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- PDB-4bm7: Crystal Structure of IgG Fc F241A mutant with native glycosylation -

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Basic information

Entry
Database: PDB / ID: 4bm7
TitleCrystal Structure of IgG Fc F241A mutant with native glycosylation
ComponentsIG GAMMA-1 CHAIN C REGION
KeywordsIMMUNE SYSTEM / GLYCAN
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / Classical antibody-mediated complement activation / immunoglobulin complex, circulating / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / Classical antibody-mediated complement activation / immunoglobulin complex, circulating / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / 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 / 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
Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsYu, X. / Baruah, K. / Harvey, D.J. / Vasiljevic, S. / Alonzi, D.S. / Song, B. / Higgins, M.K. / Bowden, T.A. / Crispin, M. / Scanlan, C.N.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Engineering Hydrophobic Protein-Carbohydrate Interactions to Fine-Tune Monoclonal Antibodies.
Authors: Yu, X. / Baruah, K. / Harvey, D.J. / Vasiljevic, S. / Alonzi, D.S. / Song, B. / Higgins, M.K. / Bowden, T.A. / Scanlan, C.N. / Crispin, M.
History
DepositionMay 7, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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.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_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 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 2.2Oct 16, 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

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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)53,8554
Polymers52,5592
Non-polymers1,2962
Water5,350297
1
A: IG GAMMA-1 CHAIN C REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5753
Polymers26,2801
Non-polymers1,2962
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: IG GAMMA-1 CHAIN C REGION


Theoretical massNumber of molelcules
Total (without water)26,2801
Polymers26,2801
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.868, 73.375, 135.951
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: Protein IG GAMMA-1 CHAIN C REGION


Mass: 26279.691 Da / Num. of mol.: 2 / Fragment: IMMUNOGLOBULIN GAMMA, FC, RESIDUES 101-329 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: P01857
#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)-[beta-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[LFucpb1-6]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-1b_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)][b-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSEQUENCE INCLUDES A SITE-DIRECTED F241A MUTATION FOR ANALYSIS OF EFFECTS UPON PROTEIN-CARBOHYDRATE ...SEQUENCE INCLUDES A SITE-DIRECTED F241A MUTATION FOR ANALYSIS OF EFFECTS UPON PROTEIN-CARBOHYDRATE INTERACTIONS AND GLYCAN BIOSYNTHESIS

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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: 2.75 Å3/Da / Density % sol: 55 % / Description: NONE
Crystal growpH: 6.5
Details: 28% POLYETHYLENE GLYCOL MONOMETHYL ETHER 2,000 IN 0.1M BIS-TRIS BUFFER AT PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.917
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 5, 2011 / Details: MIRRORS
RadiationMonochromator: SINGLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 36211 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.4
Reflection shellResolution: 1.95→2 Å / Redundancy: 6 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AVE

3ave


Resolution: 1.95→49.92 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.424 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23428 1832 5.1 %RANDOM
Rwork0.19787 ---
obs0.19974 34319 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.812 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20 Å2
2--0.04 Å20 Å2
3---0.95 Å2
Refinement stepCycle: LAST / Resolution: 1.95→49.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3120 0 86 297 3503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193345
X-RAY DIFFRACTIONr_bond_other_d0.0010.023131
X-RAY DIFFRACTIONr_angle_refined_deg1.3111.9814571
X-RAY DIFFRACTIONr_angle_other_deg0.7172.9957253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2235398
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86425.035143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31415565
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9141512
X-RAY DIFFRACTIONr_chiral_restr0.0780.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213638
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02708
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8061.6411575
X-RAY DIFFRACTIONr_mcbond_other0.8061.641574
X-RAY DIFFRACTIONr_mcangle_it1.352.4541965
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3412.0451770
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.947→1.997 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 111 -
Rwork0.265 2241 -
obs--88.62 %
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)
14.73160.3869-1.04417.62420.79437.58370.03791.0420.2698-2.0126-0.0092-0.2153-0.5836-0.1151-0.02880.61570.00230.05270.27890.05110.1472-17.82821.773513.8159
213.38081.24986.81752.71981.05168.46040.2618-0.942-0.4220.26890.08430.03730.4972-0.4095-0.34610.09190.0229-0.01650.09410.01240.0956-6.80077.424340.4275
35.9359-0.69641.59713.49140.76173.0747-0.085-0.04880.45080.00550.0791-0.3571-0.20820.1680.00590.02340.0176-0.00820.1244-0.03940.1081-2.279913.20937.4357
411.70362.87548.34034.41943.60699.75480.043-0.73240.110.55790.1587-0.23870.15720.0027-0.20170.09960.0445-0.02410.1298-0.05220.1002-9.417116.954743.5314
53.3474-0.66722.23281.6578-1.192614.21560.18620.2803-0.2122-0.5585-0.09970.18570.5249-0.7161-0.08650.2927-0.0414-0.04920.1307-0.04350.131814.5301-8.583117.5463
640.5668-17.4766-16.71717.55217.34679.2905-0.34040.8242-1.10930.0216-0.34680.5149-0.2502-0.5510.68720.7516-0.149-0.10440.6263-0.05280.32928.0198-15.4828-5.2541
74.36992.24223.01995.02923.68988.5847-0.05231.1827-0.5204-1.05930.2831-0.24760.2550.4579-0.23080.52910.01220.05330.3917-0.12610.212318.5943-9.9187.8505
85.7252-0.6106-1.29152.9801-0.36572.4447-0.1227-0.1951-0.28970.22280.14980.26830.1128-0.1285-0.02710.03330.02380.00720.09590.01950.07664.92860.095439.258
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B238 - 339
2X-RAY DIFFRACTION2B340 - 358
3X-RAY DIFFRACTION3B359 - 417
4X-RAY DIFFRACTION4B418 - 445
5X-RAY DIFFRACTION5A237 - 264
6X-RAY DIFFRACTION6A265 - 269
7X-RAY DIFFRACTION7A270 - 339
8X-RAY DIFFRACTION8A340 - 443

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