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- PDB-3f7q: First pair of Fibronectin type III domains and part of the connec... -

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Basic information

Entry
Database: PDB / ID: 3f7q
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 / 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 / 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: 1.75 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
B: Integrin beta-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,03111
Polymers52,1292
Non-polymers9029
Water9,044502
1
A: Integrin beta-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5686
Polymers26,0641
Non-polymers5045
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Integrin beta-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4625
Polymers26,0641
Non-polymers3984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.110, 49.470, 74.360
Angle α, β, γ (deg.)107.22, 96.06, 106.60
Int Tables number1
Space group name H-MP1
DetailsThe monomeric form is believed to be the biological unit.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Integrin beta-4 / GP150


Mass: 26064.348 Da / Num. of mol.: 2 / Fragment: Fibronectin type-III, residues 1126-1355
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

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Non-polymers , 6 types, 511 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / 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-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 502 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCE IS BASED ON REFERENCE 2 IN THE DATABASE, ITB4_HUMAN.

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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: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M Tris-HCl, 0.3M NaCl, 24% PEG 200, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 23, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→69.48 Å / Num. all: 50835 / Num. obs: 50835 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Biso Wilson estimate: 25.7 Å2 / Net I/σ(I): 16.3
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 3.8 / % possible all: 84.8

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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: 1.75→22.272 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.87 / Phase error: 17.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1816 2589 5.09 %RANDOM
Rwork0.1552 48246 --
all0.1566 50835 --
obs0.1566 50835 91.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.664 Å2 / ksol: 0.434 e/Å3
Displacement parametersBiso max: 93.23 Å2 / Biso mean: 26.825 Å2 / Biso min: 8.71 Å2
Baniso -1Baniso -2Baniso -3
1--2.4382 Å23.8015 Å2-1.0771 Å2
2---5.4484 Å21.3235 Å2
3----8.2638 Å2
Refinement stepCycle: LAST / Resolution: 1.75→22.272 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6832 0 43 516 7391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056981
X-RAY DIFFRACTIONf_angle_d0.87812628
X-RAY DIFFRACTIONf_chiral_restr0.068513
X-RAY DIFFRACTIONf_plane_restr0.0041111
X-RAY DIFFRACTIONf_dihedral_angle_d17.1451804
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.78360.30791320.25482411X-RAY DIFFRACTION82
1.7836-1.820.22051350.22312585X-RAY DIFFRACTION89
1.82-1.85960.23321590.20482644X-RAY DIFFRACTION90
1.8596-1.90280.26171430.19912638X-RAY DIFFRACTION90
1.9028-1.95040.24041390.18042598X-RAY DIFFRACTION89
1.9504-2.00310.21131520.16432616X-RAY DIFFRACTION90
2.0031-2.0620.18561290.15572711X-RAY DIFFRACTION91
2.062-2.12850.1711370.14992599X-RAY DIFFRACTION90
2.1285-2.20450.18571400.13922660X-RAY DIFFRACTION92
2.2045-2.29270.16191410.13792660X-RAY DIFFRACTION90
2.2927-2.39690.1861500.13412757X-RAY DIFFRACTION93
2.3969-2.52310.1791130.13272744X-RAY DIFFRACTION94
2.5231-2.6810.15021600.13812713X-RAY DIFFRACTION94
2.681-2.88760.16671590.14332761X-RAY DIFFRACTION94
2.8876-3.17740.20921390.14342783X-RAY DIFFRACTION95
3.1774-3.63550.16331630.13952777X-RAY DIFFRACTION95
3.6355-4.57380.13171540.13162799X-RAY DIFFRACTION96
4.5738-22.27350.15461440.15472790X-RAY DIFFRACTION95
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)
10.29050.0068-0.36961.0082-0.17551.03260.0549-0.0958-0.0195-0.0137-0.0454-0.0801-0.10110.114900.1365-0.0237-0.00130.1649-0.00690.167316.2218-3.891943.8523
2-0.12960.0354-0.26520.07950.1980.0652-0.02760.11170.0791-0.03830.04360.0443-0.0610.00460.00010.22810.0184-0.0120.21710.00190.223310.0968-16.494426.9127
30.4463-0.2367-0.2710.1274-0.2070.518-0.066-0.04650.0957-0.08020.04320.0558-0.2308-0.1585-00.1960.0351-0.00940.20210.00620.17532.4776-27.431814.2894
40.4528-0.4281-0.25840.19050.67910.405-0.0730.021-0.10650.16220.0671-0.1749-0.05640.044500.18770.0197-0.00880.18210.01980.17947.3804-36.314311.5727
50.6008-0.0093-0.04240.3258-0.39510.13530.0651-0.0016-0.11950.03970.0989-0.00450.0086-0.08900.1603-0.0039-0.01510.20750.01780.21094.2901-37.115212.6306
60.2935-0.07040.38220.14020.1168-0.0825-0.3178-0.03550.06980.11870.2345-0.1283-0.09190.00500.247-0.025-0.02070.29690.02520.2578-3.2646-32.61681.7199
70.1664-0.16870.26190.3956-0.52340.5210.04310.08360.03420.0245-0.0298-0.08940.1120.037500.1810.02620.00610.1664-0.02210.177320.5622-38.400628.4976
8-0.0656-0.28480.09270.73080.0170.51140.06140.07290.01650.05160.00650.00230.0667-0.1355-00.17740.00320.00450.160.00620.159514.2193-37.254430.9006
90.271-0.15370.44330.1935-0.26010.56290.01980.1458-0.0136-0.02540.01120.05540.1949-0.2238-00.1835-0.0510.02460.1915-0.00950.2051.7599-13.973855.6634
100.18980.11790.07640.13820.28070.5624-0.0327-0.03860.0462-0.23140.03-0.111-0.0743-0.0288-00.1878-0.0147-0.01160.17850.01260.16258.3549-4.508760.4161
110.25030.1777-0.32650.1003-0.34930.4059-0.0228-0.06470.04180.14030.11620.00730.0373-0.082500.179-0.00520.0160.1795-0.00340.17522.8647-6.040663.3346
120.551-0.3855-0.2026-0.0533-0.18870.078-0.0853-0.044-0.0440.05590.08420.00490.0748-0.016500.17430.00430.00140.1941-0.00690.19640.0904-8.768564.3113
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 1126-1207
2X-RAY DIFFRACTION2chain A and resseq 1208-1229
3X-RAY DIFFRACTION3chain A and resseq 1230-1254
4X-RAY DIFFRACTION4chain A and resseq 1255-1282
5X-RAY DIFFRACTION5chain A and resseq 1283-1317
6X-RAY DIFFRACTION6chain A and resseq 1318-1339
7X-RAY DIFFRACTION7chain B and resseq 1126-1163
8X-RAY DIFFRACTION8chain B and resseq 1164-1215
9X-RAY DIFFRACTION9chain B and resseq 1216-1249
10X-RAY DIFFRACTION10chain B and resseq 1250-1277
11X-RAY DIFFRACTION11chain B and resseq 1278-1301
12X-RAY DIFFRACTION12chain B and resseq 1302-1339

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