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- PDB-6uqc: Mouse IgG2a Bispecific Fc -

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Basic information

Entry
Database: PDB / ID: 6uqc
TitleMouse IgG2a Bispecific Fc
Components(Ig gamma-2A chain C region, membrane-bound ...) x 2
KeywordsIMMUNE SYSTEM / Bispecific / Electrostatic Steering / Fc
Function / homology
Function and homology information


positive regulation of B cell activation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / immunoglobulin complex, circulating / phagocytosis, engulfment ...positive regulation of B cell activation / phagocytosis, recognition / humoral immune response mediated by circulating immunoglobulin / early endosome to late endosome transport / positive regulation of type IIa hypersensitivity / positive regulation of type I hypersensitivity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / immunoglobulin complex, circulating / phagocytosis, engulfment / immunoglobulin receptor binding / IgG immunoglobulin complex / antigen processing and presentation / endosome to lysosome transport / immunoglobulin mediated immune response / regulation of proteolysis / complement activation, classical pathway / positive regulation of endocytosis / antigen binding / multivesicular body / positive regulation of phagocytosis / response to bacterium / positive regulation of immune response / antibacterial humoral response / : / 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 / Immunoglobulin-like fold ...: / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
alpha-L-fucopyranose / Immunoglobulin heavy constant gamma 2A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsWang, F. / Tsai, J.C. / Davis, J.H. / West, S.M. / Strop, P.
CitationJournal: Mabs / Year: 2019
Title: Design and characterization of mouse IgG1 and IgG2a bispecific antibodies for use in syngeneic models.
Authors: Wang, F. / Tsai, J.C. / Davis, J.H. / Chau, B. / Dong, J. / West, S.M. / Hogan, J.M. / Wheeler, M.L. / Bee, C. / Morishige, W. / Cayton, T. / David-Brown, D. / Zhang, C. / Kozhich, A. / ...Authors: Wang, F. / Tsai, J.C. / Davis, J.H. / Chau, B. / Dong, J. / West, S.M. / Hogan, J.M. / Wheeler, M.L. / Bee, C. / Morishige, W. / Cayton, T. / David-Brown, D. / Zhang, C. / Kozhich, A. / Sproul, T. / Dollinger, G. / Rajpal, A. / Strop, P.
History
DepositionOct 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
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_unobs_or_zero_occ_atoms / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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.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 11, 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
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Ig gamma-2A chain C region, membrane-bound form
D: Ig gamma-2A chain C region, membrane-bound form
E: Ig gamma-2A chain C region, membrane-bound form
F: Ig gamma-2A chain C region, membrane-bound form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,88914
Polymers94,9284
Non-polymers5,96110
Water14,898827
1
C: Ig gamma-2A chain C region, membrane-bound form
E: Ig gamma-2A chain C region, membrane-bound form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2806
Polymers47,4642
Non-polymers2,8174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint45 kcal/mol
Surface area23120 Å2
MethodPISA
2
D: Ig gamma-2A chain C region, membrane-bound form
F: Ig gamma-2A chain C region, membrane-bound form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6098
Polymers47,4642
Non-polymers3,1456
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint52 kcal/mol
Surface area23470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.270, 64.400, 88.980
Angle α, β, γ (deg.)76.185, 72.170, 61.482
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'C' and (resid 237 through 267 or resid 269...C237 - 266
121(chain 'C' and (resid 237 through 267 or resid 269...C269 - 291
131(chain 'C' and (resid 237 through 267 or resid 269...C294 - 320
141(chain 'C' and (resid 237 through 267 or resid 269...C323 - 324
151(chain 'C' and (resid 237 through 267 or resid 269...C327 - 338
