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- PDB-8ttm: IgG1 Fc Heterodimer combYSelect1 -

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Basic information

Entry
Database: PDB / ID: 8ttm
TitleIgG1 Fc Heterodimer combYSelect1
Components(Immunoglobulin gamma-1 heavy chain) x 2
KeywordsIMMUNE SYSTEM / IgG1 Fc / heterodimer
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 / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / 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/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulin / 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 gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens x Mus musculus hybrid cell line (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 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 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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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)55,2224
Polymers52,2952
Non-polymers2,9272
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint49 kcal/mol
Surface area21800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.782, 79.394, 142.902
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: 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
#2: Antibody Immunoglobulin gamma-1 heavy chain


Mass: 26148.592 Da / Num. of mol.: 1 / Mutation: L368S, D399Y
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.: 6 / 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: 2.7 Å3/Da / Density % sol: 54.45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1M BisTris pH 6.5 and 21% PEG MME 5000

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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: Mar 4, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→40.88 Å / Num. obs: 19700 / % possible obs: 98.13 % / Redundancy: 10.2 % / CC1/2: 0.993 / Rmerge(I) obs: 0.24 / Rpim(I) all: 0.079 / Rrim(I) all: 0.254 / Net I/σ(I): 30.3
Reflection shellResolution: 2.51→2.6 Å / Rmerge(I) obs: 0.961 / Mean I/σ(I) obs: 2.25 / Num. unique obs: 1814 / CC1/2: 0.852 / Rpim(I) all: 0.336 / Rrim(I) all: 1.02

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Processing

Software
NameVersionClassification
PDB-REDOrefinement
PHENIXv1.21refinement
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→40.88 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 21.273 / SU ML: 0.213 / Cross valid method: THROUGHOUT / ESU R: 0.529 / ESU R Free: 0.284 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 1970 10 %RANDOM
Rwork0.20192 ---
obs0.20601 17731 98.13 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.516 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å20 Å20 Å2
2--0.38 Å2-0 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.51→40.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 198 6 3526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0163659
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163209
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.8325021
X-RAY DIFFRACTIONr_angle_other_deg0.4761.5717590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5495.14428
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09810576
X-RAY DIFFRACTIONr_chiral_restr0.0740.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023895
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02655
X-RAY DIFFRACTIONr_mcbond_it2.2593.7111661
X-RAY DIFFRACTIONr_mcbond_other2.2593.7111661
X-RAY DIFFRACTIONr_mcangle_it3.4795.5662075
X-RAY DIFFRACTIONr_mcangle_other3.4785.5662076
X-RAY DIFFRACTIONr_scbond_it3.5354.7041998
X-RAY DIFFRACTIONr_scbond_other3.5344.7091999
X-RAY DIFFRACTIONr_scangle_other5.3576.9482946
X-RAY DIFFRACTIONr_long_range_B_refined7.19148.9493666
X-RAY DIFFRACTIONr_long_range_B_other7.1948.9893667
LS refinement shellResolution: 2.51→2.575 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 128 -
Rwork0.302 1147 -
obs--88.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.848-0.81990.42482.1661-0.74383.197-0.1119-0.02040.1437-0.13170.0921-0.1294-0.19480.24710.01980.0426-0.03250.04790.0542-0.01070.353414.46711.38926.776
22.8212-0.38550.0163.08560.13323.4991-0.10470.0405-0.4388-0.61480.07520.20310.185-0.22310.02960.1531-0.0444-0.05860.06720.05880.530432.554-8.7625.217
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A237 - 443
2X-RAY DIFFRACTION2B237 - 443

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