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- PDB-5y56: Fc mutant (K392D/K409D/D399K) -

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Basic information

Entry
Database: PDB / ID: 5y56
TitleFc mutant (K392D/K409D/D399K)
ComponentsImmunoglobulin gamma-1 heavy chain
KeywordsIMMUNE SYSTEM / IgG Fc / homodimer / triple mutantion (K392D/K409D/D399K)
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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 gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.653 Å
AuthorsYe, S. / Xu, T. / Yu, J. / Wang, X. / Xu, T. / Jin, Q. / Duan, J. / Wu, J. / Wu, H.
Funding support China, 5items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0500404 China
Ministry of Science and Technology (China)2014CB910300 China
Ministry of Science and Technology (China)31525001 China
Ministry of Science and Technology (China)31430019 China
Ministry of Science and Technology (China)31370721 China
CitationJournal: J. Biol. Chem. / Year: 2017
Title: A rational approach to enhancing antibody Fc homodimer formation for robust production of antibody mixture in a single cell line
Authors: Yu, J. / Wang, X. / Xu, T. / Jin, Q. / Duan, J. / Wu, J. / Wu, H. / Xu, T. / Ye, S.
History
DepositionAug 7, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
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_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_symm_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_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 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)50,0834
Polymers47,1812
Non-polymers2,9022
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7140 Å2
ΔGint50 kcal/mol
Surface area22100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.130, 65.130, 477.521
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-657-

HOH

21B-632-

HOH

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Components

#1: Antibody Immunoglobulin gamma-1 heavy chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 23590.555 Da / Num. of mol.: 2 / Fragment: UNP residues 238-445 / Mutation: K392D/K409D/D399K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK / Production host: Mammalian expression vector pCBio (others) / References: UniProt: P0DOX5
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1625.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAca1-2DManpa1-6[DGlcpNAcb1-2DManpb1-3]DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/6,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1b_1-5]/1-1-2-2-1-3-4-5-6/a4-b1_a6-i1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[beta-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: 1276.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAca1-2DManpa1-6[DManpb1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-1-2-2-3-4-5/a4-b1_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)][b-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.92 Å3/Da / Density % sol: 57.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.5M (NH4)2SO4, 10% Glycerol, 0.1M Tris-Hcl (pH 7.5)

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.65→48.57 Å / Num. obs: 18054 / % possible obs: 95.2 % / Observed criterion σ(I): 2 / Redundancy: 13.1 % / Net I/σ(I): 50.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DN2