161(chain 'C' and (resid 237 through 267 or resid 269...C341 - 354
171(chain 'C' and (resid 237 through 267 or resid 269...C357 - 359
181(chain 'C' and (resid 237 through 267 or resid 269...C362
191(chain 'C' and (resid 237 through 267 or resid 269...C365 - 366
1101(chain 'C' and (resid 237 through 267 or resid 269...C371 - 384
1111(chain 'C' and (resid 237 through 267 or resid 269...C387 - 397
1121(chain 'C' and (resid 237 through 267 or resid 269...C400 - 407
1131(chain 'C' and (resid 237 through 267 or resid 269...C412 - 417
1141(chain 'C' and (resid 237 through 267 or resid 269...C421 - 437
1151(chain 'C' and (resid 237 through 267 or resid 269...C440
1161(chain 'C' and (resid 237 through 267 or resid 269...C501 - 508
211(chain 'D' and (resid 237 through 267 or resid 269...D237 - 266
221(chain 'D' and (resid 237 through 267 or resid 269...D269 - 291
231(chain 'D' and (resid 237 through 267 or resid 269...D294 - 320
241(chain 'D' and (resid 237 through 267 or resid 269...D323 - 324
251(chain 'D' and (resid 237 through 267 or resid 269...D327 - 338
261(chain 'D' and (resid 237 through 267 or resid 269...D341 - 354
271(chain 'D' and (resid 237 through 267 or resid 269...D357 - 359
281(chain 'D' and (resid 237 through 267 or resid 269...D362
291(chain 'D' and (resid 237 through 267 or resid 269...D365 - 366
2101(chain 'D' and (resid 237 through 267 or resid 269...D371 - 384
2111(chain 'D' and (resid 237 through 267 or resid 269...D387 - 397
2121(chain 'D' and (resid 237 through 267 or resid 269...D400 - 407
2131(chain 'D' and (resid 237 through 267 or resid 269...D412 - 417
2141(chain 'D' and (resid 237 through 267 or resid 269...D421 - 437
2151(chain 'D' and (resid 237 through 267 or resid 269...D440
2161(chain 'D' and (resid 237 through 267 or resid 269...D501 - 508
311(chain 'E' and (resid 237 through 267 or resid 269...E237 - 266
321(chain 'E' and (resid 237 through 267 or resid 269...E269 - 291
331(chain 'E' and (resid 237 through 267 or resid 269...E294 - 320
341(chain 'E' and (resid 237 through 267 or resid 269...E323 - 324
351(chain 'E' and (resid 237 through 267 or resid 269...E327 - 338
361(chain 'E' and (resid 237 through 267 or resid 269...E341 - 354
371(chain 'E' and (resid 237 through 267 or resid 269...E357 - 359
381(chain 'E' and (resid 237 through 267 or resid 269...E362
391(chain 'E' and (resid 237 through 267 or resid 269...E365 - 366
3101(chain 'E' and (resid 237 through 267 or resid 269...E371 - 384
3111(chain 'E' and (resid 237 through 267 or resid 269...E387 - 397
3121(chain 'E' and (resid 237 through 267 or resid 269...E400 - 407
3131(chain 'E' and (resid 237 through 267 or resid 269...E412 - 417
3141(chain 'E' and (resid 237 through 267 or resid 269...E421 - 437
3151(chain 'E' and (resid 237 through 267 or resid 269...E440
3161(chain 'E' and (resid 237 through 267 or resid 269...E501 - 508
411(chain 'F' and (resid 237 through 267 or resid 269...F237 - 266
421(chain 'F' and (resid 237 through 267 or resid 269...F269 - 291
431(chain 'F' and (resid 237 through 267 or resid 269...F294 - 320
441(chain 'F' and (resid 237 through 267 or resid 269...F323 - 324
451(chain 'F' and (resid 237 through 267 or resid 269...F327 - 338
461(chain 'F' and (resid 237 through 267 or resid 269...F341 - 354
471(chain 'F' and (resid 237 through 267 or resid 269...F357 - 359
481(chain 'F' and (resid 237 through 267 or resid 269...F362
491(chain 'F' and (resid 237 through 267 or resid 269...F365 - 366
4101(chain 'F' and (resid 237 through 267 or resid 269...F371 - 384
4111(chain 'F' and (resid 237 through 267 or resid 269...F387 - 397
4121(chain 'F' and (resid 237 through 267 or resid 269...F400 - 407
4131(chain 'F' and (resid 237 through 267 or resid 269...F412 - 417
4141(chain 'F' and (resid 237 through 267 or resid 269...F421 - 437
4151(chain 'F' and (resid 237 through 267 or resid 269...F440
4161(chain 'F' and (resid 237 through 267 or resid 269...F501 - 508

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Components

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Ig gamma-2A chain C region, membrane-bound ... , 2 types, 4 molecules CDEF

