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- PDB-4wi9: Structural mapping of the human IgG1 binding site for FcRn: hu3S1... -

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Basic information

Entry
Database: PDB / ID: 4wi9
TitleStructural mapping of the human IgG1 binding site for FcRn: hu3S193 Fc mutation I253A/H310A
ComponentsIg gamma-1 chain C region
KeywordsIMMUNE SYSTEM / Human IgG1 / FcRn binding site / Therapeutic antibody
Function / homology
Function and homology information


complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / 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 / Interleukin-4 and Interleukin-13 signaling / 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-like fold ...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
Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.65 Å
AuthorsFarrugia, W. / Burvenich, I.J.G. / Scott, A.M. / Ramsland, P.A.
Funding support Australia, 2items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)542512 Australia
National Health and Medical Research Council (NHMRC, Australia)1030469 Australia
CitationJournal: To Be Published
Title: Structural and functional mapping of human IgG1 binding site for FcRn in vivo using human FcRn transgenic mice
Authors: Burvenich, I.J.G. / Farrugia, W. / Lee, F.T. / Catimel, B. / Liu, Z. / Makris, D. / Cao, D. / O'Keefe, G. / Brechbiel, M.W. / King, D. / Spirkoska, V. / Allan, L. / Ramsland, P.A. / Scott, A.M.
History
DepositionSep 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Data collection / Derived calculations
Category: diffrn_source / pdbx_audit_support / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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 2.1Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ig gamma-1 chain C region
B: Ig gamma-1 chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9965
Polymers47,0512
Non-polymers2,9453
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7340 Å2
ΔGint50 kcal/mol
Surface area21830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.163, 77.654, 140.897
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: Protein Ig gamma-1 chain C region


Mass: 23525.525 Da / Num. of mol.: 2 / Fragment: unp residues 120-327 / Mutation: I253A/H310A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: P01857
#2: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#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


Type: oligosaccharide / Mass: 1114.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-3-1-3-1/a4-b1_b3-c1_b6-e1_c2-d1_e2-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-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]{}}}}LINUCSPDB-CARE
#4: 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)][a-D-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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 6000, 0.1 M MES, 25% v/v ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.65→30 Å / Num. obs: 16296 / % possible obs: 99.5 % / Redundancy: 7.2 % / Net I/σ(I): 24.5

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.3_928) / Classification: refinement
RefinementResolution: 2.65→29.782 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 29.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2737 1628 10 %
Rwork0.2063 --
obs0.2131 16281 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.196 Å2 / ksol: 0.326 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--17.3366 Å2-0 Å20 Å2
2---4.0895 Å2-0 Å2
3---21.4261 Å2
Refinement stepCycle: LAST / Resolution: 2.65→29.782 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 198 30 3540
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083619
X-RAY DIFFRACTIONf_angle_d1.2724952
X-RAY DIFFRACTIONf_dihedral_angle_d28.1921430
X-RAY DIFFRACTIONf_chiral_restr0.073590
X-RAY DIFFRACTIONf_plane_restr0.006606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6502-2.72810.37191350.31651215X-RAY DIFFRACTION100
2.7281-2.81610.37581310.29941180X-RAY DIFFRACTION100
2.8161-2.91670.33291350.29041206X-RAY DIFFRACTION100
2.9167-3.03340.35571310.23931187X-RAY DIFFRACTION100
3.0334-3.17130.28741330.23521211X-RAY DIFFRACTION100
3.1713-3.33830.30411340.20911195X-RAY DIFFRACTION100
3.3383-3.54710.32751370.21921230X-RAY DIFFRACTION100
3.5471-3.82050.31631340.22761211X-RAY DIFFRACTION100
3.8205-4.2040.27531360.21261221X-RAY DIFFRACTION100
4.204-4.81010.20971370.16471231X-RAY DIFFRACTION100
4.8101-6.05190.26041390.18131256X-RAY DIFFRACTION100
6.0519-100.22361460.18391310X-RAY DIFFRACTION99
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)
11.778-0.1332-0.74032.29470.03683.0247-0.70791.3188-0.8303-0.54750.74860.70530.8398-1.2446-0.15120.6256-0.4609-0.09950.8852-0.32570.6507-10.7235-13.8419.4598
20.4051-0.2332-0.45810.7152-0.36741.2356-0.02980.48660.4825-0.72040.0723-0.54510.3996-0.5516-0.00421.103-0.24750.1571.1329-0.28120.69-8.6324-15.04761.4518
31.8210.66050.81560.977-0.46421.05520.63330.18080.8181-1.0885-0.6213-0.26720.5551-0.3398-0.13180.9766-0.08030.22461.2275-0.22751.2516-11.1194-18.84136.7551
41.2959-1.0393-1.90161.19011.18743.1224-0.97620.8896-0.5491-1.49230.219-1.07150.1015-0.0768-0.02471.1283-0.31940.25250.6863-0.04280.7193-4.2448-10.591512.3501
53.8826-0.3194-0.51773.38951.012.76990.064-0.6984-0.73180.36310.0563-0.24230.22730.0784-0.01670.36430.0232-0.12610.44540.02520.5104-20.2495-7.402241.0211
60.9329-0.60140.46471.6911-0.39014.2324-0.12420.34030.1752-2.18960.2393-0.5924-0.35170.3867-0.11711.8065-0.30260.33160.5395-0.00170.5772-31.261713.62287.8231
70.0108-0.01080.24130.07720.93126.8499-0.19120.6436-0.0042-2.27960.63080.3931-0.0143-0.79230.27181.63650.0685-0.17950.7004-0.16140.4634-37.15149.1677.573
83.3858-1.3409-0.41993.0303-0.16172.83660.0609-0.72780.5030.16490.0967-0.0899-0.10870.0815-0.12070.3212-0.04630.04210.4991-0.10070.5306-30.29766.548639.4896
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 237:264)
2X-RAY DIFFRACTION2chain 'A' and (resseq 265:279)
3X-RAY DIFFRACTION3chain 'A' and (resseq 280:301)
4X-RAY DIFFRACTION4chain 'A' and (resseq 302:336)
5X-RAY DIFFRACTION5chain 'A' and (resseq 337:444)
6X-RAY DIFFRACTION6chain 'B' and (resseq 237:300)
7X-RAY DIFFRACTION7chain 'B' and (resseq 301:336)
8X-RAY DIFFRACTION8chain 'B' and (resseq 337:444)

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