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

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Basic information

Entry
Database: PDB / ID: 6ytb
TitleGLYCOSYLATED KNOB/DUMMY-HOLE/DUMMY FC FRAGMENT
Components(Immunoglobulin gamma-1 heavy chain) x 2
KeywordsIMMUNE SYSTEM / BISPECIFIC ANTIBODY FC ENGINEERING / KNOB-INTO-HOLE / FORMAT CHAIN EXCHANGE / FORCE
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / 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 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
Immunoglobulin gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsKuglstatter, A. / Leibrock, L. / Benz, J.
Citation
Journal: 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.
#1: Journal: To Be Published
Title: Format Chain Exchange (FORCE) - a robust high throughput approach for combinatorial generation of bispecific antibodies in different formats
Authors: Dengl, S.
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
Revision 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Immunoglobulin gamma-1 heavy chain
B: Immunoglobulin gamma-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8124
Polymers53,9682
Non-polymers2,8452
Water4,197233
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint57 kcal/mol
Surface area21640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.158, 75.218, 149.476
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: P0DOX5
#2: Antibody Immunoglobulin gamma-1 heavy chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 26881.332 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HOLE-DUMMY PROTEIN (E357K,T366S,L368A,Y407V) / Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Homo sapiens (human) / References: UniProt: P0DOX5
#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


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.57 Å3/Da / Density % sol: 52.12 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG3350, 0.2M potassium formate

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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 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→74.85 Å / Num. obs: 61292 / % possible obs: 95.1 % / Redundancy: 6.6 % / CC1/2: 1 / Rpim(I) all: 0.024 / Net I/σ(I): 16.2
Reflection shellResolution: 1.65→1.73 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3069 / CC1/2: 0.57 / Rpim(I) all: 0.568 / % possible all: 51.5

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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: 1.65→46.7 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2487 3022 4.93 %RANDOM
Rwork0.2159 58270 --
obs0.2176 61292 91.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 108.56 Å2 / Biso mean: 38.2323 Å2 / Biso min: 15.76 Å2
Refinement stepCycle: final / Resolution: 1.65→46.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3415 0 192 233 3840
Biso mean--51.8 37.07 -
Num. residues----416
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.680.2446160.375832734312
1.68-1.710.3937470.36993898533
1.71-1.740.4151120.33012032214472
1.74-1.770.31081290.3222732286195
1.77-1.80.35571380.30042827296599
1.8-1.840.33471520.290628633015100
1.84-1.880.27921550.269928813036100
1.88-1.920.27651430.247128532996100
1.92-1.970.27021460.245628753021100
1.97-2.030.2761570.253128453002100
2.03-2.080.28341530.239228913044100
2.08-2.150.26161430.237128833026100
2.15-2.230.27791640.225428673031100
2.23-2.320.22351600.225628523012100
2.32-2.420.30021570.233829103067100
2.42-2.550.25751390.229128803019100
2.55-2.710.24621460.235429213067100
2.71-2.920.25331390.236129293068100
2.92-3.210.2461570.228429103067100
3.21-3.680.26451480.207129523100100
3.68-4.630.20761590.17529773136100
4.64-46.70.20811620.172431253287100

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