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- PDB-7q3p: Crystal structure of IgG1-Fc-MST-HN (efgartigimod) -

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Basic information

Entry
Database: PDB / ID: 7q3p
TitleCrystal structure of IgG1-Fc-MST-HN (efgartigimod)
ComponentsIgG1-Fc-MST-HN
KeywordsIMMUNE SYSTEM / Fc / IgG1-Fc-MST-HN / efgartigimod / ARGX-113 / FcRn / FcRn-binding protein
Function / homologybeta-D-mannopyranose / alpha-L-fucopyranose / alpha-D-mannopyranose
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPannecoucke, E. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO) Belgium
CitationJournal: Nat Commun / Year: 2022
Title: The Fab region of IgG impairs the internalization pathway of FcRn upon Fc engagement.
Authors: Brinkhaus, M. / Pannecoucke, E. / van der Kooi, E.J. / Bentlage, A.E.H. / Derksen, N.I.L. / Andries, J. / Balbino, B. / Sips, M. / Ulrichts, P. / Verheesen, P. / de Haard, H. / Rispens, T. / ...Authors: Brinkhaus, M. / Pannecoucke, E. / van der Kooi, E.J. / Bentlage, A.E.H. / Derksen, N.I.L. / Andries, J. / Balbino, B. / Sips, M. / Ulrichts, P. / Verheesen, P. / de Haard, H. / Rispens, T. / Savvides, S.N. / Vidarsson, G.
History
DepositionOct 28, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IgG1-Fc-MST-HN
B: IgG1-Fc-MST-HN
C: IgG1-Fc-MST-HN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,02617
Polymers76,4793
Non-polymers4,54714
Water8,305461
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.408, 87.935, 106.093
Angle α, β, γ (deg.)90.000, 114.041, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11C-684-

HOH

21C-687-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 237 through 255 or (resid 256...A237 - 291
121(chain 'A' and (resid 237 through 255 or (resid 256...A293 - 343
131(chain 'A' and (resid 237 through 255 or (resid 256...A345 - 415
141(chain 'A' and (resid 237 through 255 or (resid 256...A417 - 419
151(chain 'A' and (resid 237 through 255 or (resid 256...A422 - 444
161(chain 'A' and (resid 237 through 255 or (resid 256...A446
171(chain 'A' and (resid 237 through 255 or (resid 256...A450
281(chain 'B' and (resid 237 through 268 or (resid 269...B237 - 291
291(chain 'B' and (resid 237 through 268 or (resid 269...B293 - 343
2101(chain 'B' and (resid 237 through 268 or (resid 269...B345 - 415
2111(chain 'B' and (resid 237 through 268 or (resid 269...B417 - 419
2121(chain 'B' and (resid 237 through 268 or (resid 269...B422 - 445
2131(chain 'B' and (resid 237 through 268 or (resid 269...B449
3141(chain 'C' and (resid 237 through 255 or (resid 256...C237 - 291
3151(chain 'C' and (resid 237 through 255 or (resid 256...C293 - 343
3161(chain 'C' and (resid 237 through 255 or (resid 256...C345 - 415
3171(chain 'C' and (resid 237 through 255 or (resid 256...C417 - 419
3181(chain 'C' and (resid 237 through 255 or (resid 256...C422 - 444
3191(chain 'C' and (resid 237 through 255 or (resid 256...C446
3201(chain 'C' and (resid 237 through 255 or (resid 256...C450

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Components

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Antibody / Non-polymers , 2 types, 464 molecules ABC

#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 461 / Source method: isolated from a natural source / Formula: H2O
#1: Antibody IgG1-Fc-MST-HN


Mass: 25492.846 Da / Num. of mol.: 3 / Mutation: M252Y, S254T, T256E, N433K, H434F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 8 types, 14 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-3-1/a4-b1_b6-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a1122h-1a_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(2+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 707.630 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-3-3/a4-b1_b3-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / 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
#7: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#8: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#9: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: 20% w/v PEG3350 pH 5.1. Cyroprotectant: mother liquid + 20% ethylene glycol (final concentration)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.097→48.14 Å / Num. obs: 46871 / % possible obs: 98.76 % / Redundancy: 7 % / Biso Wilson estimate: 40.42 Å2 / CC1/2: 0.998 / Net I/σ(I): 12.42
Reflection shellResolution: 2.097→2.172 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.09 / Num. unique obs: 4414 / CC1/2: 0.464 / % possible all: 93.89

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Processing

Software
NameVersionClassification
MxCuBE1.17.1_3660data collection
XDSdata scaling
PHASERphasing
Cootmodel building
PHENIX1.17.1_3660refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N0U

4n0u


Resolution: 2.1→48.14 Å / SU ML: 0.2576 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.2682
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2139 2344 5 %
Rwork0.1887 44507 -
obs0.19 46851 98.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.78 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5231 0 0 461 5692
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095415
X-RAY DIFFRACTIONf_angle_d1.33117401
X-RAY DIFFRACTIONf_chiral_restr0.1164890
X-RAY DIFFRACTIONf_plane_restr0.0071914
X-RAY DIFFRACTIONf_dihedral_angle_d20.12862073
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.140.36271240.31382351X-RAY DIFFRACTION90.49
2.14-2.190.31451390.29842622X-RAY DIFFRACTION98.57
2.19-2.240.33591360.28062596X-RAY DIFFRACTION99.24
2.24-2.290.3441380.26982626X-RAY DIFFRACTION99.46
2.29-2.360.27111380.26412625X-RAY DIFFRACTION99.25
2.36-2.420.27431410.24642660X-RAY DIFFRACTION99.68
2.42-2.50.29641370.24772611X-RAY DIFFRACTION98.88
2.5-2.590.25411370.23272611X-RAY DIFFRACTION99.42
2.59-2.70.24531380.22592623X-RAY DIFFRACTION99.03
2.7-2.820.26661380.21562610X-RAY DIFFRACTION98.99
2.82-2.970.26211380.21962635X-RAY DIFFRACTION99.28
2.97-3.150.25611390.21152625X-RAY DIFFRACTION99.82
3.15-3.40.20931390.18172657X-RAY DIFFRACTION99.75
3.4-3.740.23071390.17332637X-RAY DIFFRACTION99.68
3.74-4.280.15561400.15092665X-RAY DIFFRACTION99.64
4.28-5.390.13921400.13122656X-RAY DIFFRACTION98.94
5.39-48.140.16651430.1642697X-RAY DIFFRACTION99.02

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