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- PDB-6bz4: Human IgG1 lacking complement-dependent cytotoxicity: hu3S193 Fc ... -

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Basic information

Entry
Database: PDB / ID: 6bz4
TitleHuman IgG1 lacking complement-dependent cytotoxicity: hu3S193 Fc mutant K322A
ComponentsImmunoglobulin gamma-1 heavy chain
KeywordsIMMUNE SYSTEM / Immunoglobulin G / Fc engineering / complement dependent cytotoxicity
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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 gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFarrugia, W. / Burvenich, I.G.J. / 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: Biochem. J. / Year: 2018
Title: Global conformational changes in IgG-Fc upon mutation of the FcRn-binding site are not associated with altered antibody-dependent effector functions.
Authors: Burvenich, I.J.G. / Farrugia, W. / Liu, Z. / Makris, D. / King, D. / Gloria, B. / Perani, A. / Allan, L.C. / Scott, A.M. / Ramsland, P.A.
History
DepositionDec 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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: 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_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 2.1Oct 4, 2023Group: Data collection / Database references ...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 / 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: Immunoglobulin gamma-1 heavy chain
B: Immunoglobulin gamma-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5895
Polymers47,1532
Non-polymers2,4363
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint38 kcal/mol
Surface area22000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.324, 79.502, 138.221
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: Antibody Immunoglobulin gamma-1 heavy chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 23576.572 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PEE6.4 / Details (production host): PEE6.4 / Cell line (production host): 293F / Production host: Homo sapiens (human) / References: UniProt: P0DOX5
#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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1260.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-1-4/a4-b1_a6-g1_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]{}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: 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
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / 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: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 21683 / % possible obs: 98.7 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 22
Reflection shellResolution: 2.4→2.55 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.4 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WI2

4wi2


Resolution: 2.4→28.3 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 26.53
RfactorNum. reflection% reflection
Rfree0.249 2000 9.23 %
Rwork0.212 --
obs0.216 21679 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→28.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 164 58 3506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033564
X-RAY DIFFRACTIONf_angle_d0.6354841
X-RAY DIFFRACTIONf_dihedral_angle_d11.6242171
X-RAY DIFFRACTIONf_chiral_restr0.044563
X-RAY DIFFRACTIONf_plane_restr0.004601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4011-2.46110.34841340.32921317X-RAY DIFFRACTION94
2.4611-2.52760.31021420.30541392X-RAY DIFFRACTION99
2.5276-2.6020.34541410.28941389X-RAY DIFFRACTION99
2.602-2.68590.30991390.26721371X-RAY DIFFRACTION99
2.6859-2.78180.2761410.24711394X-RAY DIFFRACTION99
2.7818-2.89310.30111440.25751412X-RAY DIFFRACTION100
2.8931-3.02460.331420.26121400X-RAY DIFFRACTION100
3.0246-3.18390.30021420.23711401X-RAY DIFFRACTION100
3.1839-3.38310.25511440.23151404X-RAY DIFFRACTION100
3.3831-3.64380.2781450.22481423X-RAY DIFFRACTION100
3.6438-4.00950.27761430.21551421X-RAY DIFFRACTION100
4.0095-4.58760.21161460.16781438X-RAY DIFFRACTION100
4.5876-5.77180.18431480.15931454X-RAY DIFFRACTION99
5.7718-28.3030.21121490.20111463X-RAY DIFFRACTION95
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)
16.4517-1.99731.52572.4286-1.51056.39620.35280.89-0.6947-0.63250.15580.2340.4379-0.3057-0.65060.5899-0.1537-0.05860.5108-0.1450.8399-9.6695-14.787112.8768
24.7145-1.33621.07051.07881.24867.25730.30920.6002-0.2935-0.6450.1996-0.28420.00790.2463-0.5010.5896-0.11960.03720.536-0.10260.8725-6.5178-12.390913.4455
35.2428-1.0118-0.5765.08160.12762.7548-0.2976-1.2011-0.78560.73390.35350.13470.29610.13080.00860.37180.10110.00490.70340.17790.5863-21.9805-7.492241.8784
43.08180.0612-1.6441.9952-0.1254.9589-0.25060.5630.4057-2.6026-0.02470.2805-1.008-0.2063-0.19141.8558-0.15710.02740.51780.10430.5817-33.920912.33397.9903
55.1820.26570.99944.91540.79373.1563-0.3226-1.03550.59640.34710.14950.1273-0.0720.07160.18870.28830.02290.04040.6512-0.13550.5923-30.36747.10939.259
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 237 THROUGH 279 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 280 THROUGH 346 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 347 THROUGH 443 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 237 THROUGH 336 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 337 THROUGH 444 )

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