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- PDB-1qg3: CRYSTAL STRUCTURE OF A TANDEM PAIR OF FIBRONECTIN TYPE III DOMAIN... -

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Basic information

Entry
Database: PDB / ID: 1qg3
TitleCRYSTAL STRUCTURE OF A TANDEM PAIR OF FIBRONECTIN TYPE III DOMAINS FROM THE CYTOPLASMIC TAIL OF INTEGRIN ALPHA6 BETA4
ComponentsPROTEIN (INTEGRIN BETA-4 SUBUNIT)
KeywordsSTRUCTURAL PROTEIN / INTEGRIN / HEMIDESMOSOME / FIBRONECTIN / CARCINOMA
Function / homology
Function and homology information


Type I hemidesmosome assembly / nail development / hemidesmosome assembly / hemidesmosome / peripheral nervous system myelin formation / trophoblast cell migration / skin morphogenesis / Laminin interactions / filopodium assembly / mesodermal cell differentiation ...Type I hemidesmosome assembly / nail development / hemidesmosome assembly / hemidesmosome / peripheral nervous system myelin formation / trophoblast cell migration / skin morphogenesis / Laminin interactions / filopodium assembly / mesodermal cell differentiation / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / 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 / cell motility / cell-cell adhesion / G protein-coupled receptor binding / response to wounding / autophagy / integrin binding / cell junction / cell migration / 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 / Domains in Na-Ca exchangers and integrin-beta4 / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / CalX-like domain superfamily / Teneurin-like EGF domain / 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-4 subunit / Domains in Na-Ca exchangers and integrin-beta4 / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / CalX-like domain superfamily / Teneurin-like EGF domain / 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 / Integrins beta chain EGF (I-EGF) domain profile. / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain EGF (I-EGF) domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / Fibronectin type III domain / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CACODYLATE ION / Integrin beta-4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.15 Å
Authorsde Pereda, J.M. / Wiche, G. / Liddington, R.C.
CitationJournal: EMBO J. / Year: 1999
Title: Crystal structure of a tandem pair of fibronectin type III domains from the cytoplasmic tail of integrin alpha6beta4.
Authors: de Pereda, J.M. / Wiche, G. / Liddington, R.C.
History
DepositionApr 19, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Aug 20, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Dec 25, 2019Group: Advisory / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_struct_assembly ...pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: PROTEIN (INTEGRIN BETA-4 SUBUNIT)
B: PROTEIN (INTEGRIN BETA-4 SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8997
Polymers43,3372
Non-polymers5625
Water6,864381
1
A: PROTEIN (INTEGRIN BETA-4 SUBUNIT)
hetero molecules

B: PROTEIN (INTEGRIN BETA-4 SUBUNIT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8997
Polymers43,3372
Non-polymers5625
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_455x-1/2,-y+1/2,-z+1/41
Buried area3670 Å2
ΔGint-30 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.040, 59.040, 246.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-383-

CAC

21B-382-

CAC

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Components

#1: Protein PROTEIN (INTEGRIN BETA-4 SUBUNIT)


Mass: 21668.338 Da / Num. of mol.: 2 / Fragment: FIRST TANDEM PAIR OF FIBRONECTIN TYPE III DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P16144
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.47 Å3/Da / Density % sol: 41 %
Crystal growpH: 6.2
Details: 100 MM CACODYLIC ACID/NAOH PH 6.2 200 MM LI2SO4 30% 400 MM POLYETHYLENE GLYCOL
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMcacodylic acid/NaOH1
2200 mM1reservoirLi2SO4
330 %(v/v)PEG4001reservoir
420 mg/mlprotein1drop
510 mMTris-HCl1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.037
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.037 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 22644 / % possible obs: 91.5 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Biso Wilson estimate: 14.8 Å2 / Rsym value: 0.035 / Net I/σ(I): 34
Reflection shellResolution: 2.15→2.21 Å / Mean I/σ(I) obs: 20 / Rsym value: 0.068 / % possible all: 98.9
Reflection
*PLUS
Rmerge(I) obs: 0.035
Reflection shell
*PLUS
Rmerge(I) obs: 0.068

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Processing

Software
NameVersionClassification
SOLVEphasing
CCP4model building
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.15→20 Å / Rfactor Rfree error: 0.008 / Data cutoff high rms absF: 2163566.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1100 5 %RANDOM
Rwork0.201 ---
obs-22644 91.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.49 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å20 Å2
2--1.28 Å20 Å2
3----2.56 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.15→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3027 0 25 381 3433
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.471.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it2.352
X-RAY DIFFRACTIONc_scangle_it3.382.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.283 169 4.7 %
Rwork0.219 3451 -
obs--90.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CAC.PARAMCAC.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 26.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.283 / % reflection Rfree: 4.7 % / Rfactor Rwork: 0.219

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