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- PDB-6yt7: GLYCOSYLATED KNOB/DUMMY-HOLE FC FRAGMENT -

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Basic information

Entry
Database: PDB / ID: 6yt7
TitleGLYCOSYLATED KNOB/DUMMY-HOLE FC FRAGMENT
Components
  • Ig gamma-1 chain C region
  • Immunoglobulin gamma-1 heavy chain
KeywordsIMMUNE SYSTEM / BISPECIFIC ANTIBODY FC ENGINEERING / KNOB-INTO-HOLE / FORMAT CHAIN EXCHANGE / FORCE
Function / homology
Function and homology information


complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin complex / FCGR activation ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin complex / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / blood microparticle / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / 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
Immunoglobulin heavy constant gamma 1 / Immunoglobulin gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsKuglstatter, A. / Leibrock, L. / Benz, J.
CitationJournal: Nat Commun / Year: 2020
Title: Format chain exchange (FORCE) for high-throughput generation of bispecific antibodies in combinatorial binder-format matrices.
Authors: Dengl, S. / Mayer, K. / Bormann, F. / Duerr, H. / Hoffmann, E. / Nussbaum, B. / Tischler, M. / Wagner, M. / Kuglstatter, A. / Leibrock, L. / Buldun, C. / Georges, G. / Brinkmann, U.
History
DepositionApr 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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: Immunoglobulin gamma-1 heavy chain
B: Ig gamma-1 chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3324
Polymers52,4872
Non-polymers2,8452
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7440 Å2
ΔGint55 kcal/mol
Surface area21300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.015, 75.103, 149.445
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 Immunoglobulin gamma-1 heavy chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 27086.453 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: KNOB-DUMMY PROTEIN (T366W,K370E) / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: P0DOX5
#2: Protein Ig gamma-1 chain C region


Mass: 25400.775 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HOLE PROTEIN (Y349C,T366S,L368A,Y407V) / Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: P01857
#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)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1422.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-3-1-4-5/a4-b1_a6-h1_b4-c1_c3-d1_c6-e1_e2-f1_f4-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.62 Å3/Da / Density % sol: 53.06 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 25% (w/v) PEG2000 MME, 0.1M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→74.83 Å / Num. obs: 64377 / % possible obs: 95.4 % / Redundancy: 6.6 % / Biso Wilson estimate: 26.94 Å2 / CC1/2: 1 / Rpim(I) all: 0.02 / Net I/σ(I): 23.1
Reflection shellResolution: 1.55→1.69 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3224 / CC1/2: 0.7 / Rsym value: 0.542 / % possible all: 61.8

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Processing

Software
NameVersionClassification
PHENIXdev_3893refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HY9

5hy9


Resolution: 1.55→67.11 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 35.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2731 3215 4.99 %RANDOM
Rwork0.2341 61162 --
obs0.236 64377 79.05 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.21 Å2 / Biso mean: 36.5367 Å2 / Biso min: 13.97 Å2
Refinement stepCycle: final / Resolution: 1.55→67.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3408 0 192 205 3805
Biso mean--48.96 34.55 -
Num. residues----416
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.570.684910.487757582
1.57-1.590.4311120.40612022146
1.59-1.620.2957290.398946549414
1.62-1.650.3363430.372168773021
1.65-1.680.379560.35081092114833
1.68-1.710.4253780.34311725180351
1.71-1.750.37971710.34132870304187
1.75-1.780.33851720.31773261343399
1.78-1.830.36881520.300333683520100
1.83-1.870.29321790.287733333512100
1.87-1.920.33061990.272433093508100
1.92-1.980.2991730.276233453518100
1.98-2.040.29241650.272633763541100
2.04-2.110.28631650.267233183483100
2.11-2.20.30111950.263233593554100
2.2-2.30.28291630.248833613524100
2.3-2.420.30341880.262633793567100
2.42-2.570.28731870.24833483535100
2.57-2.770.25961700.259833973567100
2.77-3.050.31421630.25934113574100
3.05-3.490.28151750.227534273602100
3.49-4.40.23892030.196634433646100
4.4-67.110.21681760.173636293805100

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