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- PDB-5jii: Crystal structure of human IgG1-Fc -

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Basic information

Entry
Database: PDB / ID: 5jii
TitleCrystal structure of human IgG1-Fc
ComponentsIg gamma-1 chain C region
KeywordsIMMUNE SYSTEM / antibody / immunoglobulin G1 / Fc fragment / glycosylations
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 / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding ...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 / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Regulation of Complement cascade / antigen binding / 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 / adaptive immune response / blood microparticle / 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
PHOSPHATE ION / Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsHumm, A. / Lobner, E. / Mlynek, G. / Obinger, C. / Djinovic-Carugo, K.
Funding support Austria, 2items
OrganizationGrant numberCountry
Christian Doppler Research AssociationChristian Doppler Laboratory for Antibody Engineering Austria
Austrian Science FundFWF W1224 (Doctoral Program on Biomolecular Technology of Proteins , BioToP) Austria
CitationJournal: Structure / Year: 2017
Title: Fcab-HER2 Interaction: a Menage a Trois. Lessons from X-Ray and Solution Studies.
Authors: Lobner, E. / Humm, A.S. / Goritzer, K. / Mlynek, G. / Puchinger, M.G. / Hasenhindl, C. / Ruker, F. / Traxlmayr, M.W. / Djinovic-Carugo, K. / Obinger, C.
History
DepositionApr 22, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1May 31, 2017Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
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.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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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 2.1Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / 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)52,9399
Polymers49,9372
Non-polymers3,0037
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7900 Å2
ΔGint30 kcal/mol
Surface area21760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.384, 75.088, 149.403
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ig gamma-1 chain C region


Mass: 24968.254 Da / Num. of mol.: 2 / Fragment: Hinge-CH2-CH3, UNP Residues 108-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Cell line (production host): HEK293-6E / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: P01857

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Sugars , 2 types, 2 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(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
DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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]/1-1-2-3-3-1/a4-b1_b4-c1_c3-d1_c6-e1_e2-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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: 1422.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-3-1-4-5/a4-b1_a6-h1_b4-c1_c3-d1_c6-e1_e2-f1_f4-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 290 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

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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: 2.76 Å3/Da / Density % sol: 55.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.05 M Sodium phosphate, 16% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Mar 2, 2014 / Details: KB mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.79→46.89 Å / Num. obs: 52192 / % possible obs: 97.82 % / Redundancy: 4.7 % / Biso Wilson estimate: 28.83 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04695 / Net I/σ(I): 15.87
Reflection shellResolution: 1.79→1.854 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.9299 / Mean I/σ(I) obs: 1.52 / % possible all: 95.97

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Processing

Software
NameVersionClassification
EDNAdata collection
XDSVERSION January 10, 2014data reduction
PHENIX1.10-2247phasing
PHENIXdev_1894refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OQO

1oqo


Resolution: 1.79→46.889 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.4 / Details: TLS group refinement
RfactorNum. reflection% reflection
Rfree0.2206 2655 5.09 %
Rwork0.1808 --
obs0.1828 52118 97.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49.2 Å2
Refinement stepCycle: LAST / Resolution: 1.79→46.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 199 285 3806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133626
X-RAY DIFFRACTIONf_angle_d1.4034962
X-RAY DIFFRACTIONf_dihedral_angle_d13.9581401
X-RAY DIFFRACTIONf_chiral_restr0.063583
X-RAY DIFFRACTIONf_plane_restr0.009607
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7901-1.82260.30391450.28822488X-RAY DIFFRACTION95
1.8226-1.85770.31211500.26582523X-RAY DIFFRACTION97
1.8577-1.89560.26431490.24462541X-RAY DIFFRACTION97
1.8956-1.93680.29331250.22742560X-RAY DIFFRACTION97
1.9368-1.98190.24591370.222574X-RAY DIFFRACTION97
1.9819-2.03140.22111390.20542568X-RAY DIFFRACTION98
2.0314-2.08630.25221580.22559X-RAY DIFFRACTION98
2.0863-2.14770.23881500.18962571X-RAY DIFFRACTION98
2.1477-2.21710.23531050.18422604X-RAY DIFFRACTION98
2.2171-2.29630.23641440.18432601X-RAY DIFFRACTION98
2.2963-2.38820.22811570.18562568X-RAY DIFFRACTION98
2.3882-2.49690.22331530.17122590X-RAY DIFFRACTION98
2.4969-2.62860.23051400.17912597X-RAY DIFFRACTION98
2.6286-2.79320.22381350.18082611X-RAY DIFFRACTION98
2.7932-3.00890.24891250.18322660X-RAY DIFFRACTION99
3.0089-3.31160.25351300.18482671X-RAY DIFFRACTION99
3.3116-3.79060.19041270.17712672X-RAY DIFFRACTION98
3.7906-4.7750.18231370.15312696X-RAY DIFFRACTION98
4.775-46.90490.20051490.16912809X-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)
10.3202-0.1238-0.15280.38380.31030.4912-0.1277-0.72420.41660.3202-0.09970.2349-0.1357-0.1728-0.41670.46110.06510.03520.8601-0.71680.494941.958649.070663.6221
21.5352-0.0020.19991.4671-0.17491.163-0.02960.11390.3031-0.21030.06860.0343-0.0686-0.0837-0.03420.2857-0.0023-0.03810.20260.03360.318529.564642.067732.6157
30.36020.05040.5940.68530.29711.07840.0279-0.9253-0.38580.3912-0.17520.12070.26530.05810.0350.4899-0.02890.01110.81080.17070.32799.162117.850861.0322
41.7168-0.0403-0.35751.12790.20251.1992-0.05640.2121-0.1578-0.1432-0.0287-0.02780.068-0.10760.08110.2189-0.0192-0.01320.1838-0.04960.225919.214528.627431.5004
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 237 through 340 )
2X-RAY DIFFRACTION2chain 'A' and (resid 341 through 443 )
3X-RAY DIFFRACTION3chain 'B' and (resid 237 through 340 )
4X-RAY DIFFRACTION4chain 'B' and (resid 341 through 443 )

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