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- PDB-2odv: Crystal structure of a fragment of the plakin domain of plectin, ... -

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Basic information

Entry
Database: PDB / ID: 2odv
TitleCrystal structure of a fragment of the plakin domain of plectin, Cys to Ala mutant.
ComponentsPlectin 1
KeywordsSTRUCTURAL PROTEIN / PLAKIN DOMAIN / SPECTRIN REPEAT / CYTOSKELETON / HEMIDESMOSOMES / EPIDERMOLYSIS BULLOSA
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
S-1,2-PROPANEDIOL / Plectin / Plectin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
Authorsde Pereda, J.M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The structure of a tandem pair of spectrin repeats of plectin reveals a modular organization of the plakin domain.
Authors: Sonnenberg, A. / Rojas, A.M. / de Pereda, J.M.
History
DepositionDec 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Plectin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4972
Polymers27,4211
Non-polymers761
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.620, 26.510, 58.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is the monomeric molecule as presented in the coordinates

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Components

#1: Protein Plectin 1 / HD1


Mass: 27420.512 Da / Num. of mol.: 1 / Fragment: RESIDUES 300-530 / Mutation: C420A, C435A, E506K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLEC1 / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q6S383, UniProt: Q15149*PLUS
#2: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.28 Å3/Da / Density % sol: 46.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M Citrate Phosphate pH 4.6, 24% 1,2-propanediol, 6% PEG 3000, 3% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9785, 0.9185
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 5, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97851
20.91851
ReflectionResolution: 2.05→39 Å / Num. obs: 15444 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 34.6 Å2 / Net I/σ(I): 31.7
Reflection shellResolution: 2.05→2.15 Å / Redundancy: 14.2 % / Mean I/σ(I) obs: 6 / % possible all: 99.6

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Processing

Software
NameVersionClassification
SHELXmodel building
REFMAC5.2.0019refinement
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→38.66 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.911 / SU B: 10.227 / SU ML: 0.137 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25599 764 4.9 %RANDOM
Rwork0.21006 ---
obs0.21227 14679 97.7 %-
all-15443 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.265 Å2
Baniso -1Baniso -2Baniso -3
1--0.84 Å20 Å20 Å2
2--1.83 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 2.05→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1793 0 5 52 1850
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221893
X-RAY DIFFRACTIONr_angle_refined_deg1.5451.9712552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3715227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62423.689103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.68615369
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8881521
X-RAY DIFFRACTIONr_chiral_restr0.1120.2270
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021453
X-RAY DIFFRACTIONr_nbd_refined0.2210.2886
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21303
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.214
X-RAY DIFFRACTIONr_mcbond_it1.0891.51161
X-RAY DIFFRACTIONr_mcangle_it1.59321792
X-RAY DIFFRACTIONr_scbond_it2.9163836
X-RAY DIFFRACTIONr_scangle_it4.4344.5760
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 49 -
Rwork0.213 1061 -
obs--100 %
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)
121.7198-13.682320.272216.6042-18.468634.9733-0.66060.27621.18180.0795-0.4949-0.8794-1.290.92951.15540.3999-0.11790.0621-0.07340.02790.212126.91226.594-3.807
22.6649-2.8554.97624.1895-6.711812.05610.2482-0.0657-0.0326-0.58910.0274-0.04150.5458-0.0984-0.27560.1704-0.00270.0287-0.1087-0.00880.105627.66516.5294.952
37.4568-5.35941.2035.21-0.66893.0777-0.4227-1.0821-0.19090.17460.5468-0.0770.25790.065-0.12410.04870.0271-0.00710.0040.02680.125959.241-11.85837.139
416.3113-16.723411.594120.506-12.690412.5668-0.3061-0.17841.27-0.3375-0.3428-1.7157-0.02610.4030.64890.1051-0.05610.0214-0.0269-0.03990.502764.655-7.00632.21
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA303 - 3318 - 36
2X-RAY DIFFRACTION2AA333 - 42238 - 127
3X-RAY DIFFRACTION3AA423 - 489128 - 194
4X-RAY DIFFRACTION4AA490 - 520195 - 225

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