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- PDB-3f7p: Crystal structure of a complex between integrin beta4 and plectin -

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Open data


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Basic information

Entry
Database: PDB / ID: 3f7p
TitleCrystal structure of a complex between integrin beta4 and plectin
Components
  • Integrin beta-4
  • Plectin-1
KeywordsSTRUCTURAL PROTEIN/CELL ADHESION / INTEGRIN / PLAKIN / HEMIDESMOSOME / CELL ADHESION / EPIDERMOLYSIS BULLOSA / Actin-binding / Alternative splicing / Coiled coil / Cytoplasm / Cytoskeleton / Disease mutation / Phosphoprotein / Structural protein / Glycoprotein / Membrane / Polymorphism / Receptor / Transmembrane / STRUCTURAL PROTEIN-CELL ADHESION COMPLEX
Function / homology
Function and homology information


protein-containing complex organization / actomyosin contractile ring assembly actin filament organization / tight junction organization / Type I hemidesmosome assembly / skeletal myofibril assembly / hemidesmosome assembly / nail development / hemidesmosome / leukocyte migration involved in immune response / peripheral nervous system myelin formation ...protein-containing complex organization / actomyosin contractile ring assembly actin filament organization / tight junction organization / Type I hemidesmosome assembly / skeletal myofibril assembly / hemidesmosome assembly / nail development / hemidesmosome / leukocyte migration involved in immune response / peripheral nervous system myelin formation / trophoblast cell migration / intermediate filament organization / intermediate filament cytoskeleton organization / skin morphogenesis / dystroglycan binding / Laminin interactions / fibroblast migration / cellular response to hydrostatic pressure / regulation of vascular permeability / T cell chemotaxis / filopodium assembly / costamere / cellular response to fluid shear stress / intermediate filament cytoskeleton / peripheral nervous system myelin maintenance / adherens junction organization / mesodermal cell differentiation / myoblast differentiation / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / cardiac muscle cell development / integrin complex / podosome / structural constituent of muscle / response to food / ankyrin binding / Assembly of collagen fibrils and other multimeric structures / sarcomere organization / cell adhesion mediated by integrin / Syndecan interactions / keratinocyte development / nucleus organization / transmission of nerve impulse / cell leading edge / brush border / basement membrane / sarcoplasm / Caspase-mediated cleavage of cytoskeletal proteins / establishment of skin barrier / skeletal muscle fiber development / basal plasma membrane / cell-matrix adhesion / respiratory electron transport chain / integrin-mediated signaling pathway / mitochondrion organization / cell motility / G protein-coupled receptor binding / wound healing / cell morphogenesis / sarcolemma / multicellular organism growth / cell-cell adhesion / structural constituent of cytoskeleton / autophagy / response to wounding / Z disc / cellular response to mechanical stimulus / actin filament binding / integrin binding / cell junction / intracellular protein localization / cell migration / myelin sheath / gene expression / nuclear membrane / mitochondrial outer membrane / receptor complex / cell adhesion / cadherin binding / axon / focal adhesion / dendrite / nucleolus / perinuclear region of cytoplasm / cell surface / RNA binding / extracellular exosome / metal ion binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Integrin beta-4 subunit / Spectrin repeat / : / Spectrin-like repeat / Desmoplakin, spectrin-like domain / Spectrin like domain / Plectin repeat / Plectin repeat / Plakin repeat superfamily / Desmoplakin, SH3 domain ...Integrin beta-4 subunit / Spectrin repeat / : / Spectrin-like repeat / Desmoplakin, spectrin-like domain / Spectrin like domain / Plectin repeat / Plectin repeat / Plakin repeat superfamily / Desmoplakin, SH3 domain / SH3 domain / Spectrin-like repeat / Plectin repeat / Plakin / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / CalX-like domain superfamily / Teneurin-like EGF domain / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Spectrin/alpha-actinin / Spectrin repeats / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / 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) / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / PSI domain / domain found in Plexins, Semaphorins and Integrins / Plectin/S10, N-terminal / Plectin/S10 domain / 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 / Src homology 3 (SH3) domain profile. / SH3 domain / Winged helix-like DNA-binding domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Integrin beta-4 / Plectin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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: Plectin-1
B: Plectin-1
C: Integrin beta-4
D: Integrin beta-4
E: Integrin beta-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,6809
Polymers149,4105
Non-polymers2704
Water36020
1
A: Plectin-1
C: Integrin beta-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0353
Polymers60,9722
Non-polymers621
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2310 Å2
ΔGint-5 kcal/mol
Surface area21140 Å2
MethodPISA
2
B: Plectin-1
D: Integrin beta-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1815
Polymers60,9722
Non-polymers2083
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-6 kcal/mol
Surface area20980 Å2
MethodPISA
3
E: Integrin beta-4