1dn2


Resolution: 2.653→36.445 Å / SU ML: 0.52 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 33.56
RfactorNum. reflection% reflection
Rfree0.2977 1804 10 %
Rwork0.2602 --
obs0.264 18043 96.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.653→36.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 196 95 3613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093630
X-RAY DIFFRACTIONf_angle_d1.1764977
X-RAY DIFFRACTIONf_dihedral_angle_d18.1592210
X-RAY DIFFRACTIONf_chiral_restr0.058592
X-RAY DIFFRACTIONf_plane_restr0.007611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6526-2.72430.45691380.45681244X-RAY DIFFRACTION98
2.7243-2.80440.45281360.41111213X-RAY DIFFRACTION98
2.8044-2.89490.46321350.40161226X-RAY DIFFRACTION98
2.8949-2.99830.43521370.37771236X-RAY DIFFRACTION98
2.9983-3.11830.39441380.35561238X-RAY DIFFRACTION98
3.1183-3.26020.36981390.32781252X-RAY DIFFRACTION98
3.2602-3.43190.36341370.31051234X-RAY DIFFRACTION97
3.4319-3.64680.32951380.28151245X-RAY DIFFRACTION97
3.6468-3.9280.31361370.27911232X-RAY DIFFRACTION97
3.928-4.32270.24881420.23051275X-RAY DIFFRACTION96
4.3227-4.94690.23631390.19811241X-RAY DIFFRACTION94
4.9469-6.22760.25471400.21471262X-RAY DIFFRACTION93
6.2276-36.44860.27971480.24151341X-RAY DIFFRACTION89
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)
15.97054.63784.8083.9684.34245.16041.0609-1.5211.3329-0.20190.10510.8008-1.75970.22641.09261.0997-0.43510.51251.0247-0.53260.921243.42070.7319-27.3972
23.76591.43491.4388.61042.55425.56490.16350.21490.7733-0.04770.49570.7437-0.20980.785-1.42970.8423-0.25530.20630.9078-0.12140.632843.526-0.8976-34.297
32.8349-1.2278-2.42747.8159-0.19287.37261.2786-0.34541.43050.3007-1.1202-1.3247-1.10990.2077-1.58860.9808-0.59060.38061.5546-0.70171.267555.896311.7986-28.2811
47.39920.96792.22999.68071.65283.91090.5585-1.46250.9053-0.26040.66110.0396-0.72690.7435-1.05280.6969-0.39510.341.1996-0.4091.013850.07510.7404-31.6072
53.34371.31260.10828.3361-0.5412.48090.2741-0.60970.24570.3375-0.0349-1.0552-0.30360.829-0.18270.5566-0.24670.12681.0343-0.18710.687750.9417-3.5236-30.3372
64.22012.1631-2.26216.57191.92272.37290.6789-0.8839-0.38971.494-0.1026-1.1647-0.44581.4667-0.61590.9456-0.3043-0.28541.2105-0.10630.674248.6346-4.5612-21.8686
77.8855-1.2074-2.17985.5129-0.88993.3503-0.69010.09351.6522-0.53630.32020.47570.298-1.39430.42330.6087-0.1973-0.0441.1812-0.34440.969510.2431-14.4329-29.3156
84.2853-1.60652.04441.95012.56977.6111-0.1068-0.0586-0.2255-0.2179-0.04180.06340.2538-0.20050.08660.5739-0.21260.08790.5577-0.06380.699824.5636-11.5599-29.9099
97.3495-2.4005-1.05845.04080.76273.9467-0.20480.680.3746-0.3715-0.370.91450.411-0.67620.32340.5395-0.1880.06660.682-0.06570.754415.1651-11.4876-32.7151
104.3814-0.92693.85565.5489-1.14693.9516-0.37141.8232-0.4175-0.3667-0.18520.272-0.33630.94420.5680.6322-0.09980.2420.9247-0.13410.637424.3177-17.0559-35.86
112.4766-1.62320.74293.5538-3.36863.6147-0.07161.7731-0.17210.5236-0.40350.29170.81160.39270.34310.6747-0.0837-0.03960.8781-0.28120.790926.0915-21.1426-35.7653
124.9979-1.40981.03435.57492.79226.5018-0.89320.47081.9094-0.94510.4944-0.1518-2.65731.99190.3281.6413-0.6474-0.15191.22470.05250.835826.251113.2637-2.4374
139.7042-4.48216.9398.388-6.26876.84442.56672.28631.3953-3.6627-2.5065-0.7817-2.39753.77950.37942.48270.1996-0.2741.5323-0.17691.246630.383813.7592.8707
142.5427-3.1569-2.89587.7725-0.22136.7837-0.07240.4620.0037-1.1814-0.8458-0.5356-3.33491.31970.57851.5673-0.3798-0.24971.08990.16230.86620.769516.957-8.9355
156.1173-0.79510.61269.23351.74977.4767-0.6185-0.2068-0.37180.764-0.07791.2360.8695-1.45610.53330.6052-0.20930.21940.9794-0.29290.722612.5753-10.8221-17.1732
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 236 through 251 )
2X-RAY DIFFRACTION2chain 'A' and (resid 252 through 264 )
3X-RAY DIFFRACTION3chain 'A' and (resid 265 through 279 )
4X-RAY DIFFRACTION4chain 'A' and (resid 280 through 301 )
5X-RAY DIFFRACTION5chain 'A' and (resid 302 through 325 )
6X-RAY DIFFRACTION6chain 'A' and (resid 326 through 346 )
7X-RAY DIFFRACTION7chain 'A' and (resid 347 through 361 )
8X-RAY DIFFRACTION8chain 'A' and (resid 362 through 403 )
9X-RAY DIFFRACTION9chain 'A' and (resid 404 through 418 )
10X-RAY DIFFRACTION10chain 'A' and (resid 419 through 432 )
11X-RAY DIFFRACTION11chain 'A' and (resid 433 through 443 )
12X-RAY DIFFRACTION12chain 'B' and (resid 236 through 279 )
13X-RAY DIFFRACTION13chain 'B' and (resid 280 through 301 )
14X-RAY DIFFRACTION14chain 'B' and (resid 302 through 346 )
15X-RAY DIFFRACTION15chain 'B' and (resid 347 through 443 )

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