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- PDB-6gvk: Second pair of Fibronectin type III domains of integrin beta4 (T1... -

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Basic information

Entry
Database: PDB / ID: 6gvk
TitleSecond pair of Fibronectin type III domains of integrin beta4 (T1663R mutant) bound to the bullous pemphigoid antigen BP230 (BPAG1e)
Components
  • Dystonin
  • Integrin beta-4
KeywordsSTRUCTURAL PROTEIN / CYTOSKELETON / PLAKIN / HEMIDESMOSOME
Function / homology
Function and homology information


intermediate filament bundle assembly / trophoblast cell migration / Type I hemidesmosome assembly / keratin filament / hemidesmosome assembly / nail development / hemidesmosome / keratin filament binding / peripheral nervous system myelin formation / H zone ...intermediate filament bundle assembly / trophoblast cell migration / Type I hemidesmosome assembly / keratin filament / hemidesmosome assembly / nail development / hemidesmosome / keratin filament binding / peripheral nervous system myelin formation / H zone / skin morphogenesis / intermediate filament cytoskeleton organization / Laminin interactions / microtubule plus-end / maintenance of cell polarity / filopodium assembly / microtubule plus-end binding / mesodermal cell differentiation / retrograde axonal transport / integrin complex / RND1 GTPase cycle / RND2 GTPase cycle / intermediate filament cytoskeleton / RND3 GTPase cycle / Assembly of collagen fibrils and other multimeric structures / cell adhesion mediated by integrin / Syndecan interactions / RHOV GTPase cycle / cell leading edge / RHOU GTPase cycle / basement membrane / stress fiber / axon cytoplasm / cytoskeleton organization / basal plasma membrane / cell-matrix adhesion / integrin-mediated signaling pathway / G protein-coupled receptor binding / cell motility / wound healing / autophagy / Z disc / cell-cell adhesion / response to wounding / microtubule cytoskeleton organization / microtubule cytoskeleton / actin cytoskeleton / integrin binding / cell junction / nuclear envelope / actin binding / cell cortex / cytoplasmic vesicle / microtubule binding / nuclear membrane / receptor complex / cell adhesion / axon / focal adhesion / calcium ion binding / endoplasmic reticulum membrane / nucleolus / structural molecule activity / cell surface / protein homodimerization activity / extracellular exosome / nucleoplasm / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
GAR domain / GAR domain superfamily / Growth-Arrest-Specific Protein 2 Domain / GAR domain profile. / Growth-Arrest-Specific Protein 2 Domain / Integrin beta-4 subunit / : / Spectrin-like repeat / Spectrin repeat / Spectrin-like repeat ...GAR domain / GAR domain superfamily / Growth-Arrest-Specific Protein 2 Domain / GAR domain profile. / Growth-Arrest-Specific Protein 2 Domain / Integrin beta-4 subunit / : / Spectrin-like repeat / Spectrin repeat / Spectrin-like repeat / Desmoplakin, spectrin-like domain / Spectrin like domain / Plectin repeat / Plectin repeat / Plakin repeat superfamily / Desmoplakin, SH3 domain / SH3 domain / Plectin repeat / Plakin / 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 / Spectrin repeat / Spectrin repeat / 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) / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats / Actinin-type actin-binding domain, conserved site / EGF-like domain, extracellular / EGF-like domain / Calponin homology domain / Calponin homology (CH) domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / 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 / EF-hand domain pair / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / EF-hand domain pair / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Integrin beta-4 / Dystonin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsManso, J.A. / Gomez-Hernandez, M. / Alonso-Garcia, N. / de Pereda, J.M.
Funding support Spain, 2items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2009-08389 Spain
Spanish Ministry of Economy and CompetitivenessBFU2015-69499-P Spain
CitationJournal: Structure / Year: 2019
Title: Integrin alpha 6 beta 4 Recognition of a Linear Motif of Bullous Pemphigoid Antigen BP230 Controls Its Recruitment to Hemidesmosomes.
Authors: Manso, J.A. / Gomez-Hernandez, M. / Carabias, A. / Alonso-Garcia, N. / Garcia-Rubio, I. / Kreft, M. / Sonnenberg, A. / de Pereda, J.M.
History
DepositionJun 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_database_related
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_database_related.db_id
Revision 1.2Jun 19, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Dec 25, 2019Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
Revision 1.4Jan 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: Integrin beta-4
B: Dystonin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8314
Polymers26,6472
Non-polymers1842
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, This fragment of beta4 is a monomer (by SAXS, gel-filtration, and EPR). When BP230 binds to beta4, the latter remains monomeric (as judged by EPR)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
ΔGint-20 kcal/mol
Surface area11250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.580, 59.520, 42.400
Angle α, β, γ (deg.)90.00, 113.50, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1832-

HOH

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Components

#1: Protein Integrin beta-4 / GP150


Mass: 23438.285 Da / Num. of mol.: 1 / Mutation: T1663R
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: Protein/peptide Dystonin / 230 kDa bullous pemphigoid antigen / 230/240 kDa bullous pemphigoid antigen / Bullous pemphigoid ...230 kDa bullous pemphigoid antigen / 230/240 kDa bullous pemphigoid antigen / Bullous pemphigoid antigen 1 / Bullous pemphigoid antigen / Dystonia musculorum protein / Hemidesmosomal plaque protein