Theoretical massNumber of molelcules
Total (without water)27,4651
Polymers27,4651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)107.250, 107.250, 203.970
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11D-101-

CA

21D-1-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24
34
15
25
35
16
26
17
27
18
28
19
29
39
110
210
111
211
112
212
113
213
114
214
115
215

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and resseq 60:62 and (name CA or name C or name N or name O or name CB)
211chain B and resseq 60:62 and (name CA or name C or name N or name O or name CB)
112chain A and (resseq 65:144 or resseq 146:179 ) and...
212chain B and (resseq 65:144 or resseq 146:179 ) and...
113chain A and resseq 180:290
213chain B and resseq 180:290
114chain D and (resseq 1127:1138 or resseq 1142:1157 or resseq...
214chain C and (resseq 1127:1138 or resseq 1142:1157 or resseq...
314chain E and (resseq 1127:1138 or resseq 1142:1157 or resseq...
115chain D and resseq 1163:1171
215chain C and resseq 1163:1171
315chain E and resseq 1163:1171
116chain D and resseq 1158 and sidechain
216chain C and resseq 1158 and sidechain
117chain E and resseq 1193 and sidechain
217chain C and resseq 1193 and sidechain
118chain D and resseq 1139:1141
218chain C and resseq 1139:1141
119chain C and (resseq 1217:1224 or resseq 1226:1261 or resseq...
219chain D and (resseq 1217:1224 or resseq 1226:1261 or resseq...
319chain E and (resseq 1217:1224 or resseq 1226:1261 or resseq...
1110chain C and resseq 1225 and sidechain
2110chain D and resseq 1225 and sidechain
1111chain C and resseq 1262:1270
2111chain D and resseq 1262:1270
1112chain C and resseq 1274
2112chain D and resseq 1274
1113chain E and resseq 1275:1282
2113chain C and resseq 1275:1282
1114chain C and resseq 1328:1330
2114chain D and resseq 1328:1330
1115chain A and resseq 294
2115chain B and resseq 294

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
DetailsThe biological unit is the beta4-plectin heterodimer. The asymmetric unit contains two copies of the beta4-plectin heterodimer and a beta4 molecule not bound to plectin.

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Components

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Protein , 2 types, 5 molecules ABCDE

#1: Protein Plectin-1 / Plectin 1C / PLTN / PCN / Hemidesmosomal protein 1 / HD1 / Plectin-6 / Plectin-11


Mass: 33507.797 Da / Num. of mol.: 2 / Fragment: Actin-binding domain, residues 1-293
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLEC-1 (Isoform 1C), PLEC1 / Plasmid: Derivative of pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15149
#2: Protein Integrin beta-4 / GP150


Mass: 27464.674 Da / Num. of mol.: 3 / 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

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Non-polymers , 4 types, 24 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE SEQUENCES OF PLECTIN-1, INTEGRIN BETA-4 ARE BASED ON REFERENCE 2 IN THE DATABASE, PLEC1_HUMAN, ...THE SEQUENCES OF PLECTIN-1, INTEGRIN BETA-4 ARE BASED ON REFERENCE 2 IN THE DATABASE, PLEC1_HUMAN, 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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.8
Details: 0.1M Sodium Acetate, 0.2M CaCl2, 10% PEG 6000, pH 5.8, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2006
RadiationMonochromator: Single Silicon (111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.75→84.53 Å / Num. all: 35944 / Num. obs: 35944 / % possible obs: 99.73 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Biso Wilson estimate: 63.6 Å2 / Net I/σ(I): 20.4
Reflection shellResolution: 2.75→2.9 Å / Redundancy: 9.9 % / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1QG3 and 1MB8

