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- PDB-4bsw: Heterodimeric Fc Antibody Azymetric Variant 2 -

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Basic information

Entry
Database: PDB / ID: 4bsw
TitleHeterodimeric Fc Antibody Azymetric Variant 2
Components(HETERODIMERIC FC ANTIBODY AZYMETRIC VARIANT ...) x 2
KeywordsIMMUNE SYSTEM / BISPECIFIC / SCAFFOLD / ANTIBODY ENGINEERING / FC DOMAIN / IGG / IGG1 / IMMUNOGLOBULIN G / ZYMEWORKS INC.
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
IODIDE ION / Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSuits, M.D.L. / Spreter, T. / Cabrera, E.E. / Dixit, S.B. / Lario, P.I. / Poon, D.K.Y. / D'Angelo, I.E.P. / Boulanger, M.J.
CitationJournal: Mabs / Year: 2013
Title: Improving Biophysical Properties of a Bispecific Antibody Scaffold to Aid Developability: Quality by Molecular Design.
Authors: Von Kreudenstein, T.S. / Escobar-Carbrera, E. / Lario, P.I. / D'Angelo, I. / Brault, K. / Kelly, J. / Durocher, Y. / Baardsnes, J. / Woods, R.J. / Xie, M.H. / Girod, P. / Suits, M.D.L. / ...Authors: Von Kreudenstein, T.S. / Escobar-Carbrera, E. / Lario, P.I. / D'Angelo, I. / Brault, K. / Kelly, J. / Durocher, Y. / Baardsnes, J. / Woods, R.J. / Xie, M.H. / Girod, P. / Suits, M.D.L. / Boulanger, M.J. / Poon, D.K.Y. / Ng, G.Y.K. / Dixit, S.B.
History
DepositionJun 11, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 23, 2014Group: Database references
Revision 1.2Sep 23, 2015Group: Data collection
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _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.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_alt_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_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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_label_seq_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 2.1Dec 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HETERODIMERIC FC ANTIBODY AZYMETRIC VARIANT 2
B: HETERODIMERIC FC ANTIBODY AZYMETRIC VARIANT 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,71712
Polymers50,7752
Non-polymers3,94210
Water6,684371
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-9.2 kcal/mol
Surface area31450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.677, 74.715, 148.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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HETERODIMERIC FC ANTIBODY AZYMETRIC VARIANT ... , 2 types, 2 molecules AB

#1: Protein HETERODIMERIC FC ANTIBODY AZYMETRIC VARIANT 2


Mass: 25301.643 Da / Num. of mol.: 1 / Fragment: IG GAMMA 1 FC DOMAIN, RESIDUES 106-330 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P01857
#2: Protein HETERODIMERIC FC ANTIBODY AZYMETRIC VARIANT 2


Mass: 25472.904 Da / Num. of mol.: 1 / Fragment: IG GAMMA 1 FC DOMAIN, RESIDUES 106-330 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P01857

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Sugars , 1 types, 2 molecules

#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)-[alpha-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[LFucpa1-6]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-1a_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)][a-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 379 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsFC HETERODIMERS WERE CONSTRUCTED VIA INTRODUCTION OF THE FOLLOWING MUTATIONS - T350V, L351Y, F405A, ...FC HETERODIMERS WERE CONSTRUCTED VIA INTRODUCTION OF THE FOLLOWING MUTATIONS - T350V, L351Y, F405A, Y407V (MOLECULE A, A), AND T350V, T366L, K392L, T394W (MOLECULE B, B) FC HETERODIMERS WERE CONSTRUCTED VIA INTRODUCTION OF THE FOLLOWING MUTATIONS - T350V, L351Y, F405A, Y407V (MOLECULE A, A), AND T350V, T366L, K392L, T394W (MOLECULE B, B)

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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: 2.55 Å3/Da / Density % sol: 51.82 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop
Details: VIA HANGING DROP VAPOR DIFFUSION METHOD AT A RATIO OF 2:1 OF 8.5 MG/ML OF AZYMETRIC VARIANT 2 ABOVE A MOTHER LIQUOR SOLUTION COMPOSED OF 5% (V/V) ETHYLENE GLYCOL, 18% (W/V) POLYETHYLENE ...Details: VIA HANGING DROP VAPOR DIFFUSION METHOD AT A RATIO OF 2:1 OF 8.5 MG/ML OF AZYMETRIC VARIANT 2 ABOVE A MOTHER LIQUOR SOLUTION COMPOSED OF 5% (V/V) ETHYLENE GLYCOL, 18% (W/V) POLYETHYLENE GLYCOL 3350, AND 0.15 M AMMONIUM IODIDE WITH AID OF MICROSEEDING.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.98005
DetectorType: MARRESEARCH MX300HE / Detector: CCD / Date: Sep 12, 2012
Details: COLLIMATING MIRROR WITH TWO STRIPES (SI, RH AND PT)
RadiationMonochromator: KOHZU DOUBLE CRYSTAL MONOCHROMATOR (DCM), FEATURING INDIRECTLY WATER- COOLED FIRST CRYSTAL AND FLAT, LONG SECOND CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98005 Å / Relative weight: 1
ReflectionResolution: 2.1→47 Å / Num. obs: 33200 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J6E

2j6e


Resolution: 2.15→36.26 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 9.679 / SU ML: 0.255 / Cross valid method: THROUGHOUT / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. IN ORDER TO ACCOMMODATE THE PREFECT 50-50 MIXTURE, RECIPROCAL RELATIONSHIP OF THE AZYMETRIC HETERODIMER ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. IN ORDER TO ACCOMMODATE THE PREFECT 50-50 MIXTURE, RECIPROCAL RELATIONSHIP OF THE AZYMETRIC HETERODIMER PRESENT IN THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT, TWO POSSIBLE HETERODIMER PAIRS, EACH WITH 0.5 ATOMIC OCCUPANCIES, WERE MODELED. FOR EXAMPLE, THE OCCUPANCY OF ALTERNATIV CONFORMER A CAN BE EQUALLY BE DESCRIBED BY ALTERNATIVE CONFORMER B AND VICE VERSA.
RfactorNum. reflection% reflectionSelection details
Rfree0.25937 1557 5 %RANDOM
Rwork0.19999 ---
obs0.20296 29307 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.511 Å2
Baniso -1Baniso -2Baniso -3
1--2.3 Å20 Å20 Å2
2--0.94 Å20 Å2
3---1.35 Å2
Refinement stepCycle: LAST / Resolution: 2.15→36.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 243 371 4072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197413
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5262.03410148
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.5895836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.1425304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.076151158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7221524
X-RAY DIFFRACTIONr_chiral_restr0.1060.21210
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0225350
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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: 2.145→2.201 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 95 -
Rwork0.219 1991 -
obs--92.83 %

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