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- PDB-8qya: J22.9-FNY, fully humanized, CDR optimized Fab Fragment based on c... -

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Basic information

Entry
Database: PDB / ID: 8qya
TitleJ22.9-FNY, fully humanized, CDR optimized Fab Fragment based on chimeric J22.9-xi IgG against BCMA; with VH CDR2 glycosylation
Components
  • (J22.9-FNY Fab antibody ...) x 2
  • Tumor necrosis factor receptor superfamily member 17
KeywordsIMMUNE SYSTEM / Fab fragment / humanized / CDR derivatized / BCMA binding
Function / homology
Function and homology information


lymphocyte homeostasis / TNFs bind their physiological receptors / tumor necrosis factor-mediated signaling pathway / endomembrane system / signaling receptor activity / adaptive immune response / signal transduction / membrane / plasma membrane
Similarity search - Function
BCMA, TALL-1 binding / Tumour necrosis factor receptor 17 / BCMA, TALL-1 binding / Tumor necrosis factor receptor 13C/17
Similarity search - Domain/homology
COPPER (II) ION / Tumor necrosis factor receptor superfamily member 17
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsMarino, S.F. / Daumke, O.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: J.Mol.Med. / Year: 2024
Title: Structure-based humanization of a therapeutic antibody for multiple myeloma.
Authors: Marino, S.F. / Daumke, O.
#1: Journal: Mol Oncol / Year: 2015
Title: Potent anti-tumor response by targeting B cell maturation antigen (BCMA) in a mouse model of multiple myeloma.
Authors: Marino, S.F. / Damke, O.
History
DepositionOct 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 2.0Sep 4, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / database_PDB_caveat / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_branch_scheme / pdbx_contact_author / pdbx_database_related / pdbx_entity_branch_descriptor / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _pdbx_branch_scheme.auth_asym_id / _pdbx_branch_scheme.auth_seq_num / _pdbx_branch_scheme.pdb_asym_id / _pdbx_entity_branch_descriptor.descriptor / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_close_contact.dist / _pdbx_validate_polymer_linkage.dist / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_number_reflns_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_vdw_probe_radii / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _reflns.number_obs / _software.version / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.auth_comp_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.label_comp_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_mon_prot_cis.pdbx_auth_comp_id_2 / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_mon_prot_cis.pdbx_label_comp_id_2 / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.db_code / _struct_ref.db_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq.seq_align_end
Description: Chirality error / Details: NAG chirality problem solved / Provider: author / Type: Coordinate replacement
Revision 2.1Sep 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 2.2Nov 6, 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
L: J22.9-FNY Fab antibody light chain
H: J22.9-FNY Fab antibody heavy chain
A: Tumor necrosis factor receptor superfamily member 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0355
Polymers50,5473
Non-polymers4882
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-40 kcal/mol
Surface area21320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.266, 55.371, 69.486
Angle α, β, γ (deg.)90.000, 108.009, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Antibody , 2 types, 2 molecules LH

#1: Antibody J22.9-FNY Fab antibody light chain


Mass: 23321.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): 293_6E / Production host: Homo sapiens (human)
#2: Antibody J22.9-FNY Fab antibody heavy chain


Mass: 23141.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): 293_6E / Production host: Homo sapiens (human)

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Protein/peptide / Sugars , 2 types, 2 molecules A

#3: Protein/peptide Tumor necrosis factor receptor superfamily member 17 / B-cell maturation protein


Mass: 4083.632 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF17, BCM, BCMA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q02223
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 2 types, 75 molecules

#5: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 3350 CuCl2 BisTris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 21, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.72→21.76 Å / Num. obs: 13497 / % possible obs: 99.42 % / Redundancy: 3.6 % / Biso Wilson estimate: 49.72 Å2 / CC1/2: 0.993 / Net I/σ(I): 9.98
Reflection shellResolution: 2.72→2.817 Å / Num. unique obs: 1323 / CC1/2: 0.747

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Processing

Software
NameVersionClassification
PHENIXdev_5407refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→21.76 Å / SU ML: 0.461 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.2812
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2986 675 5 %
Rwork0.2314 12822 -
obs0.2347 13497 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.2 Å2
Refinement stepCycle: LAST / Resolution: 2.72→21.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3546 0 29 74 3649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213657
X-RAY DIFFRACTIONf_angle_d0.47514979
X-RAY DIFFRACTIONf_chiral_restr0.0414563
X-RAY DIFFRACTIONf_plane_restr0.0039638
X-RAY DIFFRACTIONf_dihedral_angle_d14.50761337
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.930.38351320.36172508X-RAY DIFFRACTION98.18
2.93-3.220.40421340.29952562X-RAY DIFFRACTION99.81
3.22-3.680.30461350.26152563X-RAY DIFFRACTION99.78
3.68-4.630.30921360.20372574X-RAY DIFFRACTION99.6
4.63-21.760.22451380.17852615X-RAY DIFFRACTION99.49

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