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- PDB-5m3v: BEAT Fc -

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Basic information

Entry
Database: PDB / ID: 5m3v
TitleBEAT Fc
Components
  • Ig gamma-1 chain C region
  • Ig gamma-1 chain C region,Ig gamma-3 chain C region
KeywordsIMMUNE SYSTEM / Antibody TCR Bispecific Interface
Function / homology
Function and homology information


complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / IgG immunoglobulin complex / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / FCGR3A-mediated IL10 synthesis / antigen binding / Regulation of Complement cascade / 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-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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1 / Immunoglobulin heavy constant gamma 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsSkegro, D. / Stutz, C. / Bourquin, F. / Blein, S.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Immunoglobulin domain interface exchange as a platform technology for the generation of Fc heterodimers and bispecific antibodies.
Authors: Skegro, D. / Stutz, C. / Ollier, R. / Svensson, E. / Wassmann, P. / Bourquin, F. / Monney, T. / Gn, S. / Blein, S.
History
DepositionOct 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Category: citation / citation_author
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 / _citation_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 2024Group: 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: Ig gamma-1 chain C region,Ig gamma-3 chain C region
B: Ig gamma-1 chain C region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2564
Polymers52,0052
Non-polymers3,2512
Water8,881493
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7360 Å2
ΔGint51 kcal/mol
Surface area21520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.780, 73.650, 141.530
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,Ig gamma-3 chain C region / HDC / Heavy chain disease protein / BEAT Fc (A)


Mass: 26496.016 Da / Num. of mol.: 1
Mutation: S364K T366V K370T K392Y F405S Y407V K409W T411N,S364K T366V K370T K392Y F405S Y407V K409W T411N,S364K T366V K370T K392Y F405S Y407V K409W T411N,S364K T366V K370T K392Y F405S Y407V K409W T411N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1, IGHG3 / Production host: Homo sapiens (human) / References: UniProt: P01857, UniProt: P01860
#2: Protein Ig gamma-1 chain C region / BEAT Fc (B)


Mass: 25508.832 Da / Num. of mol.: 1
Mutation: Q347E Y349A L351F S364T T366V K370T T394D V397L D399E F405A Y407S K409R T411R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Production host: Homo sapiens (human) / References: UniProt: P01857
#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)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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: 1625.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1b_1-5]/1-1-2-3-1-3-1-4-5/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)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 493 / 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: 2.49 Å3/Da / Density % sol: 50.69 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 10.2 MG/ML PROTEIN IN 10 MM TRIS-HCL PH8.0, 100 MM NACL, 1 MM EDTA, EQUALLY WITH 27.00 %(W/V) PEG 1500

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Data collection

DiffractionMean temperature: 93.15 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.97→30 Å / Num. obs: 35360 / % possible obs: 99.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.119 / Net I/σ(I): 5.2
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 1.3 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H3T

1h3t


Resolution: 1.97→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.227 / SU ML: 0.188 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27893 1883 5.1 %RANDOM
Rwork0.20978 ---
obs0.21327 35360 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 56.556 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2---0.32 Å20 Å2
3----0.38 Å2
Refinement stepCycle: 1 / Resolution: 1.97→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3078 0 220 493 3791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193434
X-RAY DIFFRACTIONr_bond_other_d0.0020.023158
X-RAY DIFFRACTIONr_angle_refined_deg1.6942.0354694
X-RAY DIFFRACTIONr_angle_other_deg0.96437363
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.3925.064390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83524.722144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.08315537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3281515
X-RAY DIFFRACTIONr_chiral_restr0.0830.2565
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213603
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02710
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_it1.5232.391541
X-RAY DIFFRACTIONr_mcbond_other1.5232.391540
X-RAY DIFFRACTIONr_mcangle_it2.4613.571920
X-RAY DIFFRACTIONr_mcangle_other2.4613.5711921
X-RAY DIFFRACTIONr_scbond_it1.9372.9681893
X-RAY DIFFRACTIONr_scbond_other1.9372.9681893
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0234.3592772
X-RAY DIFFRACTIONr_long_range_B_refined16.46935.9243921
X-RAY DIFFRACTIONr_long_range_B_other16.39633.6063754
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.021 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 130 -
Rwork0.378 2533 -
obs--96.94 %
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)
10.92040.54980.26560.99990.26212.510.0145-0.10810.0384-0.01990.14850.20870.1061-0.1953-0.16290.0062-0.018-0.0260.09680.0420.50135.7495.571-24.367
23.5299-0.0638-2.19983.04541.5973.9268-0.1974-0.4422-0.17840.34060.3825-0.38140.12190.6005-0.18510.06640.0534-0.04220.1118-0.03880.439114.683-16.402-29.277
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A237 - 1011
2X-RAY DIFFRACTION2B240 - 1011

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