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- PDB-4q58: Crystal structure of the plectin 1a actin-binding domain/integrin... -

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Basic information

Entry
Database: PDB / ID: 4q58
TitleCrystal structure of the plectin 1a actin-binding domain/integrin beta 4 fragment complex
Components
  • Integrin beta-4
  • Plectin
KeywordsSTRUCTURAL PROTEIN/PROTEIN BINDING / calponin homology domain / STRUCTURAL PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


trophoblast cell migration / protein-containing complex organization / actomyosin contractile ring assembly actin filament organization / skeletal myofibril assembly / tight junction organization / Type I hemidesmosome assembly / hemidesmosome assembly / nail development / hemidesmosome / leukocyte migration involved in immune response ...trophoblast cell migration / protein-containing complex organization / actomyosin contractile ring assembly actin filament organization / skeletal myofibril assembly / tight junction organization / Type I hemidesmosome assembly / hemidesmosome assembly / nail development / hemidesmosome / leukocyte migration involved in immune response / peripheral nervous system myelin formation / intermediate filament organization / : / skin morphogenesis / regulation of vascular permeability / intermediate filament cytoskeleton organization / Laminin interactions / dystroglycan binding / cellular response to hydrostatic pressure / fibroblast migration / costamere / T cell chemotaxis / filopodium assembly / mesodermal cell differentiation / cellular response to fluid shear stress / peripheral nervous system myelin maintenance / cardiac muscle cell development / myoblast differentiation / integrin complex / adherens junction organization / intermediate filament cytoskeleton / response to food / structural constituent of muscle / ankyrin binding / Assembly of collagen fibrils and other multimeric structures / intermediate filament / cell adhesion mediated by integrin / Syndecan interactions / sarcomere organization / nucleus organization / keratinocyte development / transmission of nerve impulse / cell leading edge / brush border / sarcoplasm / basement membrane / Caspase-mediated cleavage of cytoskeletal proteins / establishment of skin barrier / skeletal muscle fiber development / respiratory electron transport chain / mitochondrion organization / cell-matrix adhesion / basal plasma membrane / integrin-mediated signaling pathway / G protein-coupled receptor binding / cell motility / wound healing / cell morphogenesis / protein localization / multicellular organism growth / structural constituent of cytoskeleton / sarcolemma / autophagy / cell-cell adhesion / Z disc / response to wounding / cellular response to mechanical stimulus / : / actin filament binding / integrin binding / cell junction / myelin sheath / gene expression / nuclear membrane / mitochondrial outer membrane / receptor complex / cell adhesion / cadherin binding / axon / focal adhesion / dendrite / nucleolus / perinuclear region of cytoplasm / cell surface / RNA binding / extracellular exosome / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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 / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / 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) / 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. / Plectin/S10, N-terminal / Plectin/S10 domain / 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 / Src homology 3 (SH3) domain profile. / SH3 domain / Winged helix-like DNA-binding domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Integrin beta-4 / Plectin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.001 Å
AuthorsSong, J.-G. / Kostan, J. / Grishkovskaya, I. / Djinovic-Carugo, K.
CitationJournal: To be Published
Title: Crystal structure of the plectin 1a actin-binding domain/integrin beta 4 fragment complex
Authors: Song, J.-G. / Kostan, J. / Grishkovskaya, I. / Djinovic-Carugo, K.
History
DepositionApr 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Plectin
B: Plectin
C: Integrin beta-4
D: Integrin beta-4


Theoretical massNumber of molelcules
Total (without water)96,1934
Polymers96,1934
Non-polymers00
Water0
1
A: Plectin
D: Integrin beta-4


Theoretical massNumber of molelcules
Total (without water)48,0972
Polymers48,0972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Plectin


Theoretical massNumber of molelcules
Total (without water)26,4281
Polymers26,4281
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Integrin beta-4


Theoretical massNumber of molelcules
Total (without water)21,6681
Polymers21,6681
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.341, 96.341, 208.025
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Plectin / / PCN / PLTN / Hemidesmosomal protein 1 / HD1 / Plectin-1


Mass: 26428.162 Da / Num. of mol.: 2 / Fragment: actin-binding domain (UNP residues 175-400) / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q15149
#2: Protein Integrin beta-4 / GP150


Mass: 21668.338 Da / Num. of mol.: 2
Fragment: fibronectin type III domains 1 and 2 (UNP residues 1126-1320)
Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P16144

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.54 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20 mM HEPES, pH 6.5, 150 mM sodium formate, 7.5% PEG550 MME, 3% sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 4→48.16 Å / Num. obs: 9188 / Redundancy: 5.7 % / Rmerge(I) obs: 0.272 / Net I/σ(I): 7.4
Reflection shellResolution: 4→4.47 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 3.9 / Num. unique all: 2594

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 4.001→46.929 Å / SU ML: 0.51 / σ(F): 1.35 / Phase error: 33.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2869 440 4.82 %
Rwork0.2237 --
obs0.2268 9130 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.001→46.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6619 0 0 0 6619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046763
X-RAY DIFFRACTIONf_angle_d0.8929166
X-RAY DIFFRACTIONf_dihedral_angle_d13.0862565
X-RAY DIFFRACTIONf_chiral_restr0.06995
X-RAY DIFFRACTIONf_plane_restr0.0051198
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.001-4.57910.32071420.26392913X-RAY DIFFRACTION99
4.5791-5.76750.30231480.23662891X-RAY DIFFRACTION99
5.7675-46.9320.26041500.19282886X-RAY DIFFRACTION98

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