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- PDB-3f7r: First pair of Fibronectin type III domains and part of the connec... -

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Basic information

Entry
Database: PDB / ID: 3f7r
TitleFirst pair of Fibronectin type III domains and part of the connecting segment of the integrin beta4
ComponentsIntegrin beta-4
KeywordsCELL ADHESION / INTEGRIN / HEMIDESMOSOME / CARCINOMA / EPIDERMOLYSIS BULLOSA / Alternative splicing / Disease mutation / Glycoprotein / Membrane / Phosphoprotein / Polymorphism / Receptor / Transmembrane
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 / mesodermal cell differentiation / filopodium assembly ...trophoblast cell migration / Type I hemidesmosome assembly / hemidesmosome assembly / nail development / hemidesmosome / peripheral nervous system myelin formation / skin morphogenesis / Laminin interactions / mesodermal cell differentiation / filopodium assembly / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / integrin complex / Assembly of collagen fibrils and other multimeric structures / Syndecan interactions / cell leading edge / basement membrane / cell-matrix adhesion / basal plasma membrane / integrin-mediated signaling pathway / cell motility / G protein-coupled receptor binding / cell-cell adhesion / response to wounding / autophagy / 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
DI(HYDROXYETHYL)ETHER / Integrin beta-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.036 Å
Authorsde Pereda, J.M.
CitationJournal: Embo J. / Year: 2009
Title: Structural basis of the interaction between integrin alpha6beta4 and plectin at the hemidesmosomes
Authors: de Pereda, J.M. / Lillo, M.P. / Sonnenberg, A.
History
DepositionNov 10, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin beta-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9065
Polymers27,5961
Non-polymers3104
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)137.500, 42.150, 56.910
Angle α, β, γ (deg.)90.00, 109.92, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Integrin beta-4 / GP150


Mass: 27595.871 Da / Num. of mol.: 1 / Fragment: Fibronectin type-III, residues 1126-1370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB4 / Plasmid: Derivative of pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16144
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#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.: 142 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE IS BASED ON REFERENCE 2 IN THE DATABASE, ITB4_HUMAN, RESPECTIVELY.

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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: 2.81 Å3/Da / Density % sol: 56.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M Cacodylate, 18.75% PEG 600, 6.25% Glycerol, 0.7M NaCl, pH 6.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 26, 2005
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.036→35.674 Å / Num. all: 19573 / Num. obs: 19563 / % possible obs: 98.17 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 31.6 Å2 / Net I/σ(I): 16.6
Reflection shellResolution: 2.036→2.11 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 5.6 / % possible all: 85.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QG3

1qg3


Resolution: 2.036→35.674 Å / Occupancy max: 1 / Occupancy min: 0.39 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.01 / Phase error: 19.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2149 998 5.1 %RANDOM
Rwork0.176 18565 --
all0.178 19567 --
obs0.178 19563 98.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.661 Å2 / ksol: 0.432 e/Å3
Displacement parametersBiso max: 107.53 Å2 / Biso mean: 26.53 Å2 / Biso min: 8.34 Å2
Baniso -1Baniso -2Baniso -3
1--4.5456 Å20 Å2-0.2221 Å2
2--6.1672 Å20 Å2
3----2.1554 Å2
Refinement stepCycle: LAST / Resolution: 2.036→35.674 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3375 0 5 156 3536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123440
X-RAY DIFFRACTIONf_angle_d1.136228
X-RAY DIFFRACTIONf_chiral_restr0.094253
X-RAY DIFFRACTIONf_plane_restr0.007540
X-RAY DIFFRACTIONf_dihedral_angle_d17.599883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0361-2.14350.28141400.24872506X-RAY DIFFRACTION94
2.1435-2.27770.24071270.18652635X-RAY DIFFRACTION98
2.2777-2.45360.21151420.17322644X-RAY DIFFRACTION98
2.4536-2.70040.21861250.16362660X-RAY DIFFRACTION99
2.7004-3.0910.1941560.15162659X-RAY DIFFRACTION99
3.091-3.89350.17251540.14622692X-RAY DIFFRACTION100
3.8935-35.67980.21651540.17182769X-RAY DIFFRACTION99
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)
11.0685-0.2881-0.3846-0.04190.44770.809-0.0099-0.03820.08250.0503-0.04-0.031-0.0339-0.2724-0.00040.1769-0.0071-0.00760.17080.01290.1251-12.3166-2.951444.2208
20.87340.00760.40.551-0.46160.4492-0.0286-0.0523-0.26140.033-0.0089-0.12780.03530.201500.1181-0.01810.00790.17320.00140.1815-21.6132-16.12697.2893
30.1679-0.00980.07390.1444-0.02180.06680.0901-0.0584-0.0556-0.11350.05050.0935-0.2721-0.0608-0.00010.1812-0.00710.0010.17390.05420.274-28.8039-12.03555.2536
40.14210.1675-0.20940.3343-0.10020.0193-0.1704-0.0733-0.3032-0.23880.0520.1134-0.0874-0.0579-0.00050.1776-0.0143-0.02280.0951-0.01050.1764-24.0623-16.0864-1.62
5-0.05020.2955-0.33240.65370.1101-0.0533-0.0649-0.1103-0.1216-0.03-0.0153-0.0428-0.0131-0.023100.1890.00870.0090.1372-0.01360.2148-27.9371-19.42352.4084
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 1126-1216
2X-RAY DIFFRACTION2chain A and resseq 1217-1266
3X-RAY DIFFRACTION3chain A and resseq 1267-1282
4X-RAY DIFFRACTION4chain A and resseq 1283-1301
5X-RAY DIFFRACTION5chain A and resseq 1302-1339

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