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- PDB-8ftb: Crystal structure of integrin beta-2 tail bound to the FERM-folde... -

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Basic information

Entry
Database: PDB / ID: 8ftb
TitleCrystal structure of integrin beta-2 tail bound to the FERM-folded talin head domain with a K306Q mutation
ComponentsIntegrin beta-2,Talin-1
KeywordsCELL ADHESION / integrin / beta-2 / talin / FERM / complex / K306Q
Function / homology
Function and homology information


Toll Like Receptor 4 (TLR4) Cascade / integrin alphaD-beta2 complex / integrin alphaX-beta2 complex / cellular extravasation / integrin alphaM-beta2 complex / positive regulation of neutrophil degranulation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling ...Toll Like Receptor 4 (TLR4) Cascade / integrin alphaD-beta2 complex / integrin alphaX-beta2 complex / cellular extravasation / integrin alphaM-beta2 complex / positive regulation of neutrophil degranulation / integrin alphaL-beta2 complex / ICAM-3 receptor activity / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / leukocyte adhesion to vascular endothelial cell / p130Cas linkage to MAPK signaling for integrins / MAP2K and MAPK activation / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / activated T cell proliferation / Cell surface interactions at the vascular wall / Integrin cell surface interactions / cell-substrate junction assembly / leukocyte migration involved in inflammatory response / LIM domain binding / complement component C3b binding / Smooth Muscle Contraction / Platelet degranulation / neutrophil migration / vinculin binding / cortical microtubule organization / neuron cell-cell adhesion / integrin activation / cell-cell adhesion mediated by integrin / cortical actin cytoskeleton organization / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of leukocyte adhesion to vascular endothelial cell / integrin complex / phagocytosis, engulfment / heterotypic cell-cell adhesion / cell adhesion mediated by integrin / regulation of peptidyl-tyrosine phosphorylation / leukocyte cell-cell adhesion / centriolar satellite / phosphatidylserine binding / receptor clustering / amyloid-beta clearance / cellular response to low-density lipoprotein particle stimulus / plasma membrane raft / endothelial cell migration / cell-matrix adhesion / phagocytosis / neutrophil chemotaxis / positive regulation of superoxide anion generation / ruffle / heat shock protein binding / Neutrophil degranulation / cell adhesion molecule binding / phosphatidylinositol binding / receptor-mediated endocytosis / integrin-mediated signaling pathway / adherens junction / cell-cell adhesion / receptor internalization / integrin binding / ruffle membrane / positive regulation of nitric oxide biosynthetic process / structural constituent of cytoskeleton / positive regulation of angiogenesis / actin filament binding / actin cytoskeleton organization / amyloid-beta binding / signaling receptor complex / cell adhesion / membrane raft / external side of plasma membrane / focal adhesion / protein kinase binding / protein-containing complex binding / cell surface / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Integrin beta-2 subunit / : / Talin VBS2 domain / Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily / Talin-1/2, rod-segment / : / : / Vinculin Binding Site ...Integrin beta-2 subunit / : / Talin VBS2 domain / Vinculin-binding site-containing domain / Talin, central / Talin, central domain superfamily / Talin-1/2, rod-segment / : / : / Vinculin Binding Site / Talin, middle domain / Talin, R4 domain / Talin 1-like, rod segment domain / Talin, N-terminal F0 domain / : / N-terminal or F0 domain of Talin-head FERM / Talin IBS2B domain / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / Phosphotyrosine-binding domain / IRS-type PTB domain / PTB domain (IRS-1 type) / Alpha-catenin/vinculin-like superfamily / FERM domain signature 1. / FERM conserved site / Integrin beta subunit, cytoplasmic domain / Integrin beta tail domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / : / Integrin EGF domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / FERM domain signature 2. / : / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / Integrin domain superfamily / FERM/acyl-CoA-binding protein superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / EGF-like domain signature 1. / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Integrin beta-2 / Talin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsWu, J. / Gao, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Cell Rep / Year: 2025
Title: Molecular basis of beta 2 integrin activation by talin unveils subunit-specific mechanisms of integrin signaling
Authors: Gao, T. / Maskalenko, N.A. / Kabir, S. / Campbell, K.S. / Wu, J.
History
DepositionJan 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Integrin beta-2,Talin-1


Theoretical massNumber of molelcules
Total (without water)47,4051
Polymers47,4051
Non-polymers00
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.006, 68.394, 110.617
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein Integrin beta-2,Talin-1 / Cell surface adhesion glycoproteins LFA-1/CR3/p150 / 95 subunit beta / Complement receptor C3 subunit beta


Mass: 47405.414 Da / Num. of mol.: 1 / Mutation: K306Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Itgb2, Tln1, Tln / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P11835, UniProt: P26039
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / 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: 2.67 Å3/Da / Density % sol: 53.99 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: PEG4000 15%, NaCl 0.1M, DTT 2mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92011 Å / Relative weight: 1
ReflectionResolution: 1.97→29.37 Å / Num. obs: 36669 / % possible obs: 99.6 % / Redundancy: 6.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.15 / Net I/σ(I): 8.7
Reflection shellResolution: 1.97→2.02 Å / Rmerge(I) obs: 0.819 / Num. unique obs: 2559 / CC1/2: 0.78

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIX1.20.1refinement
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→29.09 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2107 1824 4.98 %
Rwork0.1833 --
obs0.1846 36621 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3045 0 0 489 3534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008
X-RAY DIFFRACTIONf_angle_d0.978
X-RAY DIFFRACTIONf_dihedral_angle_d5.588412
X-RAY DIFFRACTIONf_chiral_restr0.06455
X-RAY DIFFRACTIONf_plane_restr0.008538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.020.27321300.22492536X-RAY DIFFRACTION95
2.02-2.080.23491430.21262640X-RAY DIFFRACTION100
2.08-2.150.22351340.19982651X-RAY DIFFRACTION100
2.15-2.230.2231470.19382642X-RAY DIFFRACTION100
2.23-2.310.22581360.1932653X-RAY DIFFRACTION100
2.31-2.420.25171410.1992642X-RAY DIFFRACTION100
2.42-2.550.27241400.19662673X-RAY DIFFRACTION100
2.55-2.710.24641400.19682671X-RAY DIFFRACTION100
2.71-2.920.20481440.19992682X-RAY DIFFRACTION100
2.92-3.210.20411410.19222685X-RAY DIFFRACTION100
3.21-3.670.21931420.16922708X-RAY DIFFRACTION100
3.67-4.620.15211400.15282750X-RAY DIFFRACTION100
4.62-29.090.19861460.1752864X-RAY DIFFRACTION100

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