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- PDB-11zt: Kindlin-3/Integrin Beta2 Cytoplasmic Tail Complex -

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Basic information

Entry
Database: PDB / ID: 11zt
TitleKindlin-3/Integrin Beta2 Cytoplasmic Tail Complex
ComponentsFermitin family homolog 3,Fermitin family homolog 3,Integrin beta-2
KeywordsCELL ADHESION / Complex
Function / homology
Function and homology information


cell-substrate junction / regulation of cell-cell adhesion mediated by integrin / integrin activation / podosome / leukocyte cell-cell adhesion / substrate adhesion-dependent cell spreading / cell-matrix adhesion / platelet alpha granule lumen / integrin-mediated signaling pathway / platelet aggregation ...cell-substrate junction / regulation of cell-cell adhesion mediated by integrin / integrin activation / podosome / leukocyte cell-cell adhesion / substrate adhesion-dependent cell spreading / cell-matrix adhesion / platelet alpha granule lumen / integrin-mediated signaling pathway / platelet aggregation / integrin binding / Platelet degranulation / positive regulation of cell migration / lipid binding / extracellular exosome / extracellular region / membrane
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 central domain / FERM superfamily, second domain / Band 4.1 domain / Band 4.1 homologues ...Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / FERM domain signature 2. / FERM central domain / 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
Similarity search - Domain/homology
Fermitin family homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39670522411 Å
AuthorsXu, Z. / Ma, Y.Q.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL160861 United States
CitationJournal: J.Thromb.Haemost. / Year: 2026
Title: Structural basis of kindlin-3 in leukocyte adhesion deficiency III.
Authors: Xu, Z. / Ma, S. / Zhou, Y. / Ma, Y.Q.
History
DepositionMar 20, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 8, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2026Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fermitin family homolog 3,Fermitin family homolog 3,Integrin beta-2
B: Fermitin family homolog 3,Fermitin family homolog 3,Integrin beta-2


Theoretical massNumber of molelcules
Total (without water)113,4192
Polymers113,4192
Non-polymers00
Water1,38777
1
A: Fermitin family homolog 3,Fermitin family homolog 3,Integrin beta-2


Theoretical massNumber of molelcules
Total (without water)56,7101
Polymers56,7101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fermitin family homolog 3,Fermitin family homolog 3,Integrin beta-2


Theoretical massNumber of molelcules
Total (without water)56,7101
Polymers56,7101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.256, 102.976, 114.598
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Fermitin family homolog 3,Fermitin family homolog 3,Integrin beta-2 / Kindlin-3 / MIG2-like protein / Unc-112-related protein 2


Mass: 56709.613 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FERMT3, KIND3, MIG2B, URP2, ITGB2, CD18, MFI7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86UX7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 0.1M sodium thiocyanate, 10% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 28, 2018
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.3967→35.4568 Å / Num. obs: 41545 / % possible obs: 97.5 % / Redundancy: 7.2 % / Biso Wilson estimate: 40.6886769077 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Net I/σ(I): 22.54
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 4019 / CC1/2: 0.883

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.12_2829refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39670522411→35.4526805631 Å / SU ML: 0.280856222548 / Cross valid method: FREE R-VALUE / σ(F): 1.33723867896 / Phase error: 26.480877794
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.25465674975 1993 4.80715887986 %
Rwork0.221907381623 39466 -
obs0.22346191161 41459 97.3421614895 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.1211873767 Å2
Refinement stepCycle: LAST / Resolution: 2.39670522411→35.4526805631 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6761 0 0 77 6838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002619432525846925
X-RAY DIFFRACTIONf_angle_d0.5571472432059374
X-RAY DIFFRACTIONf_chiral_restr0.04141675770311012
X-RAY DIFFRACTIONf_plane_restr0.003800900874451199
X-RAY DIFFRACTIONf_dihedral_angle_d6.705061422924148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.45660.3158718539341340.2744655132492678X-RAY DIFFRACTION94.3307614894
2.4566-2.5230.3114455950581230.2654842222672744X-RAY DIFFRACTION96.014735432
2.523-2.59730.3064994714961380.2564439972072752X-RAY DIFFRACTION96.0771276596
2.5973-2.68110.3099812835591540.2616612532032712X-RAY DIFFRACTION95.5651883961
2.6811-2.77680.3161939953211510.2554463052252716X-RAY DIFFRACTION95.375914837
2.7768-2.8880.2869538787361380.2712136840712766X-RAY DIFFRACTION95.9682749504
2.888-3.01930.2913255779071540.2692875539332774X-RAY DIFFRACTION97.0822281167
3.0193-3.17840.3165167840131330.2541274692522832X-RAY DIFFRACTION97.9841374752
3.1784-3.37740.3042869283821290.2612696055112818X-RAY DIFFRACTION97.4859411181
3.3774-3.6380.2685091724941320.2398970333132870X-RAY DIFFRACTION98.6526454157
3.638-4.00360.2417304275431520.2099821769322864X-RAY DIFFRACTION99.1127177128
4.0036-4.58190.2016214196951500.1732385644782938X-RAY DIFFRACTION99.8383446492
4.5819-5.76870.2154967808121360.1828957931222956X-RAY DIFFRACTION99.6455043506
5.7687-35.450.2074716185041690.1958604804953046X-RAY DIFFRACTION99.3203583565

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