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- PDB-3fq4: Crystal structure of the Calx-beta domain of integrin beta4 -

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Basic information

Entry
Database: PDB / ID: 3fq4
TitleCrystal structure of the Calx-beta domain of integrin beta4
ComponentsIntegrin beta-4
KeywordsCELL ADHESION / Immunoglobulin fold / integrin / Alternative splicing / Disease mutation / Epidermolysis bullosa / 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 / filopodium assembly / mesodermal cell differentiation ...trophoblast cell migration / Type I hemidesmosome assembly / hemidesmosome assembly / nail development / hemidesmosome / peripheral nervous system myelin formation / skin morphogenesis / Laminin interactions / filopodium assembly / mesodermal cell differentiation / 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 / G protein-coupled receptor binding / cell motility / autophagy / cell-cell adhesion / response to wounding / 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 / CalX-beta domain / 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-4 subunit / CalX-beta domain / 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 / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.487 Å
AuthorsAlonso-Garcia, N. / Ingles-Prieto, A. / de Pereda, J.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of the Calx-beta domain of the integrin beta4 subunit: insights into function and cation-independent stability
Authors: Alonso-Garcia, N. / Ingles-Prieto, A. / Sonnenberg, A. / de Pereda, J.M.
History
DepositionJan 7, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Integrin beta-4
B: Integrin beta-4


Theoretical massNumber of molelcules
Total (without water)27,9332
Polymers27,9332
Non-polymers00
Water5,927329
1
A: Integrin beta-4


Theoretical massNumber of molelcules
Total (without water)13,9671
Polymers13,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Integrin beta-4


Theoretical massNumber of molelcules
Total (without water)13,9671
Polymers13,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.310, 51.660, 87.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Integrin beta-4 / GP150


Mass: 13966.667 Da / Num. of mol.: 2 / Fragment: Calx-beta domain, residues 989-1107
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB4 / Plasmid: Modified pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16144
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.03 Å3/Da / Density % sol: 39.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 50mM Tris-HCl, 26% PEG 1500, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 3, 2007
RadiationMonochromator: HELIOS OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.48→27.81 Å / Num. all: 38089 / Num. obs: 38089 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Biso Wilson estimate: 14.8 Å2 / Net I/σ(I): 29.5
Reflection shellResolution: 1.48→1.54 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 8.6 / Num. unique all: 3644 / % possible all: 85.4

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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: Homology model based on PDB entry 2DPK

2dpk


Resolution: 1.487→25.83 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.17 / σ(F): 1.37 / σ(I): 0 / Phase error: 15.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1885 1911 5.02 %RANDOM
Rwork0.1547 36177 --
all0.1564 38088 --
obs0.1564 38088 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.128 Å2 / ksol: 0.434 e/Å3
Displacement parametersBiso max: 138.16 Å2 / Biso mean: 20.843 Å2 / Biso min: 6.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.0143 Å20 Å20 Å2
2--1.1169 Å20 Å2
3----1.4224 Å2
Refinement stepCycle: LAST / Resolution: 1.487→25.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3783 0 0 334 4117
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083829
X-RAY DIFFRACTIONf_angle_d0.966929
X-RAY DIFFRACTIONf_chiral_restr0.079279
X-RAY DIFFRACTIONf_plane_restr0.006617
X-RAY DIFFRACTIONf_dihedral_angle_d15.5781000
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4872-1.52440.24751530.20442450X-RAY DIFFRACTION97
1.5244-1.56560.20041270.17092571X-RAY DIFFRACTION100
1.5656-1.61170.17481220.15162550X-RAY DIFFRACTION100
1.6117-1.66370.1841430.15182559X-RAY DIFFRACTION100
1.6637-1.72310.19841280.152565X-RAY DIFFRACTION100
1.7231-1.79210.18531300.14272565X-RAY DIFFRACTION100
1.7921-1.87360.1851330.14552561X-RAY DIFFRACTION100
1.8736-1.97240.16641370.13872549X-RAY DIFFRACTION100
1.9724-2.09590.14851470.13692592X-RAY DIFFRACTION100
2.0959-2.25770.18011380.13442597X-RAY DIFFRACTION100
2.2577-2.48470.1711350.14622586X-RAY DIFFRACTION100
2.4847-2.84380.20271350.14622622X-RAY DIFFRACTION100
2.8438-3.58140.16871350.13712653X-RAY DIFFRACTION100
3.5814-25.83390.19231480.16292757X-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)
10.396-0.0188-0.3190.31430.32490.4237-0.00920.0335-0.03860.0039-0.04620.00690.0201-0.156-0.0270.0627-0.00980.00310.0499-0.01160.077421.188824.15319.0495
2-0.02680.0990.02050.43360.14490.19540.00850.02730.0048-0.0077-0.00710.0188-0.00940.06300.09910.00530.01280.1215-0.010.103128.877526.31918.6302
30.2461-0.293-0.06730.53760.36720.1640.0667-0.06880.01460.1242-0.01320.0837-0.10850.124-0.00050.10520.0060.01810.1049-0.0040.105922.633529.946923.1391
40.3607-0.152-0.29470.26510.04820.06270.0064-0.0681-0.04540.0358-0.01240.05760.0371-0.0695-00.0794-0.00350.00390.09120.00260.110436.57068.78582.5637
50.503-0.0074-0.120.1601-0.04370.2068-0.0247-0.03340.0220.01190.010.0249-0.07340.0048-0.0020.08190.0080.00480.0631-0.0010.076538.535116.47593.1999
60.5915-0.2435-0.39140.25010.15230.190.00750.0336-0.0728-0.0566-0.02730.033-0.0174-0.0478-0.01530.0861-0.008-0.00580.0728-0.00870.098140.23318.4988-4.0513
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 988:1009)
2X-RAY DIFFRACTION2chain A and resid 1010:1063)
3X-RAY DIFFRACTION3chain A and resid 1064:1105)
4X-RAY DIFFRACTION4chain B and resid 987:1009)
5X-RAY DIFFRACTION5chain B and resid 1010:1063)
6X-RAY DIFFRACTION6chain B and resid 1064:1107)

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