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- PDB-5nl1: Shigella IpaA-VBS3/TBS in complex with the Talin VBS1 domain 488-512 -

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Basic information

Entry
Database: PDB / ID: 5nl1
TitleShigella IpaA-VBS3/TBS in complex with the Talin VBS1 domain 488-512
Components
  • Invasin IpaA
  • Talin-1
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


positive regulation of actin filament depolymerization / 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 ...positive regulation of actin filament depolymerization / 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 / platelet aggregation / ruffle membrane / cell-cell adhesion / actin filament binding / integrin binding / actin binding / cytoskeleton / focal adhesion / cell surface / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
SipA, vinculin binding site / SipA vinculin binding site / Salmonella invasion protein A, N-terminal / Salmonella invasion protein A, chaperone-binding / SipA N-terminal domain / Talin, central domain / A middle domain of Talin 1 / : / Talin, R4 domain / Vinculin-binding site-containing domain ...SipA, vinculin binding site / SipA vinculin binding site / Salmonella invasion protein A, N-terminal / Salmonella invasion protein A, chaperone-binding / SipA N-terminal domain / Talin, central domain / A middle domain of Talin 1 / : / 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 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Invasin IpaA / Talin-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Shigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBou-Nader, C. / Pecqueur, L. / Valencia-Gallardo, C. / Fontecave, M. / Tran Van Nhieu, G.
CitationJournal: Cell Rep / Year: 2019
Title: Shigella IpaA Binding to Talin Stimulates Filopodial Capture and Cell Adhesion.
Authors: Valencia-Gallardo, C. / Bou-Nader, C. / Aguilar-Salvador, D.I. / Carayol, N. / Quenech'Du, N. / Pecqueur, L. / Park, H. / Fontecave, M. / Izard, T. / Tran Van Nhieu, G.
History
DepositionApr 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
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.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Talin-1
B: Talin-1
C: Talin-1
D: Talin-1
E: Talin-1
F: Talin-1
G: Invasin IpaA
H: Invasin IpaA
I: Invasin IpaA
J: Invasin IpaA
K: Invasin IpaA
L: Invasin IpaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,87817
Polymers127,49312
Non-polymers3865
Water2,522140
1
A: Talin-1
B: Talin-1
H: Invasin IpaA
I: Invasin IpaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5605
Polymers42,4984
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-39 kcal/mol
Surface area15770 Å2
MethodPISA
2
C: Talin-1
E: Talin-1
J: Invasin IpaA
L: Invasin IpaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,5945
Polymers42,4984
Non-polymers961
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-59 kcal/mol
Surface area15740 Å2
MethodPISA
3
D: Talin-1
F: Talin-1
G: Invasin IpaA
K: Invasin IpaA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7257
Polymers42,4984
Non-polymers2283
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-77 kcal/mol
Surface area15420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.260, 96.360, 175.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Talin-1


Mass: 16220.107 Da / Num. of mol.: 6 / Fragment: UNP residues 480-635
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tln1, Tln / Plasmid: pet28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P26039
#2: Protein/peptide
Invasin IpaA / 70 kDa antigen


Mass: 5028.668 Da / Num. of mol.: 6 / Fragment: UNP residues 488-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: ipaA, CP0125 / Plasmid: pet28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P18010

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Non-polymers , 4 types, 145 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M ammonium sulfate 0.1 M sodium acetate pH 4.6 30 % PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.5→48.18 Å / Num. obs: 39441 / % possible obs: 99.2 % / Redundancy: 4.8 % / Biso Wilson estimate: 58.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Net I/σ(I): 9.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 0.7 / CC1/2: 0.567 / % possible all: 95.7

