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- PDB-4wi3: Structural mapping of the human IgG1 binding site for FcRn: hu3S1... -

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Basic information

Entry
Database: PDB / ID: 4wi3
TitleStructural mapping of the human IgG1 binding site for FcRn: hu3S193 Fc mutation I253A
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: 2.703 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 / 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_close_contact / 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 / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 23, 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)50,1124
Polymers47,1852
Non-polymers2,9272
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint54 kcal/mol
Surface area21700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.129, 75.908, 142.368
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 237:444 ) and (not element H) and (not element D)
211chain 'B' and (resseq 237:444 ) and (not element H) and (not element D)

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Components

#1: Protein Ig gamma-1 chain C region


Mass: 23592.594 Da / Num. of mol.: 2 / Fragment: unp residues 120-327 / Mutation: I253A
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.81 Å3/Da / Density % sol: 56.27 %
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: Mar 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 15044 / % possible obs: 99 % / Redundancy: 5.5 % / Net I/σ(I): 9.4

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.3_928) / Classification: refinement
RefinementResolution: 2.703→28.823 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 48.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2964 1472 9.95 %
Rwork0.2156 --
obs0.2236 14798 97.5 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 76.244 Å2 / ksol: 0.292 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--33.0161 Å2-0 Å20 Å2
2---30.9493 Å2-0 Å2
3---63.9654 Å2
Refinement stepCycle: LAST / Resolution: 2.703→28.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 198 32 3552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073632
X-RAY DIFFRACTIONf_angle_d1.1514968
X-RAY DIFFRACTIONf_dihedral_angle_d28.4931434
X-RAY DIFFRACTIONf_chiral_restr0.081590
X-RAY DIFFRACTIONf_plane_restr0.005608
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1661X-RAY DIFFRACTIONPOSITIONAL
12B1661X-RAY DIFFRACTIONPOSITIONAL0.038
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7034-2.79061281155X-RAY DIFFRACTION96
2.7906-2.89030.44971340.34051223X-RAY DIFFRACTION98
2.8903-3.00590.37731300.32641178X-RAY DIFFRACTION99
3.0059-3.14251330.27321208X-RAY DIFFRACTION98
3.1425-3.3080.33761370.26281219X-RAY DIFFRACTION99
3.308-3.51490.29241350.22841212X-RAY DIFFRACTION99
3.5149-3.78570.31071330.24941220X-RAY DIFFRACTION98
3.7857-4.16570.37141340.21211203X-RAY DIFFRACTION98
4.1657-4.76610.22961350.1651226X-RAY DIFFRACTION97
4.7661-5.99590.22391390.16541243X-RAY DIFFRACTION98
5.9959-100.22771340.17111239X-RAY DIFFRACTION92
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)
11.33020.11930.52736.07581.19293.1083-0.4125-0.70570.30552.21080.3259-0.1379-0.0591-0.33730.02480.97150.4939-0.29350.5367-0.24650.812413.315111.0452-11.3875
27.101-1.2772.27194.50140.51923.4826-0.32180.56630.7715-0.92130.3538-0.599-0.504-0.02970.08140.5931-0.1964-0.21850.5303-0.00650.48013.98757.467-41.607
33.01780.0418-0.33382.4763-2.33613.5482-0.1902-0.5417-0.04432.0341-0.1059-0.439-0.30020.54550.24841.35120.3151-0.01330.72230.36450.8478-10.401-9.2756-16.5398
41.9902-0.46690.61632.717-1.66114.4744-0.3813-0.846-0.23651.58080.1102-0.2325-0.55670.40.0591.66550.3042-0.16280.71590.35570.996-10.2675-14.0682-8.8046
55.4294-0.05713.20483.3957-3.63865.71960.5768-0.8894-0.84221.5971-0.05640.66840.1755-0.3223-0.40541.92250.26870.60740.78980.35821.2999-20.6825-14.9837-8.9426
67.3218-0.52142.94934.2595-2.31265.56230.3887-0.7258-0.45161.9497-0.2165-0.24490.68570.7111-0.23951.66920.3155-0.27160.63350.11821.0453-8.7436-14.7523-10.8365
71.18190.1859-1.06683.645-2.54094.5782-0.8593-1.0893-0.80342.08660.60880.4019-0.68020.39840.68461.80030.77060.32671.15740.42441.4091-16.8762-7.2499-4.9483
85.9638-0.9207-2.69996.29851.18032.9602-0.29040.4110.3780.90740.4471.0883-0.442-0.9851-0.03820.52710.0563-0.06470.4716-0.03630.9577-15.6943-1.3258-27.8475
95.5376-0.4626-2.22295.12461.35665.2896-0.38340.1657-0.8876-0.31820.3855-0.2417-0.09940.198-0.05750.1822-0.0682-0.30030.45940.0960.8107-1.1284-6.5636-40.5497
106.41431.2613-2.08774.19571.7747.0336-0.01231.0907-1.2057-0.20.26640.32620.5051-0.3132-0.23920.43080.0035-0.35730.5953-0.07590.9414-10.4946-10.9156-43.6764
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 237:346)
2X-RAY DIFFRACTION2chain 'A' and (resseq 347:444)
3X-RAY DIFFRACTION3chain 'B' and (resseq 237:250)
4X-RAY DIFFRACTION4chain 'B' and (resseq 251:276)
5X-RAY DIFFRACTION5chain 'B' and (resseq 277:290)
6X-RAY DIFFRACTION6chain 'B' and (resseq 291:314)
7X-RAY DIFFRACTION7chain 'B' and (resseq 315:331)
8X-RAY DIFFRACTION8chain 'B' and (resseq 332:351)
9X-RAY DIFFRACTION9chain 'B' and (resseq 352:418)
10X-RAY DIFFRACTION10chain 'B' and (resseq 419:444)

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