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- PDB-9c1t: Crystal structure of integrin beta-3 tail bound to the FERM-folde... -

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Basic information

Entry
Database: PDB / ID: 9c1t
TitleCrystal structure of integrin beta-3 tail bound to the FERM-folded talin head domain with a D397R mutation
ComponentsIntegrin beta-3, Talin-1
KeywordsCELL ADHESION / Talin / integrin / FERM / beta3
Function / homology
Function and homology information


GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / LIM domain binding / Smooth Muscle Contraction / Platelet degranulation / cortical microtubule organization / vinculin binding ...GRB2:SOS provides linkage to MAPK signaling for Integrins / Integrin signaling / p130Cas linkage to MAPK signaling for integrins / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / MAP2K and MAPK activation / LIM domain binding / Smooth Muscle Contraction / Platelet degranulation / cortical microtubule organization / vinculin binding / integrin activation / cell-substrate junction assembly / cortical actin cytoskeleton organization / phosphatidylserine binding / ruffle / phosphatidylinositol binding / integrin-mediated signaling pathway / adherens junction / structural constituent of cytoskeleton / ruffle membrane / actin filament binding / integrin binding / cytoskeleton / cell adhesion / focal adhesion / cell surface / cytosol
Similarity search - Function
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 ...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 / FERM domain signature 2. / 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 / PH-like domain superfamily / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWu, J. / Gao, T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)119560 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
DepositionMay 29, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 14, 2025Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin beta-3, Talin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5462
Polymers47,4501
Non-polymers961
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.425, 67.209, 115.572
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-3, Talin-1


Mass: 47449.602 Da / Num. of mol.: 1 / Mutation: D397R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Mus musculus (house mouse)
Gene: ITGB3, GP3A, Tln1, Tln / Plasmid: pET28a
Details (production host): modified to remove his-tag and cleavage site
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P26039
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M sodium chloride, 0.1 M MES pH6.5, 10 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97931 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.3→29.78 Å / Num. obs: 23199 / % possible obs: 98.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 47.03 Å2 / CC1/2: 0.996 / Net I/σ(I): 12.2
Reflection shellResolution: 2.3→2.36 Å / Num. unique obs: 1357 / CC1/2: 0.715

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→29.78 Å / SU ML: 0.3173 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.55
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2668 1153 4.98 %
Rwork0.2033 21992 -
obs0.2063 23145 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.07 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3019 0 5 81 3105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00863111
X-RAY DIFFRACTIONf_angle_d0.95384195
X-RAY DIFFRACTIONf_chiral_restr0.0549458
X-RAY DIFFRACTIONf_plane_restr0.0078540
X-RAY DIFFRACTIONf_dihedral_angle_d5.5595421
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.410.34141240.27422404X-RAY DIFFRACTION88.18
2.41-2.540.34751450.27112726X-RAY DIFFRACTION99.93
2.54-2.690.30441440.24372768X-RAY DIFFRACTION100
2.69-2.90.32861400.24252771X-RAY DIFFRACTION99.97
2.9-3.190.30691540.25072762X-RAY DIFFRACTION99.97
3.19-3.660.2631470.20682789X-RAY DIFFRACTION100
3.66-4.60.24751490.17072810X-RAY DIFFRACTION99.87
4.6-29.780.22371500.17522962X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: -26.1187588801 Å / Origin y: -2.32697266821 Å / Origin z: 11.0134731359 Å
111213212223313233
T0.348947703416 Å2-0.0203309854343 Å2-0.0322215206177 Å2-0.269172444567 Å2-0.0137152686109 Å2--0.285139969528 Å2
L1.54012404518 °20.519988229717 °2-0.58132065986 °2-0.58840247003 °2-0.432405749395 °2--0.776315252731 °2
S-0.0510637254879 Å °-0.178204066094 Å °-0.130024478959 Å °0.0591062921676 Å °0.0153395416216 Å °-0.0823399722616 Å °0.0313919657209 Å °-0.00785717599982 Å °0.049181775984 Å °
Refinement TLS groupSelection details: all

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