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1sj7

1sj7


Resolution: 2.5→36.33 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.937 / SU R Cruickshank DPI: 0.426 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.431 / SU Rfree Blow DPI: 0.244 / SU Rfree Cruickshank DPI: 0.247
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1970 4.99 %RANDOM
Rwork0.196 ---
obs0.197 39441 99.3 %-
Displacement parametersBiso mean: 68.64 Å2
Baniso -1Baniso -2Baniso -3
1-1.8015 Å20 Å20 Å2
2--0.3549 Å20 Å2
3----2.1563 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: 1 / Resolution: 2.5→36.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7167 0 20 140 7327
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017338HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.099970HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2547SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes207HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1065HARMONIC5
X-RAY DIFFRACTIONt_it7338HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.16
X-RAY DIFFRACTIONt_other_torsion19.1
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1066SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies7HARMONIC1
X-RAY DIFFRACTIONt_utility_distance4HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8490SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2482 135 4.94 %
Rwork0.2309 2596 -
all0.2318 2731 -
obs--94.24 %
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)
13.3228-0.9261-0.08953.13650.72434.61080.04460.0982-0.051-0.05020.0670.1411-0.35070.1782-0.1116-0.21-0.07160.0512-0.22540.017-0.116113.72429.673934.0619
25.4821-1.2201-0.60962.60910.1124.56410.0760.1160.1641-0.2586-0.02650.13270.5113-0.3737-0.0495-0.0631-0.06050.0124-0.20060.0042-0.19538.9522-6.219124.1421
33.99481.4923-0.69612.99610.54743.47480.0523-0.29780.1470.4286-0.0088-0.12320.74550.3149-0.04350.07670.11590.0081-0.18840.0014-0.264913.9485-9.093752.5098
41.9066-0.3245-0.74712.66030.75283.25480.11-0.07110.0976-0.39240.0054-0.0263-0.26190.0487-0.1154-0.01340.01960.0785-0.11710.0226-0.194819.97769.37335.5016
53.89563.026-1.46925.0612-0.27393.7694-0.1130.31090.2219-0.01530.1395-0.00280.1645-0.2468-0.02640.01860.03750.0524-0.14580.0137-0.21345.7842.296563.5144
62.4049-0.6910.28296.0856-0.42323.9722-0.01580.13960.0450.0115-0.02350.0359-0.1563-0.54270.0393-0.09080.09640.0187-0.06870.0237-0.2796.25044.8267-5.2316
70.8716-2.3772-0.01020.9031.4474.73150.06650.01410.0491-0.067-0.0132-0.04730.0589-0.2797-0.05330.10340.00870.04930.07310.019-0.15664.6745-1.494-15.9975
80.6514-3.33960.37283.613-0.43633.955-0.0085-0.0923-0.04460.18010.24320.0205-0.00560.1665-0.23470.11-0.05470.0364-0.048-0.0506-0.131720.677113.251944.2316
93.97560.4767-1.157402.15513.1643-0.00790.19350.1641-0.05350.08950.1680.07110.0934-0.08160.2856-0.08540.0799-0.0927-0.0283-0.236611.8827-12.999614.1582
100.12990.64772.92943.8111.63934.414-0.0181-0.02010.11780.06390.1905-0.28260.51970.212-0.17240.06710.15190.07160.0327-0.0001-0.065724.2445-7.039742.0679
110.73992.0707-2.1613.02991.55075.8227-0.00920.0723-0.0208-0.0153-0.0538-0.07480.08060.34010.0630.0165-0.02630.0550.0809-0.0038-0.109426.93912.231816.0352
121.94281.6556-0.02650.17751.84123.75240.0026-0.0060.07780.0065-0.0507-0.0854-0.0163-0.06750.04810.07840.0701-0.05830.01270.0168-0.12448.3918.196374.2742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }
6X-RAY DIFFRACTION6{ F|* }
7X-RAY DIFFRACTION7{ G|* }
8X-RAY DIFFRACTION8{ H|* }
9X-RAY DIFFRACTION9{ I|* }
10X-RAY DIFFRACTION10{ J|* }
11X-RAY DIFFRACTION11{ K|* }
12X-RAY DIFFRACTION12{ L|* }

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