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- PDB-4gdo: Structure of a fragment of the rod domain of plectin -

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Basic information

Entry
Database: PDB / ID: 4gdo
TitleStructure of a fragment of the rod domain of plectin
ComponentsPlectin
KeywordsSTRUCTURAL PROTEIN / COILED-COIL
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 / Assembly of collagen fibrils and other multimeric structures / intermediate filament / 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 / cytosol / cytoplasm
Similarity search - Function
Single Helix bin / : / Spectrin-like repeat / Spectrin repeat / Spectrin-like repeat / Desmoplakin, spectrin-like domain / Spectrin like domain / Plectin repeat / Plectin repeat / Plakin repeat superfamily ...Single Helix bin / : / Spectrin-like repeat / Spectrin repeat / Spectrin-like repeat / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Src homology 3 (SH3) domain profile. / SH3 domain / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / AB INITIO PHASING / Resolution: 1.7 Å
AuthorsDe Pereda, J.M. / Buey, R.M. / Uson, I. / Sammito, M.D. / De Marino, I.
CitationJournal: Nat.Methods / Year: 2013
Title: Exploiting tertiary structure through local folds for crystallographic phasing.
Authors: Sammito, M. / Millan, C. / Rodriguez, D.D. / de Ilarduya, I.M. / Meindl, K. / De Marino, I. / Petrillo, G. / Buey, R.M. / de Pereda, J.M. / Zeth, K. / Sheldrick, G.M. / Uson, I.
History
DepositionAug 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2013Group: Database references
Revision 1.2Nov 20, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Plectin
B: Plectin
C: Plectin
D: Plectin
E: Plectin
F: Plectin


Theoretical massNumber of molelcules
Total (without water)29,2826
Polymers29,2826
Non-polymers00
Water2,936163
1
A: Plectin
B: Plectin


Theoretical massNumber of molelcules
Total (without water)9,7612
Polymers9,7612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-13 kcal/mol
Surface area6720 Å2
MethodPISA
2
C: Plectin
D: Plectin


Theoretical massNumber of molelcules
Total (without water)9,7612
Polymers9,7612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-12 kcal/mol
Surface area6060 Å2
MethodPISA
3
E: Plectin
F: Plectin


Theoretical massNumber of molelcules
Total (without water)9,7612
Polymers9,7612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-9 kcal/mol
Surface area4340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.620, 35.870, 75.690
Angle α, β, γ (deg.)90.00, 94.11, 90.00
Int Tables number5
Space group name H-MC121
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

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


Mass: 4880.413 Da / Num. of mol.: 6
Fragment: FRAGMENT OF THE ROD DOMAIN, UNP residues 1492-1530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLEC, PLEC1 / Plasmid: Modified pGEX-4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)T1 / References: UniProt: Q15149
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.1 Å3/Da / Density % sol: 41.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M sodium acetate, 2.2M sodium chloride, 0.2M lithium sulfate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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: Apr 1, 2012
RadiationMonochromator: HELIOS OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→77 Å / Num. all: 23087 / Num. obs: 23087 / % possible obs: 85.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 %
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 3.52 / Num. unique all: 1381 / % possible all: 68.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
Arcimboldophasing
PHENIX(phenix.refine: dev_1117)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.7→45.194 Å / SU ML: 0.19 / σ(F): 1.68 / Phase error: 27.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2484 1189 5.15 %RANDOM
Rwork0.2127 ---
obs0.2148 23074 85.28 %-
all-23074 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→45.194 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1653 0 0 163 1816
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081655
X-RAY DIFFRACTIONf_angle_d0.872212
X-RAY DIFFRACTIONf_dihedral_angle_d15.388628
X-RAY DIFFRACTIONf_chiral_restr0.046245
X-RAY DIFFRACTIONf_plane_restr0.004310
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.77810.26011270.22482308X-RAY DIFFRACTION73
1.7781-1.87180.2631310.20382572X-RAY DIFFRACTION81
1.8718-1.98910.21981220.21242572X-RAY DIFFRACTION80
1.9891-2.14270.2261390.18932613X-RAY DIFFRACTION82
2.1427-2.35830.23161280.18952719X-RAY DIFFRACTION84
2.3583-2.69950.24491680.20282843X-RAY DIFFRACTION89
2.6995-3.4010.22841610.21553019X-RAY DIFFRACTION94
3.401-45.1940.26882130.22773239X-RAY DIFFRACTION98
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)
10.21590.12390.31050.139-0.07410.3383-0.0518-0.0093-0.0172-0.0130.015-0.02120.0080.0009-0.06230.0907-0.0065-0.01690.0513-0.01850.12097.113236.15811.3703
20.45470.44280.47840.18630.30640.29030.06590.19190.208-0.0470.08220.05160.0081-0.02150.00330.1460.0211-0.00140.09780.00630.137820.231642.6523-4.4255
30.2295-0.09630.01390.0356-0.14390.42290.0501-0.3156-0.41890.2401-0.02590.09730.1271-0.45420.15140.17970.05280.05780.2362-0.00480.2061-5.952728.716813.4053
40.2228-0.15380.3460.477-0.24050.2760.1232-0.03220.0477-0.06760.0356-0.0922-0.1168-0.07080.08180.13630.03090.00080.20650.01370.10276.217129.001810.4992
50.02550.0040.05260.05580.03460.07560.2093-0.0608-0.21570.2991-0.0974-0.42670.0839-0.02720.06640.37410.31050.5511.03180.39450.8984-33.305432.715826.4667
6-0.0001-0.01390.0046-0.0213-0.03010.0477-0.0987-0.0327-0.05660.0555-0.2480.09940.0472-0.016-0.0731-0.23470.05610.55071.28660.06840.66-33.780427.314732.6207
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1379:1420 )A1379 - 1420
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1380:1420 )B1380 - 1420
3X-RAY DIFFRACTION3( CHAIN C AND RESID 1383:1420 )C1383 - 1420
4X-RAY DIFFRACTION4( CHAIN D AND RESID 1380:1420 )D1380 - 1420
5X-RAY DIFFRACTION5( CHAIN E AND RESID 1390:1420 )E1390 - 1420
6X-RAY DIFFRACTION6( CHAIN F AND RESID 1388:1417 )F1388 - 1417

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