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- PDB-6wyt: Crystal structure of anti-Muscle Specific Kinase (MuSK) Fab, MuSK1B -

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Basic information

Entry
Database: PDB / ID: 6wyt
TitleCrystal structure of anti-Muscle Specific Kinase (MuSK) Fab, MuSK1B
Components
  • MuSK1B heavy chain
  • MuSK1B light chain
KeywordsIMMUNE SYSTEM / Human Fab / anti-MuSK
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsVieni, C. / Ekiert, D.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI114780 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21-AI142198 United States
Muscular Dystrophy AssociationMDA575198 United States
Colton Center for Autoimmunity United States
Brown-Coxe fellowship United States
CitationJournal: J.Exp.Med. / Year: 2020
Title: Affinity maturation is required for pathogenic monovalent IgG4 autoantibody development in myasthenia gravis.
Authors: Fichtner, M.L. / Vieni, C. / Redler, R.L. / Kolich, L. / Jiang, R. / Takata, K. / Stathopoulos, P. / Suarez, P.A. / Nowak, R.J. / Burden, S.J. / Ekiert, D.C. / O'Connor, K.C.
History
DepositionMay 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2020Group: Database references / Structure summary / Category: chem_comp / citation / citation_author
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
H: MuSK1B heavy chain
L: MuSK1B light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6476
Polymers46,1492
Non-polymers4974
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Dimeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-18 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.420, 66.690, 124.000
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: Antibody MuSK1B heavy chain


Mass: 23620.449 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pCDNA3.4-TOPO / Cell line (production host): Expi293T / Production host: Homo sapiens (human)
#2: Antibody MuSK1B light chain


Mass: 22528.744 Da / Num. of mol.: 1 / Fragment: Fab
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pCDNA3.4-TOPO / Cell line (production host): Expi293T / Production host: Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.8 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.085 M HEPES, pH 7.5, 17% PEG4000, 8.5% isopropanol, 15% glycerol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 29, 2019
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.75→42.78 Å / Num. obs: 52582 / % possible obs: 99.1 % / Redundancy: 6.618 % / Biso Wilson estimate: 36.703 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.072 / Χ2: 1.059 / Net I/σ(I): 14.17 / Num. measured all: 347976 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.85.5681.2910.8820419386736670.4731.42494.8
1.8-1.846.3150.9451.3823095375836570.7121.03197.3
1.84-1.96.9680.6782.2325162365936110.8610.73298.7
1.9-1.966.9220.5073.1324649358135610.9160.54899.4
1.96-2.026.860.4073.9423645346134470.9450.4499.6
2.02-2.096.7690.3095.2822562334533330.9680.33599.6
2.09-2.176.5530.2436.5921185324432330.9750.26499.7
2.17-2.266.5840.1988.0320346309730900.9830.21599.8
2.26-2.366.5560.1629.5519641300129960.9890.17699.8
2.36-2.477.0210.13911.6920227288628810.9920.1599.8
2.47-2.616.9560.11814.0419005273827320.9930.12899.8
2.61-2.776.8610.09317.7717817260025970.9960.199.9
2.77-2.966.6510.07222.4216242244324420.9970.078100
2.96-3.26.3980.05727.4414550228422740.9970.06299.6
3.2-3.56.4640.04434.5213711212521210.9980.04899.8
3.5-3.916.9650.03941.1613310191219110.9990.04299.9
3.91-4.526.8480.03444.9511737171517140.9990.03799.9
4.52-5.536.3590.03244.859316146714650.9990.03599.9
5.53-7.836.1680.03341.187161116211610.9990.03699.9
7.83-42.786.090.02648.8841966996890.9990.02998.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 7FAB & 8FAB

7fab

8fab


Resolution: 1.75→42.78 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2216 1995 3.8 %Random
Rwork0.1953 50513 --
obs0.1963 52508 99.13 %-
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 263.28 Å2 / Biso mean: 54.1718 Å2 / Biso min: 20.45 Å2
Refinement stepCycle: final / Resolution: 1.75→42.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3227 0 89 200 3516
Biso mean--76.56 44.47 -
Num. residues----429
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.790.35891220.32363400352295
1.79-1.840.30011510.28673461361297
1.84-1.90.28651300.27623560369099
1.9-1.960.25671470.23213585373299
1.96-2.030.28541370.221435783715100
2.03-2.110.24021580.211235613719100
2.11-2.20.26291200.207736313751100
2.2-2.320.25941520.202136043756100
2.32-2.470.26591390.21836353774100
2.47-2.660.25521490.21936103759100
2.66-2.920.20561390.213136413780100
2.92-3.350.24291460.195836843830100
3.35-4.220.18621510.171336903841100
4.22-42.780.18181540.16238734027100
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)
11.74910.45271.18971.44930.05412.3426-0.0542-0.02150.1407-0.03490.10460.0131-0.0949-0.147-0.00010.25460.056-0.02160.33080.00220.25943.831823.025610.3945
21.1007-1.04250.00982.34530.29970.64130.01110.0190.006-0.0192-0.064-0.02690.01140.0024-0.00040.2232-0.0015-0.01370.2307-0.0070.21829.293813.457522.8341
31.77721.2940.43362.30051.00632.22830.41370.6329-0.8220.63190.2714-0.55910.70530.15720.23070.5270.0269-0.26180.4141-0.16370.57730.4110.85585.5227
41.3241-1.22350.88360.9473-1.25751.54230.0676-0.0337-0.23930.01860.01980.0472-0.12720.071600.2861-0.0151-0.00320.2367-0.00390.272926.1833.057433.9883
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'L' and (resid 5 through 128 )L5 - 128
2X-RAY DIFFRACTION2chain 'L' and (resid 129 through 213 )L129 - 213
3X-RAY DIFFRACTION3chain 'H' and (resid 1 through 116 )H1 - 116
4X-RAY DIFFRACTION4chain 'H' and (resid 117 through 220 )H117 - 220

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