1qg3

1mb8


Resolution: 2.75→84.53 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 25.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2568 1803 5.02 %RANDOM
Rwork0.204 34141 --
all0.2066 35983 --
obs0.2066 35944 99.73 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.271 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso max: 211.76 Å2 / Biso mean: 82.444 Å2 / Biso min: 30.37 Å2
Baniso -1Baniso -2Baniso -3
1-7.0415 Å20 Å20 Å2
2--7.0415 Å20 Å2
3----14.083 Å2
Refinement stepCycle: LAST / Resolution: 2.75→84.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8528 0 9 27 8564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069210
X-RAY DIFFRACTIONf_angle_d0.90711833
X-RAY DIFFRACTIONf_chiral_restr0.0581286
X-RAY DIFFRACTIONf_plane_restr0.0031548
X-RAY DIFFRACTIONf_dihedral_angle_d16.093267
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A15X-RAY DIFFRACTIONPOSITIONAL
12B15X-RAY DIFFRACTIONPOSITIONAL0.041
21A921X-RAY DIFFRACTIONPOSITIONAL
22B921X-RAY DIFFRACTIONPOSITIONAL0.049
31A901X-RAY DIFFRACTIONPOSITIONAL
32B901X-RAY DIFFRACTIONPOSITIONAL0.036
41D603X-RAY DIFFRACTIONPOSITIONAL
42C603X-RAY DIFFRACTIONPOSITIONAL0.031
43E603X-RAY DIFFRACTIONPOSITIONAL0.039
51D64X-RAY DIFFRACTIONPOSITIONAL
52C64X-RAY DIFFRACTIONPOSITIONAL0.019
53E64X-RAY DIFFRACTIONPOSITIONAL0.026
61D7X-RAY DIFFRACTIONPOSITIONAL
62C7X-RAY DIFFRACTIONPOSITIONAL0.023
71E5X-RAY DIFFRACTIONPOSITIONAL
72C5X-RAY DIFFRACTIONPOSITIONAL0.008
81D21X-RAY DIFFRACTIONPOSITIONAL
82C21X-RAY DIFFRACTIONPOSITIONAL0.029
91C608X-RAY DIFFRACTIONPOSITIONAL
92D608X-RAY DIFFRACTIONPOSITIONAL0.058
93E608X-RAY DIFFRACTIONPOSITIONAL0.063
101C7X-RAY DIFFRACTIONPOSITIONAL
102D7X-RAY DIFFRACTIONPOSITIONAL0.033
111C69X-RAY DIFFRACTIONPOSITIONAL
112D69X-RAY DIFFRACTIONPOSITIONAL0.022
121C8X-RAY DIFFRACTIONPOSITIONAL
122D8X-RAY DIFFRACTIONPOSITIONAL0.029
131E66X-RAY DIFFRACTIONPOSITIONAL
132C66X-RAY DIFFRACTIONPOSITIONAL0.154
141C23X-RAY DIFFRACTIONPOSITIONAL
142D23X-RAY DIFFRACTIONPOSITIONAL0.025
151A4X-RAY DIFFRACTIONPOSITIONAL
152B4X-RAY DIFFRACTIONPOSITIONAL0.013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7502-2.82450.38011430.28792597X-RAY DIFFRACTION100
2.8245-2.90770.31021370.25972592X-RAY DIFFRACTION100
2.9077-3.00150.29461310.23422574X-RAY DIFFRACTION100
3.0015-3.10880.2681310.23032590X-RAY DIFFRACTION100
3.1088-3.23330.29191510.22782584X-RAY DIFFRACTION100
3.2333-3.38040.2861250.21542625X-RAY DIFFRACTION100
3.3804-3.55870.25111460.20292604X-RAY DIFFRACTION100
3.5587-3.78160.26661370.19192626X-RAY DIFFRACTION100
3.7816-4.07360.25661390.18952620X-RAY DIFFRACTION100
4.0736-4.48350.21851260.16232657X-RAY DIFFRACTION100