#1: Protein Ig gamma-2A chain C region, membrane-bound form


Mass: 23677.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Igh-1a / Production host: Homo sapiens (human) / References: UniProt: P01865
#2: Protein Ig gamma-2A chain C region, membrane-bound form


Mass: 23786.002 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Igh-1a / Production host: Homo sapiens (human) / References: UniProt: P01865

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Sugars , 4 types, 10 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DManpa1-6]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]/1-1-2-3-1-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1WURCSPDB2Glycan 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]{}}}}}LINUCSPDB-CARE
#4: 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)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1317.209 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-1-3-1/a4-b1_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]{}}}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#6: Sugar
ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 1 types, 827 molecules

#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 827 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.13 Å3/Da / Density % sol: 60.7 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 7.9 / Details: 21% PEG10000 and 0.1M bicine pH 7.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→35.65 Å / Num. obs: 82860 / % possible obs: 84.74 % / Redundancy: 1.8 % / Biso Wilson estimate: 30.21 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.03117 / Rpim(I) all: 0.03117 / Rrim(I) all: 0.04408 / Net I/σ(I): 13.61
Reflection shellResolution: 1.872→1.939 Å / Rmerge(I) obs: 0.282 / Mean I/σ(I) obs: 2.49 / Num. unique obs: 6078 / CC1/2: 0.873 / Rpim(I) all: 0.282 / Rrim(I) all: 0.3989

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IGT, 5VAA

1igt

5vaa


Resolution: 1.87→35.65 Å / SU ML: 0.233 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 27.3375
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2287 4113 4.96 %
Rwork0.194 78731 -
obs0.1956 82844 84.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.9 Å2
Refinement stepCycle: LAST / Resolution: 1.87→35.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6932 0 396 827 8155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00727536
X-RAY DIFFRACTIONf_angle_d0.988110380
X-RAY DIFFRACTIONf_chiral_restr0.0621240
X-RAY DIFFRACTIONf_plane_restr0.00751292
X-RAY DIFFRACTIONf_dihedral_angle_d10.35951200
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.890.34781490.29753059X-RAY DIFFRACTION93.69
1.89-1.90.3176590.2991141X-RAY DIFFRACTION80.86
1.93-1.940.37211010.26591897X-RAY DIFFRACTION90.33
1.94-1.970.3008980.25131641X-RAY DIFFRACTION52.32
1.97-1.990.27241480.22923049X-RAY DIFFRACTION94.17
1.99-2.020.26881620.22593032X-RAY DIFFRACTION94.72
2.02-2.050.26651670.21632986X-RAY DIFFRACTION94.4
2.05-2.060.2745550.22491007X-RAY DIFFRACTION82.33
2.09-2.120.24971440.2382845X-RAY DIFFRACTION91.52
2.12-2.160.27781590.2293030X-RAY DIFFRACTION94.24
2.16-2.190.29461390.22743046X-RAY DIFFRACTION94.23
2.19-2.240.28781600.22842956X-RAY DIFFRACTION93.27
2.24-2.280.31841190.22452218X-RAY DIFFRACTION68.9
2.28-2.330.26881450.23032994X-RAY DIFFRACTION93.9
2.33-2.390.2731530.23233065X-RAY DIFFRACTION94.62
2.39-2.450.26341210.22813025X-RAY DIFFRACTION93.52
2.45-2.510.31861690.22852991X-RAY DIFFRACTION93.85
2.51-2.590.26811450.23163002X-RAY DIFFRACTION94
2.59-2.660.29031450.2292763X-RAY DIFFRACTION91.42
2.67-2.760.26251480.22592797X-RAY DIFFRACTION92.67
2.76-2.880.25721810.21972970X-RAY DIFFRACTION93.89
2.88-3.010.23031710.20862992X-RAY DIFFRACTION94.36
3.01-3.160.22641670.19652982X-RAY DIFFRACTION93.44
3.16-3.360.22541960.18873005X-RAY DIFFRACTION94.12
3.36-3.620.19861590.18422719X-RAY DIFFRACTION86.01
3.62-3.990.1941180.16832484X-RAY DIFFRACTION77.19
3.99-4.560.18251400.14743019X-RAY DIFFRACTION93.19
4.56-5.740.1721970.14533045X-RAY DIFFRACTION93.62
5.74-35.650.1691980.17192971X-RAY DIFFRACTION93.95

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