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- PDB-8tud: IgG1 Fc Heterodimer combYSelect2 -

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Basic information

Entry
Database: PDB / ID: 8tud
TitleIgG1 Fc Heterodimer combYSelect2
Components(Immunoglobulin gamma-1 heavy chain) x 2
KeywordsIMMUNE SYSTEM / IgG1 Fc / heterodimer
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 x Mus musculus hybrid cell line (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAzzam, T. / Du, J.J. / Sundberg, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI149297 United States
CitationJournal: Sci Adv / Year: 2024
Title: Combinatorially restricted computational design of protein-protein interfaces to produce IgG heterodimers.
Authors: Azzam, T. / Du, J.J. / Flowers, M.W. / Ali, A.V. / Hunn, J.C. / Vijayvargiya, N. / Knagaram, R. / Bogacz, M. / Maravillas, K.E. / Sastre, D.E. / Fields, J.K. / Mirzaei, A. / Pierce, B.G. / Sundberg, E.J.
History
DepositionAug 16, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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

Downloads & links

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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)55,2064
Polymers52,2792
Non-polymers2,9272
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint50 kcal/mol
Surface area21960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.014, 79.685, 139.308
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Antibody Immunoglobulin gamma-1 heavy chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 26132.570 Da / Num. of mol.: 1 / Mutation: D399Y, K447S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens x Mus musculus hybrid cell line (mammal)
Production host: Homo sapiens (human) / References: UniProt: P0DOX5
#2: Antibody Immunoglobulin gamma-1 heavy chain


Mass: 26146.555 Da / Num. of mol.: 1 / Mutation: K409S, T411Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens x Mus musculus hybrid cell line (mammal)
Production host: Homo sapiens (human) / References: UniProt: P0DOX5
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1463.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam 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][a1221m-1a_1-5]/1-1-2-3-1-3-1-4/a4-b1_a6-h1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-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]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.65 Å3/Da / Density % sol: 53.67 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M Bis Tris pH 6.5 and 29% PEG MME 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→42.36 Å / Num. obs: 11350 / % possible obs: 96.87 % / Redundancy: 11.5 % / Biso Wilson estimate: 50.24 Å2 / CC1/2: 0.964 / Rmerge(I) obs: 0.453 / Rpim(I) all: 0.137 / Rrim(I) all: 0.474 / Net I/σ(I): 18.5
Reflection shellResolution: 3→3.108 Å / Redundancy: 10.7 % / Rmerge(I) obs: 3.074 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 993 / CC1/2: 0.628 / Rpim(I) all: 0.949 / Rrim(I) all: 3.221 / % possible all: 86.27

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Processing

Software
NameVersionClassification
PDB-REDOrefinement
PHENIX1.20.1_4487refinement
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→42.36 Å / SU ML: 0.4057 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.2829
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2852 1136 10.01 %RANDOM
Rwork0.1978 10212 --
obs0.2063 11348 96.57 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.14 Å2
Refinement stepCycle: LAST / Resolution: 3→42.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 198 3 3523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01093628
X-RAY DIFFRACTIONf_angle_d1.2214947
X-RAY DIFFRACTIONf_chiral_restr0.0564592
X-RAY DIFFRACTIONf_plane_restr0.009610
X-RAY DIFFRACTIONf_dihedral_angle_d7.307573
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.130.39521240.24961122X-RAY DIFFRACTION86.17
3.13-3.30.29591340.22721197X-RAY DIFFRACTION93.08
3.3-3.50.28921420.21331279X-RAY DIFFRACTION98.61
3.5-3.780.3191450.21061303X-RAY DIFFRACTION99.72
3.78-4.150.31211440.19671295X-RAY DIFFRACTION99.65
4.15-4.750.26691460.17051318X-RAY DIFFRACTION99.86
4.76-5.990.24331490.17961334X-RAY DIFFRACTION99.73
5.99-42.360.25851520.19581364X-RAY DIFFRACTION95.65

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