-14.9308
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 370:378)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 379:390)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 391:418)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 419:447)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 448:454)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 455:489)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 490:497)

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