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- PDB-4wtw: Crystal structure of the third FnIII domain of integrin beta4 -

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Basic information

Entry
Database: PDB / ID: 4wtw
TitleCrystal structure of the third FnIII domain of integrin beta4
ComponentsIntegrin beta-4
KeywordsCELL ADHESION / IMMUNOGLOBULIN FOLD / FIBRONECTIN TYPE III / INTEGRIN
Function / homology
Function and homology information


trophoblast cell migration / Type I hemidesmosome assembly / hemidesmosome assembly / nail development / hemidesmosome / peripheral nervous system myelin formation / skin morphogenesis / Laminin interactions / filopodium assembly / mesodermal cell differentiation ...trophoblast cell migration / Type I hemidesmosome assembly / hemidesmosome assembly / nail development / hemidesmosome / peripheral nervous system myelin formation / skin morphogenesis / Laminin interactions / filopodium assembly / mesodermal cell differentiation / integrin complex / Assembly of collagen fibrils and other multimeric structures / cell adhesion mediated by integrin / Syndecan interactions / cell leading edge / basement membrane / basal plasma membrane / cell-matrix adhesion / integrin-mediated signaling pathway / G protein-coupled receptor binding / cell motility / autophagy / cell-cell adhesion / response to wounding / integrin binding / cell junction / nuclear membrane / receptor complex / cell adhesion / focal adhesion / nucleolus / cell surface / extracellular exosome / metal ion binding / plasma membrane
Similarity search - Function
Integrin beta-4 subunit / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / CalX-like domain superfamily / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily ...Integrin beta-4 subunit / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / CalX-like domain superfamily / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / 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) / EGF-like domain, extracellular / EGF-like domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / Fibronectin type III domain / EGF-like domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.606 Å
AuthorsAlonso-Garcia, N. / Urien, H. / de Pereda, J.M.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and Competitiveness and the European Regional Development FundBFU2009-08389 Spain
Spanish Ministry of Economy and Competitiveness and the European Regional Development FundBFU2012-32847 Spain
CitationJournal: Acta Crystallogr D Biol Crystallogr / Year: 2015
Title: Combination of X-ray crystallography, SAXS and DEER to obtain the structure of the FnIII-3,4 domains of integrin α6β4.
Authors: Noelia Alonso-García / Inés García-Rubio / José A Manso / Rubén M Buey / Hector Urien / Arnoud Sonnenberg / Gunnar Jeschke / José M de Pereda /
Abstract: Integrin α6β4 is a major component of hemidesmosomes that mediate the stable anchorage of epithelial cells to the underlying basement membrane. Integrin α6β4 has also been implicated in cell ...Integrin α6β4 is a major component of hemidesmosomes that mediate the stable anchorage of epithelial cells to the underlying basement membrane. Integrin α6β4 has also been implicated in cell proliferation and migration and in carcinoma progression. The third and fourth fibronectin type III domains (FnIII-3,4) of integrin β4 mediate binding to the hemidesmosomal proteins BPAG1e and BPAG2, and participate in signalling. Here, it is demonstrated that X-ray crystallography, small-angle X-ray scattering and double electron-electron resonance (DEER) complement each other to solve the structure of the FnIII-3,4 region. The crystal structures of the individual FnIII-3 and FnIII-4 domains were solved and the relative arrangement of the FnIII domains was elucidated by combining DEER with site-directed spin labelling. Multiple structures of the interdomain linker were modelled by Monte Carlo methods complying with DEER constraints, and the final structures were selected against experimental scattering data. FnIII-3,4 has a compact and cambered flat structure with an evolutionary conserved surface that is likely to correspond to a protein-interaction site. Finally, this hybrid method is of general application for the study of other macromolecules and complexes.
History
DepositionOct 30, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Database references
Revision 1.2Apr 22, 2015Group: Database references
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _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: Integrin beta-4
B: Integrin beta-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1676
Polymers21,6742
Non-polymers4924
Water3,945219
1
A: Integrin beta-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2684
Polymers10,8371
Non-polymers4303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Integrin beta-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8992
Polymers10,8371
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.760, 68.370, 88.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-1602-

SO4

21A-1703-

HOH

31A-1731-

HOH

41A-1738-

HOH

51A-1763-

HOH

61B-1762-

HOH

71B-1766-

HOH

DetailsThe biological unit is a monomer. There are 2 biological units in the asymmetric unit

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Components

#1: Protein Integrin beta-4 / GP150


Mass: 10837.163 Da / Num. of mol.: 2 / Fragment: Third FnIII domain, UNP residues 1457-1548
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB4 / Plasmid: Modified pET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16144
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Tris-HCl, 12.5% glycerol, 36% PEG 600, 0.5 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 22, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→34.19 Å / Num. obs: 26721 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 14.15 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.039 / Χ2: 0.947 / Net I/σ(I): 41.73 / Num. measured all: 239393
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.6-1.698.10.9630.2947.6829812402636720.31391.2
1.69-1.80.9880.18412.5734865392439240.195100
1.8-1.920.9950.11719.1829699330733060.124100
1.92-2.070.9980.06831.6628445314231410.073100
2.07-2.270.9990.0541.0727325300830050.05399.9
2.27-2.540.9990.03852.0725302272427230.041100
2.54-2.9310.02965.9122135237123710.031100
2.93-3.5910.0291.0419160204520450.021100
3.59-5.0810.017108.0714746160916090.018100
5.0810.017100.7379049369250.01898.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSDecember 29, 2011data reduction
XSCALEJuly 4, 2012data scaling
PHENIX1779refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QG3

1qg3


Resolution: 1.606→33.38 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 16.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1804 1340 5.02 %Random selection
Rwork0.1508 25369 --
obs0.1522 26709 99.66 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.06 Å2 / Biso mean: 21.1827 Å2 / Biso min: 7.63 Å2
Refinement stepCycle: final / Resolution: 1.606→33.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1504 0 58 222 1784
Biso mean--27.41 30.46 -
Num. residues----188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091731
X-RAY DIFFRACTIONf_angle_d1.232383
X-RAY DIFFRACTIONf_chiral_restr0.05256
X-RAY DIFFRACTIONf_plane_restr0.007327
X-RAY DIFFRACTIONf_dihedral_angle_d11.841670
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6064-1.66380.21991430.18252456259998
1.6638-1.73040.20091140.163324992613100
1.7304-1.80920.18851370.156425502687100
1.8092-1.90450.20821260.162925052631100
1.9045-2.02380.18581310.142525252656100
2.0238-2.18010.18971430.143324972640100
2.1801-2.39940.16111410.143225282669100
2.3994-2.74650.17961310.151525502681100
2.7465-3.45970.16811370.139225822719100
3.4597-33.38720.17721370.15672677281499
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)DetailsOrigin x (Å)Origin y (Å)Origin z (Å)
10.5834-0.14360.12030.37860.03920.45570.02480.01870.02870.0105-0.0729-0.103-0.02180.0615-0.00760.08360.00360.01370.08720.01160.1077Chain A21.80914.112122.5108
20.48830.055-0.30380.6639-0.15530.25040.0402-0.06940.00570.0494-0.0218-0.08340.0046-0.0216-0.01240.1013-0.0030.00480.1092-0.0170.0835Chain B3.611731.356335.4581
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain B and resid 1456:1548)B1456 - 1548
2X-RAY DIFFRACTION2(chain B and resid 1456:1548)B1456 - 1548

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