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- PDB-2iak: Crystal Structure of a protease resistant fragment of the plakin ... -

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Basic information

Entry
Database: PDB / ID: 2iak
TitleCrystal Structure of a protease resistant fragment of the plakin domain of Bullous Pemphigoid Antigen1 (BPAG1)
ComponentsBullous pemphigoid antigen 1, isoform 5
KeywordsCELL ADHESION / Triple helical bundle / spectrin repeat
Function / homology
Function and homology information


Type I hemidesmosome assembly / neurofilament cytoskeleton / Assembly of collagen fibrils and other multimeric structures / hemidesmosome assembly / hemidesmosome / H zone / perinuclear endoplasmic reticulum / intermediate filament cytoskeleton organization / microtubule plus-end / microtubule plus-end binding ...Type I hemidesmosome assembly / neurofilament cytoskeleton / Assembly of collagen fibrils and other multimeric structures / hemidesmosome assembly / hemidesmosome / H zone / perinuclear endoplasmic reticulum / intermediate filament cytoskeleton organization / microtubule plus-end / microtubule plus-end binding / retrograde axonal transport / intermediate filament / intercalated disc / intracellular transport / regulation of microtubule polymerization or depolymerization / stress fiber / cytoplasmic microtubule organization / axon cytoplasm / axonogenesis / wound healing / cytoplasmic side of plasma membrane / sarcolemma / Z disc / microtubule cytoskeleton / actin cytoskeleton / nuclear envelope / actin binding / cell cortex / cytoplasmic vesicle / microtubule binding / membrane => GO:0016020 / postsynaptic density / cell adhesion / axon / focal adhesion / calcium ion binding / endoplasmic reticulum membrane / structural molecule activity / perinuclear region of cytoplasm / protein homodimerization activity / membrane / nucleus / cytoplasm
Similarity search - Function
: / GAR domain / GAR domain superfamily / Growth-Arrest-Specific Protein 2 Domain / GAR domain profile. / Growth-Arrest-Specific Protein 2 Domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #60 / Desmoplakin, spectrin-like domain / Spectrin like domain / Plectin repeat ...: / GAR domain / GAR domain superfamily / Growth-Arrest-Specific Protein 2 Domain / GAR domain profile. / Growth-Arrest-Specific Protein 2 Domain / 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 repeat / Spectrin repeat / 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. / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / EF-hand domain pair / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsJefferson, J.J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural analysis of the plakin domain of bullous pemphigoid antigen1 (BPAG1) suggests that plakins are members of the spectrin superfamily.
Authors: Jefferson, J.J. / Ciatto, C. / Shapiro, L. / Liem, R.K.
History
DepositionSep 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / 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 1.4Feb 21, 2024Group: 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: Bullous pemphigoid antigen 1, isoform 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7523
Polymers26,5601
Non-polymers1922
Water19811
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Bullous pemphigoid antigen 1, isoform 5
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)160,51218
Polymers159,3606
Non-polymers1,15312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
crystal symmetry operation37_545y+1/4,x-1/4,-z+3/41
crystal symmetry operation43_555-x+1/4,-z+1/4,-y+1/41
crystal symmetry operation46_445z-1/4,-y-1/4,x+1/41
Buried area11020 Å2
ΔGint-224 kcal/mol
Surface area60370 Å2
MethodPISA
3
A: Bullous pemphigoid antigen 1, isoform 5
hetero molecules

A: Bullous pemphigoid antigen 1, isoform 5
hetero molecules

A: Bullous pemphigoid antigen 1, isoform 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2569
Polymers79,6803
Non-polymers5766
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
MethodPQS
Unit cell
Length a, b, c (Å)195.800, 195.800, 195.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132

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Components

#1: Protein Bullous pemphigoid antigen 1, isoform 5 / BPA / Hemidesmosomal plaque protein / Dystonia musculorum protein / Dystonin


Mass: 26559.941 Da / Num. of mol.: 1 / Fragment: Plakin Domain, residues 226-449 / Mutation: V163A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dst, Bpag1 / Plasmid: pET SUMO / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q91ZU8, UniProt: Q91ZU6*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 5.89 Å3/Da / Density % sol: 79.11 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 9.2
Details: 1.6M ammonium sulphate, 50mM CAPSO, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 24211 / Num. obs: 24299 / % possible obs: 99.6 % / Observed criterion σ(I): -3
Reflection shellResolution: 3→3.18 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0016refinement
CBASSdata collection
XDSdata reduction
XDSdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.885 / SU B: 24.914 / SU ML: 0.211 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.313 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26655 647 4.9 %RANDOM
Rwork0.2263 ---
all0.226 24211 --
obs0.22819 12428 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.221 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 10 11 1571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211584
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.891.9482145
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2395196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.88926.11172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.23815282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.057157
X-RAY DIFFRACTIONr_chiral_restr0.1370.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021158
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2980.2823
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3240.21114
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.259
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.226
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellHighest resolution: 3 Å / Num. reflection Rwork: 892 / Total num. of bins used: 20
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)
15.40827.242-0.964132.7745-10.03227.40830.0753-0.42590.2590.4840.52121.763-0.1919-1.2829-0.5965-0.2467-0.0551-0.03910.20280.1033-0.009438.8591-9.494864.4534
20.00590.1799-0.105810.4797-5.07842.5833-0.0208-0.04550.02420.7490.1255-0.3502-0.1741-0.1756-0.1047-0.1657-0.0715-0.145-0.02430.17350.088749.3755-17.995569.7615
35.8861-1.6431.29913.4082-1.53385.7803-0.05980.3023-0.3417-0.3417-0.0239-0.42810.79490.08970.08370.04270.0505-0.1111-0.05670.0274-0.156252.6721-50.899282.9768
412.588-2.6472-17.425722.1338-13.005654.0851-0.9683-0.6559-1.53231.2240.4972-0.71242.7747-1.390.47110.43470.0565-0.2308-0.0370.04910.005851.994-64.445993.1062
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 21
2X-RAY DIFFRACTION2A22 - 112
3X-RAY DIFFRACTION3A113 - 206
4X-RAY DIFFRACTION4A207 - 213

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