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- PDB-4wi4: Structural mapping of the human IgG1 binding site for FcRn: hu3S1... -

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Basic information

Entry
Database: PDB / ID: 4wi4
TitleStructural mapping of the human IgG1 binding site for FcRn: hu3S193 Fc mutation S254A
ComponentsIg gamma-1 chain C region
KeywordsIMMUNE SYSTEM / Human IgG1 / FcRn binding site / Therapeutic antibody
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / 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 / 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
Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 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_validate_chiral / 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 / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _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
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)50,2367
Polymers47,1232
Non-polymers3,1135
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7730 Å2
ΔGint54 kcal/mol
Surface area21950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.155, 79.114, 141.207
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 240:291 or resseq 299:444 ) and (not element H) and (not element D)
211chain 'B' and (resseq 240:291 or resseq 299:444 ) and (not element H) and (not element D)

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Components

#1: Protein Ig gamma-1 chain C region


Mass: 23561.623 Da / Num. of mol.: 2 / Fragment: unp residues 120-317 / Mutation: S254A
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 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-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-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.65 %
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: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 13759 / % possible obs: 96.5 % / Redundancy: 5.1 % / Net I/σ(I): 24.7

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.3_928) / Classification: refinement
RefinementResolution: 2.8→28.673 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 34.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3079 1371 10.01 %
Rwork0.2396 --
obs0.2465 13703 96.75 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 53.103 Å2 / ksol: 0.311 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.2455 Å2-0 Å20 Å2
2---3.7715 Å2-0 Å2
3---12.0171 Å2
Refinement stepCycle: LAST / Resolution: 2.8→28.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3305 0 210 33 3548
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173623
X-RAY DIFFRACTIONf_angle_d1.9034949
X-RAY DIFFRACTIONf_dihedral_angle_d30.1831431
X-RAY DIFFRACTIONf_chiral_restr0.115590
X-RAY DIFFRACTIONf_plane_restr0.008602
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1582X-RAY DIFFRACTIONPOSITIONAL
12B1582X-RAY DIFFRACTIONPOSITIONAL0.137
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8001-2.90010.43121301166X-RAY DIFFRACTION93
2.9001-3.01610.43521300.34611173X-RAY DIFFRACTION95
3.0161-3.15320.40541300.30671180X-RAY DIFFRACTION95
3.1532-3.31920.39251360.27521221X-RAY DIFFRACTION96
3.3192-3.52680.33821350.25821218X-RAY DIFFRACTION97
3.5268-3.79860.34951360.22571223X-RAY DIFFRACTION97
3.7986-4.17980.2651390.20991253X-RAY DIFFRACTION99
4.1798-4.78220.25821400.17761252X-RAY DIFFRACTION99
4.7822-6.01590.28531430.22921296X-RAY DIFFRACTION99
6.0159-100.26821520.23321350X-RAY DIFFRACTION98
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)
14.42392.202-3.18797.6182-2.72364.4756-0.20950.6641-0.902-1.17640.83040.42510.3341-0.7757-0.44960.4067-0.14230.01550.323-0.02350.5363-9.4581-14.998522.8466
20.9972-0.03771.13440.21340.44892.4309-0.1370.3361-0.105-0.2809-0.76190.68190.8103-0.76680.47121.7688-0.3847-0.57391.6339-0.25771.0388-14.8365-15.9938-1.5187
38.36761.23760.0274.21280.29062.27570.121.4932-0.6089-1.5822-0.06211.26550.6901-0.8054-0.05721.0359-0.2109-0.24140.7434-0.15580.663-8.6863-18.07157.572
44.3236-0.4439-0.8912.66630.42471.021-0.0996-0.3062-0.2287-0.10090.1281-0.00150.00440.03760.0756-0.0420.0336-0.03880.06750.04910.4193-16.2061-8.431134.8615
55.5609-0.3197-1.04041.3396-1.01161.6382-0.11310.9585-0.0267-1.79750.0406-0.3628-0.02450.0069-0.34421.1234-0.22750.19630.31810.04650.6652-31.602912.827610.9203
61.55480.299-0.88211.6265-1.34134.0602-0.61160.81710.0629-2.14140.4426-0.36120.81860.01330.19391.4578-0.20340.17650.43520.01090.6968-35.297812.56776.5564
74.7181-1.06020.14862.86-0.5783.3723-0.5719-0.53220.7425-0.22890.0431-0.33550.2038-0.14190.33690.409-0.00850.10480.0499-0.05810.326-30.82822.433336.3042
85.2512-0.97130.93662.4185-0.90751.77-0.1832-0.87560.80720.16140.1972-0.138-0.1927-0.0447-0.09430.11440.02520.05660.3275-0.10370.5948-30.4747.767939.8119
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 240:262)
2X-RAY DIFFRACTION2chain 'A' and (resseq 263:273)
3X-RAY DIFFRACTION3chain 'A' and (resseq 274:302)
4X-RAY DIFFRACTION4chain 'A' and (resseq 303:444)
5X-RAY DIFFRACTION5chain 'B' and (resseq 238:274)
6X-RAY DIFFRACTION6chain 'B' and (resseq 275:332)
7X-RAY DIFFRACTION7chain 'B' and (resseq 333:362)
8X-RAY DIFFRACTION8chain 'B' and (resseq 363:444)

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