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- PDB-6wib: Next generation monomeric IgG4 Fc -

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Basic information

Entry
Database: PDB / ID: 6wib
TitleNext generation monomeric IgG4 Fc
ComponentsImmunoglobulin heavy constant gamma 4
KeywordsIMMUNE SYSTEM / antibody constant region / fragment crystallizable / mutated
Function / homology
Function and homology information


IgG immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis ...IgG immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / immunoglobulin receptor binding / 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 / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / 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 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsOganesyan, V.Y. / Shan, L. / Dall'Acqua, W. / van Dyk, N.
CitationJournal: Commun Biol / Year: 2021
Title: In vivo pharmacokinetic enhancement of monomeric Fc and monovalent bispecific designs through structural guidance.
Authors: Shan, L. / Dyk, N.V. / Haskins, N. / Cook, K.M. / Rosenthal, K.L. / Mazor, R. / Dragulin-Otto, S. / Jiang, Y. / Wu, H. / Dall'Acqua, W.F. / Borrok, M.J. / Damschroder, M.M. / Oganesyan, V.
History
DepositionApr 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 13, 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 heavy constant gamma 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5085
Polymers23,8481
Non-polymers1,6604
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.306, 101.731, 69.044
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Immunoglobulin heavy constant gamma 4 / Ig gamma-4 chain C region


Mass: 23847.955 Da / Num. of mol.: 1
Mutation: L351F, T366R, P395K, F405R, Y407e, L432C, H433S, N434W, Y436L, T437C, Q438 deleted
Source method: isolated from a genetically manipulated source
Details: uniprot / Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG4 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01861
#2: 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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-6-deoxy-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 3.73 Å3/Da / Density % sol: 67.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 0.01 M zinc sulfate heptahydrate; 0.1 M morpholineethanesulfonic acid (MES) monohydrate, pH 6.5, and 25% (w/v) PEG 550 MME at a protein concentration of 5.5 mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.19499 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.19499 Å / Relative weight: 1
ReflectionResolution: 2.55→35.92 Å / Num. obs: 11992 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.061 / Net I/σ(I): 11.8
Reflection shellResolution: 2.55→2.66 Å / Rmerge(I) obs: 0.958 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1429 / CC1/2: 0.8 / Rpim(I) all: 0.377

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
pointlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5hvw

5hvw


Resolution: 2.55→35.92 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.894 / SU B: 9.813 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.366 / ESU R Free: 0.273
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2656 612 5.1 %RANDOM
Rwork0.2168 ---
obs0.2193 11380 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 105.53 Å2 / Biso mean: 35.635 Å2 / Biso min: 10.49 Å2
Baniso -1Baniso -2Baniso -3
1-5.71 Å20 Å2-0 Å2
2---2.98 Å20 Å2
3----2.73 Å2
Refinement stepCycle: final / Resolution: 2.55→35.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1674 0 101 14 1789
Biso mean--56.92 27.9 -
Num. residues----210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131825
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171628
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.7342494
X-RAY DIFFRACTIONr_angle_other_deg1.1971.6453837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0595209
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.55823.52985
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.88115301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.577158
X-RAY DIFFRACTIONr_chiral_restr0.0690.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021921
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02344
LS refinement shellResolution: 2.55→2.613 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.27 40 -
Rwork0.322 824 -
obs--100 %

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