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- PDB-8t0d: Crystal structure of integrin beta-2 tail bound to the FERM-folde... -

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Basic information

Entry
Database: PDB / ID: 8t0d
TitleCrystal structure of integrin beta-2 tail bound to the FERM-folded talin head domain with E269A/Y270A/K306Q triple mutation
ComponentsIntegrin beta-2,Talin-1
KeywordsCELL ADHESION / Talin / integrin / Beta-2
Function / homology
Function and homology information


Toll Like Receptor 4 (TLR4) Cascade / cellular extravasation / integrin alphaM-beta2 complex / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / Smooth Muscle Contraction / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / Integrin cell surface interactions ...Toll Like Receptor 4 (TLR4) Cascade / cellular extravasation / integrin alphaM-beta2 complex / GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / Smooth Muscle Contraction / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / Integrin cell surface interactions / Cell surface interactions at the vascular wall / complement component C3b binding / LIM domain binding / Platelet degranulation / leukocyte migration involved in inflammatory response / vinculin binding / integrin activation / activated T cell proliferation / cell-substrate junction assembly / integrin complex / positive regulation of leukocyte adhesion to vascular endothelial cell / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cortical actin cytoskeleton organization / cell adhesion mediated by integrin / leukocyte cell-cell adhesion / phagocytosis, engulfment / phosphatidylserine binding / amyloid-beta clearance / cellular response to low-density lipoprotein particle stimulus / endothelial cell migration / ruffle / Neutrophil degranulation / phosphatidylinositol binding / neutrophil chemotaxis / cell-matrix adhesion / receptor-mediated endocytosis / integrin-mediated signaling pathway / adherens junction / receptor internalization / structural constituent of cytoskeleton / platelet aggregation / ruffle membrane / cell-cell adhesion / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / actin filament binding / integrin binding / amyloid-beta binding / cytoskeleton / receptor complex / cell adhesion / membrane raft / external side of plasma membrane / focal adhesion / protein-containing complex binding / protein kinase binding / cell surface / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Integrin beta-2 subunit / : / Talin, R4 domain / Vinculin-binding site-containing domain / Talin, central / Talin, N-terminal F0 domain / Talin, central domain superfamily / Talin-1/2, rod-segment / Vinculin Binding Site / Talin, middle domain ...Integrin beta-2 subunit / : / Talin, R4 domain / Vinculin-binding site-containing domain / Talin, central / Talin, N-terminal F0 domain / Talin, central domain superfamily / Talin-1/2, rod-segment / Vinculin Binding Site / Talin, middle domain / N-terminal or F0 domain of Talin-head FERM / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / Phosphotyrosine-binding domain / Alpha-catenin/vinculin-like superfamily / Integrin beta subunit, cytoplasmic domain / Integrin beta cytoplasmic domain / Integrin_b_cyt / FERM domain signature 1. / FERM conserved site / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / FERM domain signature 2. / Integrin domain superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / 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: 2.77 Å
AuthorsWu, J. / Gao, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM119560 United States
CitationJournal: Biorxiv / Year: 2024
Title: Structure of Talin Bound to beta 2 Integrin Unveils the Molecular Mechanism of Species-Specific Integrin Activation
Authors: Gao, T. / Kabir, S. / Wu, J.
History
DepositionMay 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,2551
Polymers47,2551
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.114, 67.092, 115.837
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 Integrin beta-2,Talin-1 / Cell surface adhesion glycoproteins LFA-1/CR3/p150 / 95 subunit beta / Complement receptor C3 subunit beta


Mass: 47255.285 Da / Num. of mol.: 1 / Mutation: E269A,Y270A,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.: 45 / 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: 2.76 Å3/Da / Density % sol: 55.43 %
Crystal growTemperature: 277 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: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.77→29.04 Å / Num. obs: 13889 / % possible obs: 99.83 % / Redundancy: 2 % / Biso Wilson estimate: 56.01 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.02713 / Net I/σ(I): 17
Reflection shellResolution: 2.77→2.869 Å / Rmerge(I) obs: 0.1737 / Num. unique obs: 1353 / CC1/2: 0.917 / CC star: 0.978

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.77→29.04 Å / SU ML: 0.3389 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.1301
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2434 696 5.01 %
Rwork0.1868 13193 -
obs0.1896 13889 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.96 Å2
Refinement stepCycle: LAST / Resolution: 2.77→29.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2989 0 0 45 3034
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00863045
X-RAY DIFFRACTIONf_angle_d0.94024107
X-RAY DIFFRACTIONf_chiral_restr0.0498457
X-RAY DIFFRACTIONf_plane_restr0.0068528
X-RAY DIFFRACTIONf_dihedral_angle_d18.37951138
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.77-2.980.33371330.24152585X-RAY DIFFRACTION99.38
2.98-3.280.30291360.24532591X-RAY DIFFRACTION100
3.28-3.750.29561370.20512620X-RAY DIFFRACTION100
3.75-4.720.21791420.16142638X-RAY DIFFRACTION100
4.72-29.040.19611480.16432759X-RAY DIFFRACTION99.86
Refinement TLS params.Method: refined / Origin x: -19.6484199246 Å / Origin y: 10.1851832103 Å / Origin z: -17.9070321627 Å
111213212223313233
T0.341586518709 Å20.0389834193628 Å20.0131223035785 Å2-0.374827175952 Å20.0569907210755 Å2--0.323433471832 Å2
L0.644577630479 °2-0.408400410553 °2-0.326570283988 °2-1.34808472009 °20.651634188846 °2--0.84092201166 °2
S0.0376004199839 Å °-0.01900520106 Å °-0.0389565464478 Å °0.138880841873 Å °-0.0466448568223 Å °0.0713263053968 Å °-0.0369201982873 Å °-0.0510797285264 Å °0.0166391065497 Å °
Refinement TLS groupSelection details: all

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