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- PDB-3g9w: Crystal Structure of Talin2 F2-F3 in Complex with the Integrin Be... -

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Basic information

Entry
Database: PDB / ID: 3g9w
TitleCrystal Structure of Talin2 F2-F3 in Complex with the Integrin Beta1D Cytoplasmic Tail
Components
  • Integrin beta-1D
  • Talin-2
KeywordsCELL ADHESION / protein-protein complex / PH domain superfold / PTB domain / helical bundle / intrinsically unstructured
Function / homology
Function and homology information


integrin alpha8-beta1 complex / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha6-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / positive regulation of glutamate uptake involved in transmission of nerve impulse / myoblast fate specification / integrin alpha9-beta1 complex ...integrin alpha8-beta1 complex / integrin alpha3-beta1 complex / integrin alpha5-beta1 complex / integrin alpha6-beta1 complex / integrin alpha7-beta1 complex / integrin alpha10-beta1 complex / integrin alpha11-beta1 complex / positive regulation of glutamate uptake involved in transmission of nerve impulse / myoblast fate specification / integrin alpha9-beta1 complex / regulation of collagen catabolic process / cardiac cell fate specification / integrin alpha1-beta1 complex / integrin binding involved in cell-matrix adhesion / integrin alpha4-beta1 complex / cell-cell adhesion mediated by integrin / collagen binding involved in cell-matrix adhesion / integrin alpha2-beta1 complex / reactive gliosis / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / formation of radial glial scaffolds / Other semaphorin interactions / Formation of the ureteric bud / myelin sheath abaxonal region / cerebellar climbing fiber to Purkinje cell synapse / Fibronectin matrix formation / CD40 signaling pathway / calcium-independent cell-matrix adhesion / positive regulation of fibroblast growth factor receptor signaling pathway / integrin alphav-beta1 complex / regulation of synapse pruning / fascia adherens / CHL1 interactions / basement membrane organization / cardiac muscle cell myoblast differentiation / MET interacts with TNS proteins / Laminin interactions / cardiac muscle cell differentiation / Platelet Adhesion to exposed collagen / germ cell migration / leukocyte tethering or rolling / cell projection organization / positive regulation of vascular endothelial growth factor signaling pathway / myoblast fusion / Elastic fibre formation / mesodermal cell differentiation / myoblast differentiation / axon extension / cell migration involved in sprouting angiogenesis / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / wound healing, spreading of epidermal cells / central nervous system neuron differentiation / regulation of spontaneous synaptic transmission / positive regulation of fibroblast migration / integrin complex / lamellipodium assembly / heterotypic cell-cell adhesion / sarcomere organization / MET activates PTK2 signaling / Molecules associated with elastic fibres / Basigin interactions / cell adhesion mediated by integrin / negative regulation of vasoconstriction / leukocyte cell-cell adhesion / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / muscle organ development / Syndecan interactions / positive regulation of wound healing / positive regulation of neuroblast proliferation / dendrite morphogenesis / negative regulation of neuron differentiation / negative regulation of Rho protein signal transduction / response to muscle activity / maintenance of blood-brain barrier / cell-substrate adhesion / homophilic cell-cell adhesion / TGF-beta receptor signaling activates SMADs / cleavage furrow / fibronectin binding / establishment of mitotic spindle orientation / negative regulation of anoikis / intercalated disc / cellular response to low-density lipoprotein particle stimulus / RHOG GTPase cycle / neuroblast proliferation / glial cell projection / RAC2 GTPase cycle / positive regulation of GTPase activity / RAC3 GTPase cycle / ECM proteoglycans / Integrin cell surface interactions / phagocytosis / cellular defense response / coreceptor activity / cell adhesion molecule binding / ruffle / laminin binding / RAC1 GTPase cycle / extracellular matrix organization / protein tyrosine kinase binding
Similarity search - Function
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 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 / Acyl-CoA Binding Protein - #10 / I/LWEQ domain / I/LWEQ domain superfamily / I/LWEQ domain / I/LWEQ domain profile. / I/LWEQ domain / Phosphotyrosine-binding domain / Acyl-CoA Binding Protein / IRS-type PTB domain / PTB domain (IRS-1 type) / Alpha-catenin/vinculin-like superfamily / FERM, N-terminal / FERM N-terminal domain / FERM conserved site / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / 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 / EGF-like domain, extracellular / EGF-like domain / 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) / FERM domain signature 2. / Integrin domain superfamily / FERM central domain / FERM/acyl-CoA-binding protein superfamily / PSI domain / domain found in Plexins, Semaphorins and Integrins / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / 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 1. / PH-like domain superfamily / Roll / Ubiquitin-like domain superfamily / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Integrin beta-1 / Talin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.165 Å
AuthorsAnthis, N.J. / Wegener, K.L. / Ye, F. / Kim, C. / Lowe, E.D. / Vakonakis, I. / Bate, N. / Critchley, D.R. / Ginsberg, M.H. / Campbell, I.D.
CitationJournal: Embo J. / Year: 2009
Title: The structure of an integrin/talin complex reveals the basis of inside-out signal transduction
Authors: Anthis, N.J. / Wegener, K.L. / Ye, F. / Kim, C. / Goult, B.T. / Lowe, E.D. / Vakonakis, I. / Bate, N. / Critchley, D.R. / Ginsberg, M.H. / Campbell, I.D.
History
DepositionFeb 15, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Talin-2
B: Talin-2
C: Integrin beta-1D
D: Integrin beta-1D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,67012
Polymers63,9054
Non-polymers7658
Water6,864381
1
A: Talin-2
D: Integrin beta-1D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2435
Polymers31,9532
Non-polymers2903
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-13 kcal/mol
Surface area15620 Å2
MethodPISA
2
B: Talin-2
C: Integrin beta-1D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4277
Polymers31,9532
Non-polymers4745
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-20 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.260, 108.720, 131.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Talin-2


