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- PDB-3pdy: Structure of the third and fourth spectrin repeats of the plakin ... -

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Basic information

Entry
Database: PDB / ID: 3pdy
TitleStructure of the third and fourth spectrin repeats of the plakin domain of plectin
ComponentsPlectin
KeywordsSTRUCTURAL PROTEIN / cytoskeleton / plakin / intermediate filament / spectrin repeat / crosslinking
Function / homology
Function and homology information


protein-containing complex organization / actomyosin contractile ring assembly actin filament organization / skeletal myofibril assembly / tight junction organization / Type I hemidesmosome assembly / hemidesmosome assembly / hemidesmosome / leukocyte migration involved in immune response / intermediate filament organization / : ...protein-containing complex organization / actomyosin contractile ring assembly actin filament organization / skeletal myofibril assembly / tight junction organization / Type I hemidesmosome assembly / hemidesmosome assembly / hemidesmosome / leukocyte migration involved in immune response / intermediate filament organization / : / regulation of vascular permeability / intermediate filament cytoskeleton organization / dystroglycan binding / cellular response to hydrostatic pressure / fibroblast migration / costamere / T cell chemotaxis / cellular response to fluid shear stress / peripheral nervous system myelin maintenance / cardiac muscle cell development / myoblast differentiation / adherens junction organization / intermediate filament cytoskeleton / response to food / structural constituent of muscle / ankyrin binding / intermediate filament / Assembly of collagen fibrils and other multimeric structures / sarcomere organization / nucleus organization / keratinocyte development / transmission of nerve impulse / brush border / sarcoplasm / Caspase-mediated cleavage of cytoskeletal proteins / establishment of skin barrier / skeletal muscle fiber development / respiratory electron transport chain / mitochondrion organization / wound healing / cell morphogenesis / protein localization / multicellular organism growth / structural constituent of cytoskeleton / sarcolemma / Z disc / cellular response to mechanical stimulus / : / actin filament binding / myelin sheath / gene expression / mitochondrial outer membrane / cadherin binding / axon / focal adhesion / dendrite / perinuclear region of cytoplasm / RNA binding / extracellular exosome / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Spectrin-like repeat / Spectrin repeat / Spectrin-like repeat / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Desmoplakin, spectrin-like domain / Spectrin like domain / Plectin repeat / Plectin repeat / Plakin repeat superfamily ...: / Spectrin-like repeat / Spectrin repeat / Spectrin-like repeat / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Desmoplakin, spectrin-like domain / Spectrin like domain / Plectin repeat / Plectin repeat / Plakin repeat superfamily / Desmoplakin, SH3 domain / SH3 domain / Plectin repeat / Plakin / Spectrin/alpha-actinin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Spectrin repeats / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Plectin/S10, N-terminal / Plectin/S10 domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Src homology 3 (SH3) domain profile. / SH3 domain / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Plectin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2182 Å
AuthorsOrtega, E. / de Pereda, J.M.
CitationJournal: J Biol Chem / Year: 2011
Title: The structure of the plakin domain of plectin reveals a non-canonical SH3 domain interacting with its fourth spectrin repeat.
Authors: Esther Ortega / Rubén M Buey / Arnoud Sonnenberg / José M de Pereda /
Abstract: Plectin belongs to the plakin family of cytoskeletal crosslinkers, which is part of the spectrin superfamily. Plakins contain an N-terminal conserved region, the plakin domain, which is formed by an ...Plectin belongs to the plakin family of cytoskeletal crosslinkers, which is part of the spectrin superfamily. Plakins contain an N-terminal conserved region, the plakin domain, which is formed by an array of spectrin repeats (SR) and a Src-homology 3 (SH3), and harbors binding sites for junctional proteins. We have combined x-ray crystallography and small angle x-ray scattering (SAXS) to elucidate the structure of the central region of the plakin domain of plectin, which corresponds to the SR3, SR4, SR5, and SH3 domains. The crystal structures of the SR3-SR4 and SR4-SR5-SH3 fragments were determined to 2.2 and 2.95 Å resolution, respectively. The SH3 of plectin presents major alterations as compared with canonical Pro-rich binding SH3 domains, suggesting that plectin does not recognize Pro-rich motifs. In addition, the SH3 binding site is partially occluded by an intramolecular contact with the SR4. Residues of this pseudo-binding site and the SR4/SH3 interface are conserved within the plakin family, suggesting that the structure of this part of the plectin molecule is similar to that of other plakins. We have created a model for the SR3-SR4-SR5-SH3 region, which agrees well with SAXS data in solution. The three SRs form a semi-flexible rod that is not altered by the presence of the SH3 domain, and it is similar to those found in spectrins. The flexibility of the plakin domain, in analogy with spectrins, might contribute to the role of plakins in maintaining the stability of tissues subject to mechanical stress.
History
DepositionOct 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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
B: Plectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6374
Polymers48,4682
Non-polymers1682
Water3,783210
1
A: Plectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4023
Polymers24,2341
Non-polymers1682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Plectin


