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- PDB-6gvl: Second pair of Fibronectin type III domains of integrin beta4 bou... -

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Basic information

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


trophoblast cell migration / Type I hemidesmosome assembly / hemidesmosome assembly / nail development / hemidesmosome / peripheral nervous system myelin formation / H zone / microtubule plus-end / intermediate filament cytoskeleton organization / Laminin interactions ...trophoblast cell migration / Type I hemidesmosome assembly / hemidesmosome assembly / nail development / hemidesmosome / peripheral nervous system myelin formation / H zone / microtubule plus-end / intermediate filament cytoskeleton organization / Laminin interactions / skin morphogenesis / maintenance of cell polarity / microtubule plus-end binding / filopodium assembly / retrograde axonal transport / mesodermal cell differentiation / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / integrin complex / RND1 GTPase cycle / RND2 GTPase cycle / RND3 GTPase cycle / intermediate filament cytoskeleton / intermediate filament / Assembly of collagen fibrils and other multimeric structures / Syndecan interactions / RHOV GTPase cycle / cell leading edge / RHOU GTPase cycle / basement membrane / stress fiber / axon cytoplasm / cytoskeleton organization / cell-matrix adhesion / basal plasma membrane / integrin-mediated signaling pathway / G protein-coupled receptor binding / cell motility / wound healing / cell-cell adhesion / Z disc / response to wounding / autophagy / 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 / cytosol / cytoplasm
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. / EF-hand domain / Src homology 3 (SH3) domain profile. / SH3 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 / FOURIER SYNTHESIS / Resolution: 2.05 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 / pdbx_database_proc
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
Revision 1.2Jun 19, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.journal_volume / _citation.page_first
Revision 1.3May 1, 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


Theoretical massNumber of molelcules
Total (without water)26,5912
Polymers26,5912
Non-polymers00
Water82946
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 area2850 Å2
ΔGint-19 kcal/mol
Surface area11230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.520, 60.730, 40.780
Angle α, β, γ (deg.)90.00, 113.71, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Integrin beta-4 / GP150


Mass: 23382.195 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.23 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 phosphate-citrate pH 4.2, 20% PEG 8000, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 14766 / % possible obs: 99.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 45.8 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.01 / Net I/σ(I): 11.7
Reflection shellResolution: 2.05→2.1 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.28 / Num. unique obs: 1091 / CC1/2: 0.694 / Rrim(I) all: 1.95 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(dev_2499: ???)refinement
XDSMay 1, 2016data reduction
XSCALEMay 1, 2016data scaling
PHENIXdev_2499phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: D_1200010415

Resolution: 2.05→47.85 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.03
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 703 4.78 %0
Rwork0.2243 ---
obs0.225 14722 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1671 0 0 46 1717
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021716
X-RAY DIFFRACTIONf_angle_d0.4962345
X-RAY DIFFRACTIONf_dihedral_angle_d14.5251028
X-RAY DIFFRACTIONf_chiral_restr0.045266
X-RAY DIFFRACTIONf_plane_restr0.003313
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0501-2.20830.33941460.34062761X-RAY DIFFRACTION99
2.2083-2.43060.34261190.30342811X-RAY DIFFRACTION99
2.4306-2.78220.29441740.28052750X-RAY DIFFRACTION100
2.7822-3.50520.23681180.2222845X-RAY DIFFRACTION100
3.5052-47.8630.20261460.19182852X-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)
10.4001-0.41620.00461.01340.02451.94340.02240.0143-0.3249-0.13590.03230.13580.5017-0.0739-00.50920.0206-0.04080.50810.00910.52596.35581.812333.1052
20.3440.15220.62580.5314-0.13372.62950.0466-0.0379-0.0116-0.2156-0.00330.02330.2408-0.047800.4097-0.0040.00950.38490.00110.43425.243821.548518.293
30.1887-0.1251-0.01280.0836-0.00110.1035-0.0424-0.82740.65940.3310.1520.0215-0.83030.04020.00050.6254-0.0436-0.05330.7130.06260.693710.842830.783228.1819
40.0252-0.0155-0.0670.12210.16450.30560.0320.09350.06950.0491-0.0072-0.45220.19560.47770.0010.6248-0.02080.02990.6095-0.00110.47269.818519.046724.2516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1457:1551)
2X-RAY DIFFRACTION2(chain A and resid 1561:1666)
3X-RAY DIFFRACTION3(chain B and resid 27:35)
4X-RAY DIFFRACTION4(chain B and resid 36:49)

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