Mass: 3208.494 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q03001
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M Na-acetate (pH 5.0), 20% PEG 6000, 0.2 M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.55→38.885 Å / Num. obs: 35010 / % possible obs: 99.7 % / Redundancy: 19.985 % / Biso Wilson estimate: 31.58 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.056 / Χ2: 1.012 / Net I/σ(I): 26.42
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.55-1.5919.3793.411.5325620.7053.50199.8
1.59-1.6320.5722.3682.1625170.8242.42799.8
1.63-1.6820.4551.8022.824200.8531.84799.6
1.68-1.7320.3621.3623.7524040.9111.39699.8
1.73-1.7919.3380.9235.3123060.9420.94899.8
1.79-1.8520.5030.5978.2922330.9790.61299.7
1.85-1.9220.4250.38512.3221330.990.39599.8
1.92-219.2740.26116.7620530.9950.269100
2-2.0921.0230.18523.0120080.9970.18999.6
2.09-2.1920.7840.13428.9518870.9980.137100
2.19-2.3120.4940.10134.9118270.9990.10399.7
2.31-2.4519.1190.08936.9917000.9990.09199.5
2.45-2.6220.2030.07443.1516180.9990.076100
2.62-2.8319.9360.05850.8515040.9990.0699.5
2.83-3.119.0260.04760.3513730.9990.04899.7
3.1-3.4720.0550.03972.23125410.0499.6
3.47-418.9630.03675.98112210.03799.5
4-4.918.8740.03385.5593310.03499.5
4.9-6.9319.1640.03583.8873710.03698.8
6.93-38.88518.9690.04181.974190.9990.04298.4

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSMarch 1, 2015data reduction
XSCALEMarch 1, 2015data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WTW, 4WTX

4wtw

4wtx


Resolution: 1.55→38.885 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.16
RfactorNum. reflection% reflectionSelection details
Rfree0.2102 1749 5 %0
Rwork0.1947 ---
obs0.1955 34993 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.55→38.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1706 0 12 105 1823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041918
X-RAY DIFFRACTIONf_angle_d0.72644
X-RAY DIFFRACTIONf_dihedral_angle_d15.0531177
X-RAY DIFFRACTIONf_chiral_restr0.051297
X-RAY DIFFRACTIONf_plane_restr0.005360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.59560.43831340.40192761X-RAY DIFFRACTION100
1.5956-1.64710.36741520.33052748X-RAY DIFFRACTION100
1.6471-1.7060.34221430.29572740X-RAY DIFFRACTION100
1.706-1.77430.3081680.25862736X-RAY DIFFRACTION100
1.7743-1.85510.25271460.24352763X-RAY DIFFRACTION100
1.8551-1.95290.22451550.21752752X-RAY DIFFRACTION100
1.9529-2.07520.241520.20842763X-RAY DIFFRACTION100
2.0752-2.23540.2341390.20242762X-RAY DIFFRACTION100
2.2354-2.46040.23921310.21122789X-RAY DIFFRACTION100
2.4604-2.81630.24681590.21532771X-RAY DIFFRACTION100
2.8163-3.54790.19351270.182828X-RAY DIFFRACTION100
3.5479-38.8970.17081430.16832831X-RAY DIFFRACTION100
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)
12.25140.8855-0.03084.7545-1.24343.88450.0518-0.2494-0.14380.0739-0.01150.18440.36670.0136-0.00090.2510.0552-0.01290.2743-0.0030.26677.31892.708335.6216
22.1512-1.52840.45662.64230.73473.0125-0.1446-0.3138-0.8354-0.2911-0.12640.12230.8462-0.2406-0.01610.39250.0066-0.06410.3215-0.01190.36683.4177-1.324732.1589
30.09920.1504-0.20540.3395-0.37780.40820.73540.5110.53790.087-0.1337-0.6105-1.4760.4973-0.00070.8336-0.05240.1180.7885-0.06140.676920.863421.762626.4969
42.14770.27810.99520.52710.17862.4213-0.03860.35960.0517-0.0325-0.0104-0.02130.03230.35040.00010.241-0.04140.03030.27820.01550.23539.356222.564518.6063
53.49690.64010.1841.6876-1.52421.82130.1202-0.0230.0301-0.12180.0962-0.11070.20720.073400.23750.0212-0.05460.2964-0.04160.21640.307118.112118.6849
62.58150.4213-0.35882.1144-1.86322.07570.11410.46020.3318-0.4429-0.07730.1061-0.3077-0.0948-0.00010.2948-0.02660.0010.30740.01490.26333.597226.166316.515
70.8726-0.0586-0.36031.0834-0.41610.65190.1720.2349-0.4043-0.3561-0.52890.38630.5601-0.5968-0.01620.4201-0.021-0.02710.3063-0.06180.3359-0.004914.1317.091
81.0784-0.607-0.13180.6606-0.3981.6213-0.0224-0.10090.0844-0.17870.1026-0.04760.00860.0767-00.2998-0.0319-0.05750.21430.00660.27764.36921.761725.743
90.9337-0.5487-0.09910.67670.38790.79570.0721-0.34310.94160.31020.0173-0.1307-0.3239-0.43720.00120.3327-0.1242-0.04750.4970.03510.461910.642530.481829.2874
100.1707-0.11590.0050.73780.06191.3654-0.03560.2495-0.03810.03520.1677-0.2999-0.04770.1365-00.3358-0.0209-0.04220.3190.03540.33488.821718.579825.7868
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1457:1528)
2X-RAY DIFFRACTION2(chain A and resid 1529:1550)
3X-RAY DIFFRACTION3(chain A and resid 1551:1567)
4X-RAY DIFFRACTION4(chain A and resid 1568:1593)
5X-RAY DIFFRACTION5(chain A and resid 1594:1620)
6X-RAY DIFFRACTION6(chain A and resid 1621:1642)
7X-RAY DIFFRACTION7(chain A and resid 1643:1653)
8X-RAY DIFFRACTION8(chain A and resid 1654:1666)
9X-RAY DIFFRACTION9(chain B and resid 27:35)
10X-RAY DIFFRACTION10(chain B and resid 36:50)

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