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- PDB-8qy9: J22.9-H, fully humanized Fab Fragment based on chimeric J22.9-xi ... -

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Basic information

Entry
Database: PDB / ID: 8qy9
TitleJ22.9-H, fully humanized Fab Fragment based on chimeric J22.9-xi IgG against BCMA
Components
  • Fab heavy chain of J22.9-H
  • Fab light chain of J22.9-H
  • Tumor necrosis factor receptor superfamily member 17
KeywordsIMMUNE SYSTEM / Fab fragment / humanized / BCMA binding
Function / homology
Function and homology information


lymphocyte homeostasis / TNFs bind their physiological receptors / endomembrane system / tumor necrosis factor-mediated signaling pathway / 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: 3.1 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.
History
DepositionOct 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 2.0Jul 24, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_contact_author / pdbx_database_related / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / 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_residues / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / pdbx_validate_symm_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_sheet_order / struct_sheet_range
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _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_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_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_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _software.version / _struct_mon_prot_cis.label_seq_id / _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.pdbx_db_accession / _struct_ref_seq.seq_align_end
Description: Real space R-factor / Details: further refinement for model improvement / Provider: author / Type: Coordinate replacement
Revision 2.1Aug 14, 2024Group: Database references / Category: citation
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
Revision 2.2Sep 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 2.3Nov 20, 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: Fab light chain of J22.9-H
H: Fab heavy chain of J22.9-H
A: Tumor necrosis factor receptor superfamily member 17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4755
Polymers50,3483
Non-polymers1272
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4880 Å2
ΔGint-48 kcal/mol
Surface area20590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.360, 55.180, 81.160
Angle α, β, γ (deg.)90.000, 121.023, 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

#1: Antibody Fab light chain of J22.9-H


Mass: 23034.570 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 Fab heavy chain of J22.9-H


Mass: 23572.344 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)
#3: Protein/peptide Tumor necrosis factor receptor superfamily member 17 / B-cell maturation protein


Mass: 3741.257 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Extracellular domain of BCMA (B-cell maturation antigen, CD269)
Source: (gene. exp.) Homo sapiens (human) / Gene: TNFRSF17, BCM, BCMA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q02223
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
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: 2.65 Å3/Da / Density % sol: 53.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 14% PEG 3350 100 mM BisTris 7.5 mM Cu(II)

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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: 3.1→34.78 Å / Num. obs: 9584 / % possible obs: 99.19 % / Redundancy: 4.14 % / Biso Wilson estimate: 68.29 Å2 / CC1/2: 0.985 / Net I/σ(I): 6.54
Reflection shellResolution: 3.1→3.211 Å / Num. unique obs: 942 / CC1/2: 0.611 / % possible all: 99.37

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Processing

Software
NameVersionClassification
PHENIX1.21.1-5286refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→34.78 Å / SU ML: 0.4842 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 34.9704
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3011 480 5.01 %
Rwork0.2535 9100 -
obs0.256 9580 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.15 Å2
Refinement stepCycle: LAST / Resolution: 3.1→34.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3496 0 2 0 3498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00193585
X-RAY DIFFRACTIONf_angle_d0.44524885
X-RAY DIFFRACTIONf_chiral_restr0.0412551
X-RAY DIFFRACTIONf_plane_restr0.0045628
X-RAY DIFFRACTIONf_dihedral_angle_d11.71451275
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.550.37761570.33442984X-RAY DIFFRACTION99.52
3.55-4.470.3351590.29243010X-RAY DIFFRACTION98.69
4.47-34.780.25091640.19923106X-RAY DIFFRACTION99.66

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