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- PDB-5w38: 1.80A resolution structure of human IgG3 Fc (N392K) -

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Basic information

Entry
Database: PDB / ID: 5w38
Title1.80A resolution structure of human IgG3 Fc (N392K)
ComponentsImmunoglobulin heavy constant gamma 3
KeywordsIMMUNE SYSTEM / Immunoglobulin G3 / Glycosylation / Fc receptor / protein A
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 / 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 / Immunoglobulins ...: / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRATE ANION / Immunoglobulin heavy constant gamma 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsLovell, S. / Mehzabeen, N. / Battaile, K.P. / Shah, I. / Tolbert, T.J.
CitationJournal: Mol. Immunol. / Year: 2017
Title: Structural characterization of the Man5 glycoform of human IgG3 Fc.
Authors: Shah, I.S. / Lovell, S. / Mehzabeen, N. / Battaile, K.P. / Tolbert, T.J.
History
DepositionJun 7, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin heavy constant gamma 3
B: Immunoglobulin heavy constant gamma 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8105
Polymers50,4472
Non-polymers1,3623
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4560 Å2
ΔGint4 kcal/mol
Surface area22060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.429, 60.443, 71.396
Angle α, β, γ (deg.)90.000, 109.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Immunoglobulin heavy constant gamma 3 / HDC / Heavy chain disease protein / Ig gamma-3 chain C region


Mass: 25223.744 Da / Num. of mol.: 2 / Fragment: Fc domain, UNP residues 155-377 / Mutation: N392K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG3 / Plasmid: pPICzalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1168 / References: UniProt: P01860
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence that was used for this structure comes from the allele IGHG3*11 (accession number ...The sequence that was used for this structure comes from the allele IGHG3*11 (accession number AJ390247). The cDNA of the Fc region of hIgG3 (ATCC: MGC-45809, accession: BC033178) was used for PCR amplification. The Fc sequence belongs to IGHG3*11, *12 allele found in the IMGT database. The expression construct encodes from T225 to K447 (EU numbering). BC033178 also has a Phe residue at position 296.

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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: 2.6 Å3/Da / Density % sol: 52.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 20% (w/v) PEG 4000, 100 mM sodium citrate/citric acid, 10% (v/v) 2-propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→37.729 Å / Num. obs: 47374 / % possible obs: 98.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 24.15 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Net I/σ(I): 12.7 / Num. measured all: 156654 / Scaling rejects: 6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
1.8-1.843.20.5750.734197.7
9-453.30.0270.999197.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.8 Å42.88 Å
Translation1.8 Å42.88 Å

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHASER2.6.1phasing
PHENIX1.11_2568refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DZ8

4dz8


Resolution: 1.8→34.729 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 22.05
RfactorNum. reflection% reflection
Rfree0.2232 2427 5.13 %
Rwork0.1835 --
obs0.1856 47353 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 68.67 Å2 / Biso mean: 28.1286 Å2 / Biso min: 10.25 Å2
Refinement stepCycle: final / Resolution: 1.8→34.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3291 0 91 351 3733
Biso mean--41.38 33.37 -
Num. residues----418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093492
X-RAY DIFFRACTIONf_angle_d1.024773
X-RAY DIFFRACTIONf_chiral_restr0.058548
X-RAY DIFFRACTIONf_plane_restr0.007604
X-RAY DIFFRACTIONf_dihedral_angle_d12.5952103
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.83680.30821200.29342648276898
1.8368-1.87670.31341550.25312625278099
1.8767-1.92030.27191310.23392614274598
1.9203-1.96840.25491460.21262644279099
1.9684-2.02160.25341410.20062638277999
2.0216-2.08110.211530.19392643279699
2.0811-2.14820.22991510.188126372788100
2.1482-2.2250.22361310.1852685281699
2.225-2.3140.24321330.192674280799
2.314-2.41930.22351400.1852634277499
2.4193-2.54690.2481290.17872658278798
2.5469-2.70640.26441520.19262649280199
2.7064-2.91520.24131400.18752666280698
2.9152-3.20840.23911400.19272622276298
3.2084-3.67220.18961710.16722577274896
3.6722-4.62490.19841440.1482620276496
4.6249-34.73530.19681500.18232692284297

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