Theoretical massNumber of molelcules
Total (without water)24,2341
Polymers24,2341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Plectin
hetero molecules

B: Plectin


Theoretical massNumber of molelcules
Total (without water)48,6374
Polymers48,4682
Non-polymers1682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x+1/2,y+1/2,-z+11
Buried area1770 Å2
ΔGint-10 kcal/mol
Surface area23200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.420, 119.400, 44.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 24234.209 Da / Num. of mol.: 2 / Fragment: SPECTRIN REPEATS 3 AND 4 (UNP Residues 653-848)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLEC, PLEC1 / Plasmid: Modified pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15149
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 17% PEG 4000, 8% ISOPROPANOL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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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: May 8, 2008
RadiationMonochromator: HELIOS OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.218→20 Å / Num. all: 26072 / Num. obs: 26072 / % possible obs: 98.38 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 33.98 Å2 / Net I/σ(I): 23.1
Reflection shellResolution: 2.218→2.3 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 2608 / % possible all: 92.1

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model based on PDB entry 2IAK

2iak


Resolution: 2.2182→19.983 Å / SU ML: 0.33 / σ(F): 1.8 / Phase error: 23.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 1315 5.04 %RANDOM
Rwork0.2035 ---
obs0.2058 26072 98.38 %-
all-26072 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.751 Å2 / ksol: 0.362 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.1136 Å2-0 Å20 Å2
2---3.4619 Å20 Å2
3---4.5755 Å2
Refinement stepCycle: LAST / Resolution: 2.2182→19.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3290 0 11 210 3511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043358
X-RAY DIFFRACTIONf_angle_d0.6794519
X-RAY DIFFRACTIONf_dihedral_angle_d13.0891275
X-RAY DIFFRACTIONf_chiral_restr0.048482
X-RAY DIFFRACTIONf_plane_restr0.002590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2182-2.30690.27981190.22342489X-RAY DIFFRACTION91
2.3069-2.41170.29551490.21662724X-RAY DIFFRACTION99
2.4117-2.53860.27571130.2192765X-RAY DIFFRACTION99
2.5386-2.69730.29261420.22552733X-RAY DIFFRACTION99
2.6973-2.9050.29091760.2372744X-RAY DIFFRACTION99
2.905-3.19630.27461590.23192743X-RAY DIFFRACTION99
3.1963-3.65630.22591660.18842770X-RAY DIFFRACTION100
3.6563-4.59730.20421380.16162835X-RAY DIFFRACTION99
4.5973-19.98360.19471530.16982954X-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)
10.1540.3651-0.010.534-0.1320.02890.1379-0.0722-0.35370.4326-0.0451-0.03730.22390.06020.00110.2556-0.0053-0.00390.24730.00610.381431.8592-7.28257.2128
20.35350.11870.18410.476-0.08990.2228-0.16040.28140.0431-0.3410.31740.31390.05850.03750.02240.1250.0047-0.07480.14820.0150.280527.1326-9.4927-0.2893
30.46860.17220.23080.7376-0.07610.1521-0.13350.32840.09670.08580.12350.0206-0.08270.0247-00.1878-0.0352-0.0390.2410.01970.186852.948229.78072.9237
40.02090.0687-0.04421.0309-0.17140.1110.0975-0.39360.11940.2462-0.05620.7098-0.0234-0.06390.00880.36970.00740.00730.2439-0.0290.164639.278223.071528.5091
50.44560.88970.18160.4633-0.1971-0.17-0.1479-0.0386-0.0363-0.1220.0718-0.0410.02490.057200.3063-0.0290.03050.2599-0.00960.25929.6147.420424.8402
60.368-0.1903-0.24851.23060.3450.26650.01910.02790.2723-0.3879-0.04990.1591-0.1889-0.065600.32290.0237-0.09730.22570.03510.208-1.6157-20.922124.1017
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 545:599)
2X-RAY DIFFRACTION2(chain A and resid 600:653)
3X-RAY DIFFRACTION3(chain A and resid 654:746)
4X-RAY DIFFRACTION4(chain B and resid 541:559)
5X-RAY DIFFRACTION5(chain B and resid 560:653)
6X-RAY DIFFRACTION6(chain B and resid 654:745)

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