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- PDB-3ivf: Crystal structure of the talin head FERM domain -

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Basic information

Entry
Database: PDB / ID: 3ivf
TitleCrystal structure of the talin head FERM domain
ComponentsTalin-1
KeywordsSTRUCTURAL PROTEIN / FERM domain / Cell membrane / Cell projection / Cytoskeleton / Membrane / Phosphoprotein / CELL ADHESION
Function / homology
Function and homology information


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 / LIM domain binding / Platelet degranulation / vinculin binding / integrin activation ...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 / LIM domain binding / Platelet degranulation / 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 / cell-cell adhesion / ruffle membrane / actin filament binding / integrin binding / cytoskeleton / focal adhesion / cell surface / plasma membrane / cytoplasm
Similarity search - Function
: / 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 ...: / 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 / Acyl-CoA Binding Protein - #10 / Phosphotyrosine-binding domain / Acyl-CoA Binding Protein / 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 / 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 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å
AuthorsElliott, P.R. / Goult, B.T. / Bate, N. / Grossmann, J.G. / Roberts, G.C.K. / Critchley, D.R. / Barsukov, I.L.
CitationJournal: Structure / Year: 2010
Title: The Structure of the talin head reveals a novel extended conformation of the FERM domain
Authors: Elliott, P.R. / Goult, B.T. / Kopp, P.M. / Bate, N. / Grossmann, J.G. / Roberts, G.C.K. / Critchley, D.R. / Barsukov, I.L.
History
DepositionSep 1, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 30, 2011Group: Database references
Revision 1.3Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Nov 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Talin-1


Theoretical massNumber of molelcules
Total (without water)42,9311
Polymers42,9311
Non-polymers00
Water10,016556
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.260, 72.160, 162.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Talin-1


Mass: 42931.441 Da / Num. of mol.: 1 / Fragment: N-terminal FERM domain, UNP residues 1-400
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tln1, Tln / Plasmid: pET151/D / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P26039
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE NUMBERS 140-168 ARE SKIPPED DUE TO DELETION

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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: 2.83 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 21% PEG4000, 0.1M Tris, 0.2M ammonium sulphate, pH7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.725 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 19, 2008
RadiationMonochromator: LN2 cooled fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.725 Å / Relative weight: 1
ReflectionResolution: 1.94→72.16 Å / Num. all: 101749 / Num. obs: 34587 / % possible obs: 76 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 8.3
Reflection shellResolution: 1.94→2.05 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 3.3 / Num. unique all: 5159 / % possible all: 71

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 52.96 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å43.38 Å
Translation2.5 Å43.38 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMAC5.5.0066refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MIX, 2KC1, 2KC2

1mix

2kc1

2kc2


Resolution: 1.94→43.38 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.892 / Occupancy max: 1 / Occupancy min: 0 / SU B: 6.867 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1721 5 %RANDOM
Rwork0.193 ---
obs0.196 34521 96.1 %-
all-46922 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 87.16 Å2 / Biso mean: 29.904 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.94→43.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2899 0 0 556 3455
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0222912
X-RAY DIFFRACTIONr_bond_other_d00.022644
X-RAY DIFFRACTIONr_angle_refined_deg1.841.9643926
X-RAY DIFFRACTIONr_angle_other_deg0.96536153
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.055356
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76624.317139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.41615532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5891519
X-RAY DIFFRACTIONr_chiral_restr0.1140.2430
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023221
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02590
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2261.51776
X-RAY DIFFRACTIONr_mcbond_other0.1841.5729
X-RAY DIFFRACTIONr_mcangle_it2.07922860
X-RAY DIFFRACTIONr_scbond_it3.12631136
X-RAY DIFFRACTIONr_scangle_it4.8574.51066
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.944→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 120 -
Rwork0.26 2491 -
all-2611 -
obs--99.58 %
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)
11.3857-0.1110.3424.36-0.09363.02040.03490.0849-0.07990.042-0.04950.19970.0049-0.07770.01450.01590.0153-0.01410.0595-0.01190.0512-31.38823.011104.249
21.49010.7446-0.18782.33940.5845.6907-0.04970.0840.0028-0.20780.0040.0168-0.3119-0.13430.04570.11850.0410.02830.1213-0.03210.1053-29.519.83778.235
32.34360.60770.23964.30341.61795.8203-0.1403-0.1150.0741-0.35350.1206-0.152-0.12890.42540.01980.0326-0.00430.00870.0389-0.00430.0105-15.4183.74457.424
41.58770.7113-0.2645.26261.02532.72330.09570.0957-0.0631-0.0447-0.14140.37670.0641-0.19060.04560.01240.0019-0.01180.0358-0.01460.0409-19.587-10.20529.882
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 83
2X-RAY DIFFRACTION2A89 - 194
3X-RAY DIFFRACTION3A211 - 305
4X-RAY DIFFRACTION4A329 - 397

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