4.4835-5.13220.20511500.14572649X-RAY DIFFRACTION100
5.1322-6.46570.21611490.17512674X-RAY DIFFRACTION100
6.4657-84.56970.25851380.21912749X-RAY DIFFRACTION97
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)
10.04430.12350.0340.091-0.0734-0.1296-0.9410.6310.638-0.89230.0941-0.27450.6897-0.6423-0.00791.32250.1527-0.14061.57910.49891.1345-53.903144.2235-13.3466
26.2686-0.47432.45572.8718-0.40376.26190.1228-0.0907-0.2496-0.3105-0.0366-0.08090.57030.621400.39190.11360.04030.3220.09070.3393-39.875629.5708-32.7705
37.0224-0.4032.66772.2979-0.28664.0410.04940.0092-0.0675-0.1888-0.0835-0.0132-0.04420.12860.00020.44270.0302-0.0110.18480.05350.305-60.499340.9305-43.9294
40.06120.06180.0608-0.01290.129-0.0362-0.23320.19360.06960.0455-0.3631-0.3459-0.10290.2901-0.00471.54160.27920.44881.0836-0.05251.53884.277-1.8238-6.9354
55.3567-0.4882-0.62663.3966-0.05392.67430.41330.86560.1276-0.084-0.74790.6489-0.0428-0.54530.00020.6040.0810.080.8119-0.22340.85224.44121.2135-20.7877
67.3882-0.5121-1.41692.93811.55453.2197-0.20550.13940.00040.32250.09560.02820.3721-0.351300.54570.00090.07910.354-0.01160.545528.588611.2262-20.4989
72.14650.14811.60452.21761.51131.6217-0.4983-0.9615-2.13230.58390.76381.27130.87560.3165-0.00020.86140.27370.23470.9840.51511.6783-27.22851.2888-5.5827
82.5517-0.27960.7863.07990.01973.6659-0.1243-0.40640.1798-0.2201-0.0486-0.0965-0.37890.1918-0.00030.32030.0129-0.04050.59450.14410.3988-40.230941.6695-11.1262
93.3603-0.01610.78181.59651.82494.1153-0.16650.3220.1418-0.42280.39690.0348-0.25960.88450.00030.3180.07420.03740.75940.13940.3936-25.98737.1683.8981
101.9659-0.8760.33071.6922-0.19351.5745-0.3141-0.1026-0.45760.35471.6156-1.07490.78580.57780.00120.73710.1668-0.06851.1255-0.32661.2265-7.40721.7008-11.0911
113.0557-1.9282-0.31552.81810.10372.6857-0.0014-0.2863-0.2398-0.05580.07640.47160.0973-0.2850.00040.4521-0.0085-0.02340.36560.01960.6844-85.41750.6078-37.4026
124.41240.75930.09682.7793-1.76242.12660.1819-1.3521-0.51030.5610.2840.32310.0913-0.92640.00090.71320.11940.03771.35490.19070.6809-63.490638.6429-1.5116
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 60-64
2X-RAY DIFFRACTION2chain A and resseq 65-179
3X-RAY DIFFRACTION3chain A and resseq 180-290
4X-RAY DIFFRACTION4chain B and resseq 60-63
5X-RAY DIFFRACTION5chain B and resseq 65-179
6X-RAY DIFFRACTION6chain B and resseq 180-290
7X-RAY DIFFRACTION7chain C and resseq 1127-1216
8X-RAY DIFFRACTION8chain C and resseq 1217-1332
9X-RAY DIFFRACTION9chain D and resseq 1126-1216
10X-RAY DIFFRACTION10chain D and resseq 1217-1330
11X-RAY DIFFRACTION11chain E and resseq 1126-1215
12X-RAY DIFFRACTION12chain E and resseq 1216-1348

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