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- PDB-7lf5: Structure of Hyperglycosylated Human IgG1 Fc (Fc267) -

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Basic information

Entry
Database: PDB / ID: 7lf5
TitleStructure of Hyperglycosylated Human IgG1 Fc (Fc267)
ComponentsIgG1 Fc (Fc267)
KeywordsSIGNALING PROTEIN / Effector / IgG / Antibody / Fc
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome / metal ion binding / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
alpha-L-fucopyranose / Uncharacterized protein DKFZp686C11235
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsFields, J.K. / Sundberg, E.J.
CitationJournal: To Be Published
Title: Silent Antibodies: Generation of Hyperglycosylated FCs to Ablate Effector Functions
Authors: Fields, J.K. / Sundberg, E.J.
History
DepositionJan 15, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Assembly

Deposited unit
A: IgG1 Fc (Fc267)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2324
Polymers26,1641
Non-polymers2,0683
Water362
1
A: IgG1 Fc (Fc267)
hetero molecules

A: IgG1 Fc (Fc267)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4638
Polymers52,3272
Non-polymers4,1366
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area7840 Å2
ΔGint57 kcal/mol
Surface area22280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.379, 146.831, 75.917
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Antibody IgG1 Fc (Fc267)


Mass: 26163.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp686C11235 / Production host: Homo sapiens (human) / References: UniProt: Q6MZV7
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1479.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5]/1-1-2-3-1-3-1-4/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: CRYSTALS GROWN BY MIXING 1 UL OF FC267 (10 MG/ML IN 10mM HEPES, 75mM NaCl pH 7.4) WITH 1 UL OF PRECIPITANT SOLUTION CONSISTING OF 0.1M HEPES pH 6.5, 8% w/v PEG6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.6→26.39 Å / Num. obs: 9106 / % possible obs: 99.4 % / Redundancy: 5 % / Biso Wilson estimate: 76.35 Å2 / Rmerge(I) obs: 0.021 / Rpim(I) all: 0.022 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsRpim(I) allDiffraction-ID
2.6-2.72211100.3871
2.6-2.72211100.3871

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDS1.18.2_3874data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CDH

4cdh


Resolution: 2.6→26.39 Å / SU ML: 0.257 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.1113
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2427 440 4.84 %
Rwork0.2238 8657 -
obs0.2247 9097 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 92.97 Å2
Refinement stepCycle: LAST / Resolution: 2.6→26.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1542 0 138 2 1682
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01021724
X-RAY DIFFRACTIONf_angle_d1.33092368
X-RAY DIFFRACTIONf_chiral_restr0.0685307
X-RAY DIFFRACTIONf_plane_restr0.0098286
X-RAY DIFFRACTIONf_dihedral_angle_d12.5209299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.980.28121540.25712825X-RAY DIFFRACTION99.77
2.98-3.750.28391340.26342883X-RAY DIFFRACTION99.47
3.75-26.390.2221520.20532949X-RAY DIFFRACTION98.29
Refinement TLS params.Method: refined / Origin x: -10.279155455 Å / Origin y: -10.6224296923 Å / Origin z: 9.25128602101 Å
111213212223313233
T0.513922374113 Å20.0228787567571 Å20.0960859482654 Å2-0.562190449543 Å2-0.0152849008812 Å2--0.433659141893 Å2
L3.91760880762 °2-0.762204570439 °21.0862986181 °2-2.38089231012 °20.670969769765 °2--1.92829390462 °2
S-0.135658260321 Å °0.540521461577 Å °-0.278004949977 Å °0.267782412398 Å °-0.164266520536 Å °0.113818257698 Å °0.150305600424 Å °0.132233255257 Å °0.252546271637 Å °
Refinement TLS groupSelection details: all

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