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- PDB-7lus: IgG2 Fc Charge Pair Mutation version 1 (CPMv1) -

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Basic information

Entry
Database: PDB / ID: 7lus
TitleIgG2 Fc Charge Pair Mutation version 1 (CPMv1)
Components(Immunoglobulin heavy constant gamma 2) x 2
KeywordsIMMUNE SYSTEM / fragment crystallizable / Fc
Function / homology
Function and homology information


IgG immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Regulation of Complement cascade ...IgG immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Regulation of Complement cascade / antigen binding / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / adaptive immune response / blood microparticle / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
Model detailsFc
AuthorsSudom, A. / Whittington, D. / Garces, F. / Wang, Z.
CitationJournal: Iscience / Year: 2021
Title: Next generation Fc scaffold for multispecific antibodies.
Authors: Estes, B. / Sudom, A. / Gong, D. / Whittington, D.A. / Li, V. / Mohr, C. / Li, D. / Riley, T.P. / Shi, S.D. / Zhang, J. / Garces, F. / Wang, Z.
History
DepositionFeb 23, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Immunoglobulin heavy constant gamma 2
A: Immunoglobulin heavy constant gamma 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1614
Polymers47,2342
Non-polymers2,9272
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.584, 112.584, 99.417
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Immunoglobulin heavy constant gamma 2 / Ig gamma-2 chain C region / Ig gamma-2 chain C region DOT / Ig gamma-2 chain C region TIL / Ig ...Ig gamma-2 chain C region / Ig gamma-2 chain C region DOT / Ig gamma-2 chain C region TIL / Ig gamma-2 chain C region ZIE


Mass: 23552.465 Da / Num. of mol.: 1 / Mutation: K392D, K409D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01859
#2: Protein Immunoglobulin heavy constant gamma 2 / Ig gamma-2 chain C region / Ig gamma-2 chain C region DOT / Ig gamma-2 chain C region TIL / Ig ...Ig gamma-2 chain C region / Ig gamma-2 chain C region DOT / Ig gamma-2 chain C region TIL / Ig gamma-2 chain C region ZIE


Mass: 23681.885 Da / Num. of mol.: 1 / Mutation: E356K, D399K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG2 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P01859
#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.: 158 / 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: 3.85 Å3/Da / Density % sol: 68.06 % / Mosaicity: 0.322 °
Crystal growTemperature: 293 K / Method: evaporation
Details: 12.5% w/v PEG550MME, 12.5% w/v PEG20K, 0.1 M Tris-HCl (pH 8.5), 20% 2,3-butanediol, 3% ethanol

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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: RAYONIX MX300-HS / Detector: CCD / Date: Jan 6, 2017
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 26116 / % possible obs: 98.8 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.033 / Rrim(I) all: 0.09 / Χ2: 0.911 / Net I/σ(I): 8.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.45-2.545.80.96123690.7370.4020.79290
2.54-2.646.90.84725950.8420.3340.80598.60.912
2.64-2.767.80.63926240.9150.2410.8499.80.684
2.76-2.98.20.43126180.960.160.8651000.459
2.9-3.098.30.29926300.9770.1110.9351000.319
3.09-3.328.30.17126460.9890.0631.1111000.183
3.32-3.668.30.11626380.9930.0431.1321000.124
3.66-4.198.30.07926350.9960.0291.0621000.084
4.19-5.288.20.05726490.9970.0210.91000.061
5.28-508.20.04227120.9990.0160.59299.90.045

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HAF

4haf


Resolution: 2.45→48.985 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2368 1208 5.06 %RANDOM
Rwork0.1814 22681 --
obs0.1842 23889 90.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.53 Å2 / Biso mean: 38.9985 Å2 / Biso min: 14.79 Å2
Refinement stepCycle: final / Resolution: 2.45→48.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 0 198 158 3677
Biso mean--37.98 39.35 -
Num. residues----415
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.45-2.54390.2968640.2445142751
2.5439-2.65970.31941020.2323194270
2.6597-2.79990.3091270.2471251890
2.7999-2.97530.27771460.24172784100
2.9753-3.2050.32951690.21192784100
3.205-3.52740.23011640.18632775100
3.5274-4.03760.22481350.1752803100
4.0376-5.08610.18181630.13982788100
5.0861-48.90.19771380.15462860100

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