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- PDB-4qmd: Crystal structure of human envoplakin plakin repeat domain -

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Basic information

Entry
Database: PDB / ID: 4qmd
TitleCrystal structure of human envoplakin plakin repeat domain
ComponentsEnvoplakin
KeywordsCELL ADHESION / Envoplakin / Periplakin / Plakin protein / Plakin repeat domain / Cornified envelope / Epidermal permeability barrier / Keratinocyte / Terminal differentiation / Intermediate filament / Vimentin / Cytoskeleton / Cell junction / Desmosome / Paraneoplastic pemphigus
Function / homology
Function and homology information


intermediate filament binding / cornification / desmosome / intermediate filament cytoskeleton organization / Formation of the cornified envelope / peptide cross-linking / cornified envelope / intermediate filament cytoskeleton / epidermis development / keratinocyte differentiation ...intermediate filament binding / cornification / desmosome / intermediate filament cytoskeleton organization / Formation of the cornified envelope / peptide cross-linking / cornified envelope / intermediate filament cytoskeleton / epidermis development / keratinocyte differentiation / wound healing / cadherin binding / structural molecule activity / extracellular exosome / membrane / cytoplasm / cytosol
Similarity search - Function
Envoplakin / beta-hairpin-alpha-hairpin repeat / Plakin repeat / Plectin repeat / Plectin repeat / Plakin repeat superfamily / Desmoplakin, SH3 domain / SH3 domain / Plectin repeat / Plakin ...Envoplakin / beta-hairpin-alpha-hairpin repeat / Plakin repeat / Plectin repeat / Plectin repeat / Plakin repeat superfamily / Desmoplakin, SH3 domain / SH3 domain / Plectin repeat / Plakin / Spectrin/alpha-actinin / Spectrin repeats / Src homology 3 (SH3) domain profile. / SH3 domain / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.601 Å
AuthorsMohammed, F. / Al-Jassar, C. / White, S.A. / Fogl, C. / Jeeves, M. / Knowles, T.J. / Odinstova, E. / Rodriguez-Zamora, P. / Overduin, M. / Chidgey, M.
CitationJournal: Nat Commun / Year: 2016
Title: Mechanism of intermediate filament recognition by plakin repeat domains revealed by envoplakin targeting of vimentin.
Authors: Fogl, C. / Mohammed, F. / Al-Jassar, C. / Jeeves, M. / Knowles, T.J. / Rodriguez-Zamora, P. / White, S.A. / Odintsova, E. / Overduin, M. / Chidgey, M.
History
DepositionJun 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envoplakin
B: Envoplakin


Theoretical massNumber of molelcules
Total (without water)42,4812
Polymers42,4812
Non-polymers00
Water7,945441
1
A: Envoplakin


Theoretical massNumber of molelcules
Total (without water)21,2401
Polymers21,2401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Envoplakin


Theoretical massNumber of molelcules
Total (without water)21,2401
Polymers21,2401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.480, 68.950, 112.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Envoplakin / 210 kDa cornified envelope precursor protein / 210 kDa paraneoplastic pemphigus antigen / p210


Mass: 21240.373 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EVPL / Plasmid: pPro-EX-HTC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q92817
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 441 / 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: 1.93 Å3/Da / Density % sol: 36.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 3350, 0.1M BIS Tris-CL, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5417 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.6→19.974 Å / % possible obs: 92.9 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rmerge(I) obs: 0.058 / Χ2: 0.898 / Net I/σ(I): 27.9
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.6-1.70.3852.09194339413167.2
1.7-1.810.3164.314692611000191.7
1.81-1.960.2167.376153511992197.3
1.96-2.140.14213.056212510583199.8
2.14-2.390.124.677546099151100
2.39-2.750.07535.977894086521100
2.75-3.360.05655.018852574751100
3.36-4.680.03195.666822657401100

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.14data extraction
CrystalCleardata collection
XDSdata reduction
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.601→19.974 Å / FOM work R set: 0.8758 / SU ML: 0.38 / σ(F): 1.99 / Phase error: 19 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2046 4207 10.02 %
Rwork0.1684 --
obs0.172 41995 94.99 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.95 Å2 / ksol: 0.375 e/Å3
Displacement parametersBiso max: 69.86 Å2 / Biso mean: 15.88 Å2 / Biso min: 0.68 Å2
Baniso -1Baniso -2Baniso -3
1-1.2471 Å20 Å20 Å2
2--1.3942 Å20 Å2
3---2.9714 Å2
Refinement stepCycle: LAST / Resolution: 1.601→19.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2963 0 0 441 3404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063038
X-RAY DIFFRACTIONf_angle_d1.0184100
X-RAY DIFFRACTIONf_chiral_restr0.066480
X-RAY DIFFRACTIONf_plane_restr0.004530
X-RAY DIFFRACTIONf_dihedral_angle_d13.3411188
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6012-1.61940.2796940.259371480856
1.6194-1.63840.3157950.2641911100670
1.6384-1.65840.31391050.24061037114279
1.6584-1.67930.28661250.22181091121683
1.6793-1.70140.28321330.20721135126888
1.7014-1.72470.24421290.20481192132191
1.7247-1.74940.22631200.20041253137396
1.7494-1.77540.23591410.18731269141095
1.7754-1.80320.26831450.19241247139297
1.8032-1.83270.21231520.18111283143598
1.8327-1.86430.23981310.17311280141197
1.8643-1.89820.21041170.166813301447100
1.8982-1.93470.21081540.16541330148499
1.9347-1.97410.2251660.157712641430100
1.9741-2.0170.16941360.153213211457100
2.017-2.06390.21591640.166713011465100
2.0639-2.11540.21631670.164712921459100
2.1154-2.17260.19761340.155313201454100
2.1726-2.23640.20891550.155813541509100
2.2364-2.30850.1851430.157413111454100
2.3085-2.39090.18271430.150213251468100
2.3909-2.48640.18331500.15513271477100
2.4864-2.59940.21331440.168813181462100
2.5994-2.73610.23651520.170913441496100
2.7361-2.9070.20831480.174413351483100
2.907-3.13070.21421500.173813521502100
3.1307-3.44430.20481510.159613401491100
3.4443-3.93940.16161510.147713641515100
3.9394-4.95070.16821520.148113891541100
4.9507-19.9760.18411600.183914591619100
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)
10.8934-0.52630.01071.55630.58531.44-0.0787-0.04850.03790.0931-0.01990.1015-0.0094-0.0862-0.07940.0003-0.01020.010.0007-0.00050.01269.178364.703946.0185
21.4233-0.167-0.71040.77180.31930.90490.0236-0.09150.0540.07470.0104-0.0191-0.02450.04880.00090.02730.0052-0.010.03260.00080.00154.402729.775136.7389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Chain AA1822 - 2014
2X-RAY DIFFRACTION2Chain BB1822 - 2014

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