Mass: 25762.516 Da / Num. of mol.: 2 / Fragment: F2-F3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tln2 / Plasmid: pET151 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q71LX4
#2: Protein Integrin beta-1D / Fibronectin receptor subunit beta / Integrin VLA-4 subunit beta


Mass: 6190.161 Da / Num. of mol.: 2 / Fragment: Cytoplasmic Tail
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB1 / Plasmid: pET16b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P05556
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF CHAIN C, D IS ISOFORM BETA-1D AS LISTED IN UNP ENTRY, P05556-5

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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: 2.99 Å3/Da / Density % sol: 58.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M ammonium acetate, 0.02M magnesium chloride, 0.05M HEPES, 5% PEG 8k, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 26, 2008
Details: Monochromator (horizontally side diffracting Silicon 111 crystal)
RadiationMonochromator: horizontally diffracting monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.165→41.95 Å / Num. all: 41528 / Num. obs: 41362 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 25.312 Å2 / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 8.3
Reflection shellResolution: 2.165→2.28 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 3.5 / Num. unique all: 5982 / Rsym value: 0.338 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1MIX, 1MK7, 1MK9

1mix

1mk7

1mk9


Resolution: 2.165→41.941 Å / SU ML: 0.32 / σ(F): 0.97 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 2068 5.07 %Selected by PHENIX Refine
Rwork0.213 ---
obs0.2148 41362 98.62 %-
all-41528 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.249 Å2 / ksol: 0.325 e/Å3
Displacement parametersBiso mean: 32.26 Å2
Baniso -1Baniso -2Baniso -3
1--2.1972 Å20 Å2-0 Å2
2--2.5887 Å2-0 Å2
3----5.1802 Å2
Refinement stepCycle: LAST / Resolution: 2.165→41.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4103 0 50 381 4534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054277
X-RAY DIFFRACTIONf_angle_d0.8745729
X-RAY DIFFRACTIONf_chiral_restr0.063597
X-RAY DIFFRACTIONf_plane_restr0.004730
X-RAY DIFFRACTIONf_dihedral_angle_d16.3171657
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.165-2.1910.2791680.2632547271597
2.191-2.2190.2761530.24827222875100
2.219-2.2480.3161050.24326402745100
2.248-2.2790.2981400.2526982838100
2.279-2.3120.2551250.24327092834100
2.312-2.3460.3171210.2426182739100
2.346-2.3830.2711740.2526902864100
2.383-2.4220.3411480.24127122860100
2.422-2.4640.2921320.2426042736100
2.464-2.5090.281480.24126652813100
2.509-2.5570.2831440.23926502794100
2.557-2.6090.3541240.2426862810100
2.609-2.6660.2831420.23826782820100
2.666-2.7280.2841340.2322648278299
2.728-2.7960.3251360.2332691282799
2.796-2.8710.2451450.2272598274399
2.871-2.9560.2491310.2252701283299
2.956-3.0510.2471590.2222565272499
3.051-3.160.2431450.2092643278898
3.16-3.2870.2241450.2012618276398
3.287-3.4360.2971230.1962587271098
3.436-3.6170.2211370.1932621275898
3.617-3.8440.2151600.1742596275697
3.844-4.140.1621360.1692598273497
4.14-4.5570.2131690.1592551272097
4.557-5.2150.1681230.1522601272497
5.215-6.5660.2061480.1632558270696
6.566-41.9490.1491270.1672568269595
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)
1-0.1339-0.10170.2667-0.01520.33351.1358-0.0491-0.01120.03030.05870.07880.0246-0.04860.0097-0.01520.1074-0.00430.00310.108-0.02380.114327.2091-3.8933-22.099
20.0123-0.0835-0.15630.48760.1371.08430.17960.08870.0422-0.161-0.06370.1473-0.002-0.0902-0.10110.10090.0302-0.01220.11550.02220.14426.9597.51757.1256
30.3819-0.23770.4421-0.3197-0.2080.64510.0627-0.0448-0.0238-0.1101-0.0922-0.0010.1964-0.0957-0.00110.1894-0.01190.00870.090.00690.103541.4702-1.720725.5769
4-0.2491-0.0979-0.10630.287-0.18780.0190.1198-0.00530.050.1366-0.17290.1144-0.09390.03270.04050.1251-0.1136-0.03180.1490.00920.154711.7068-14.0325-40.9435
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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