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- PDB-3h6a: Structure of the Calx-beta domain of integrin beta4 crystallized ... -

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Basic information

Entry
Database: PDB / ID: 3h6a
TitleStructure of the Calx-beta domain of integrin beta4 crystallized in the presence of calcium
ComponentsIntegrin beta-4
KeywordsCELL ADHESION / IMMUNOGLOBULIN FOLD / INTEGRIN / EPIDERMOLYSIS BULLOSA / GLYCOPROTEIN / MEMBRANE / RECEPTOR / TRANSMEMBRANE / Alternative splicing / Disease mutation / Disulfide bond / Phosphoprotein / Polymorphism
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 / 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 / FOURIER SYNTHESIS / Resolution: 1.608 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
DepositionApr 23, 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
Water5,332296
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, 51.700, 87.440
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.: 296 / 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: 2.04 Å3/Da / Density % sol: 39.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 50MM TRIS-HCL, 2MM CACL2, 26% PEG 1500, pH 7.9, VAPOR DIFFUSION, HANGING DROP, 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 15, 2009
RadiationMonochromator: HELIOS OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.608→19.34 Å / Num. all: 30229 / Num. obs: 30229 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 11.37 Å2 / Net I/σ(I): 17.1
Reflection shellResolution: 1.608→1.69 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 6.62 / Num. unique all: 4045 / % possible all: 88.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIX(PHENIX.REFINE)model building
PHENIX(phenix.refine: 2009_02_15_2320)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3FQ4

3fq4


Resolution: 1.608→19.34 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.23 / σ(F): 1.59 / Phase error: 18.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 1515 5.01 %RANDOM
Rwork0.1718 28711 --
all0.1738 30226 --
obs0.1738 30226 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.866 Å2 / ksol: 0.441 e/Å3
Displacement parametersBiso max: 159.23 Å2 / Biso mean: 18.61 Å2 / Biso min: 2.65 Å2
Baniso -1Baniso -2Baniso -3
1--1.1166 Å20 Å20 Å2
2--0.2335 Å20 Å2
3----2.3221 Å2
Refinement stepCycle: LAST / Resolution: 1.608→19.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3742 0 0 296 4038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011921
X-RAY DIFFRACTIONf_angle_d1.2732606
X-RAY DIFFRACTIONf_chiral_restr0.085276
X-RAY DIFFRACTIONf_plane_restr0.007358
X-RAY DIFFRACTIONf_dihedral_angle_d17.811748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDNum. reflection obs
1.6082-1.66010.26131380.21662484X-RAY DIFFRACTION2484
1.6601-1.71940.23151340.18692602X-RAY DIFFRACTION2602
1.7194-1.78820.2271290.1732553X-RAY DIFFRACTION2553
1.7882-1.86950.21761340.1712590X-RAY DIFFRACTION2590
1.8695-1.9680.21391370.16782585X-RAY DIFFRACTION2585
1.968-2.09120.21031470.17052599X-RAY DIFFRACTION2599
2.0912-2.25240.1941370.16572615X-RAY DIFFRACTION2615
2.2524-2.47870.20981430.16972593X-RAY DIFFRACTION2593
2.4787-2.83640.21731340.1672642X-RAY DIFFRACTION2642
2.8364-3.56990.1961360.15642673X-RAY DIFFRACTION2673
3.5699-19.34110.19461460.16412775X-RAY DIFFRACTION2775
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)
10.01710.01570.00730.01260.00420.006-0.0376-0.01240.0068-0.28120.03290.2614-0.0570.074900.1291-0.025-0.00590.0586-0.02440.086724.028232.36214.025
20.2682-0.04830.09330.57670.09360.25750.05780.0209-0.0018-0.0207-0.01280.04620.0085-0.00060.05610.0419-0.00510.01220.0364-0.00950.039624.313325.906718.9884
3-0.0620.0638-0.06110.0661-0.16030.14120.02350.0162-0.03020.0167-0.0012-0.02790.05750.0671-00.06940.00680.01190.0797-0.01060.067930.254923.997620.0561
40.0165-0.00660.02510.0052-0.00810.0180.07950.03030.17320.47460.01010.0930.0829-0.01570.00030.3016-0.00410.0770.01340.00420.0621.491321.181539.6899
5-0.0656-0.0226-0.07190.33120.16680.09470.0719-0.02830.06110.0657-0.0668-0.0023-0.2443-0.017200.0605-0.00320.02490.0632-0.00550.058324.502932.718318.5053
60.53960.17570.05260.2569-0.18040.3534-0.07820.2764-0.13620.3110.2422-0.02310.3210.25360.01630.15840.03150.03740.02270.03330.125516.454721.635333.5383
70.01230.0075-0.00510.111-0.01330.0078-0.0102-0.1866-0.0508-0.0529-0.04320.1527-0.06790.15570.00060.05690.00080.03450.145-0.00880.071645.080511.460819.0154
80.5047-0.095-0.01020.11740.00860.006-0.0435-0.0893-0.05680.050.02440.11810.0154-0.063900.03130.00930.01210.04880.01050.044236.121210.17485.3713
90.18880.12210.09040.1606-0.06110.1818-0.03760.01670.04420.00440.0072-0.0146-0.013-0.031900.040.01280.00430.0289-0.00340.044438.541717.3204-0.1256
100.0118-0.00130.01680.0068-0.01280.0232-0.02470.20250.1658-0.1065-0.1080.0046-0.2246-0.21950.00010.1625-0.044-0.01710.2063-0.07130.217233.42892.7135-21.246
110.3942-0.0323-0.0856-0.03920.16760.0095-0.0298-0.03420.0181-0.03020.04680.01360.01550.075500.0546-0.00670.00770.0575-0.00390.058144.431911.50032.8855
120.014-0.0224-0.01640.07880.0340.01680.1558-0.0952-0.1517-0.1347-0.17070.0789-0.0445-0.0264-0.0164-0.1853-0.2017-0.23440.0513-0.16140.065429.23331.0958-13.7966
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 988:993)A988 - 993
2X-RAY DIFFRACTION2(chain A and resid 994:1034)A994 - 1034
3X-RAY DIFFRACTION3(chain A and resid 1035:1061)A1035 - 1061
4X-RAY DIFFRACTION4(chain A and resid 1062:1075)A1062 - 1075
5X-RAY DIFFRACTION5(chain A and resid 1076:1100)A1076 - 1100
6X-RAY DIFFRACTION6(chain A and resid 1101:1105)A1101 - 1105
7X-RAY DIFFRACTION7(chain B and resid 988:992)B988 - 992
8X-RAY DIFFRACTION8(chain B and resid 993:1022)B993 - 1022
9X-RAY DIFFRACTION9(chain B and resid 1023:1063)B1023 - 1063
10X-RAY DIFFRACTION10(chain B and resid 1064:1075)B1064 - 1075
11X-RAY DIFFRACTION11(chain B and resid 1076:1102)B1076 - 1102
12X-RAY DIFFRACTION12(chain B and resid 1103:1107)B1103 - 1107

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