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- PDB-8f6o: anti-BTLA monoclonal antibody h22B3 in complex with BTLA -

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Basic information

Entry
Database: PDB / ID: 8f6o
Titleanti-BTLA monoclonal antibody h22B3 in complex with BTLA
Components
  • B- and T-lymphocyte attenuator
  • h22B3 Fab heavy chain
  • h22B3 Fab light chain
KeywordsIMMUNE SYSTEM / monoclonal antibody / complex
Function / homology
Function and homology information


immune response-regulating cell surface receptor signaling pathway / Costimulation by the CD28 family / signaling receptor activity / adaptive immune response / plasma membrane
Similarity search - Function
B- and T-lymphocyte attenuator / Immunoglobulin / Immunoglobulin domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
B- and T-lymphocyte attenuator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å
AuthorsHendle, J. / Atwell, S. / Lieu, R. / Hickey, M. / Weichert, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2023
Title: Epitope topography of agonist antibodies to the checkpoint inhibitory receptor BTLA.
Authors: Cheung, T.C. / Atwell, S. / Bafetti, L. / Cuenca, P.D. / Froning, K. / Hendle, J. / Hickey, M. / Ho, C. / Huang, J. / Lieu, R. / Lim, S. / Lippner, D. / Obungu, V. / Ward-Kavanagh, L. / ...Authors: Cheung, T.C. / Atwell, S. / Bafetti, L. / Cuenca, P.D. / Froning, K. / Hendle, J. / Hickey, M. / Ho, C. / Huang, J. / Lieu, R. / Lim, S. / Lippner, D. / Obungu, V. / Ward-Kavanagh, L. / Weichert, K. / Ware, C.F. / Vendel, A.C.
History
DepositionNov 16, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 16, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 25, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: h22B3 Fab heavy chain
B: h22B3 Fab light chain
C: B- and T-lymphocyte attenuator


Theoretical massNumber of molelcules
Total (without water)63,6563
Polymers63,6563
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.950, 88.060, 233.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody h22B3 Fab heavy chain


Mass: 25083.943 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody h22B3 Fab light chain


Mass: 23423.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein B- and T-lymphocyte attenuator / B- and T-lymphocyte-associated protein


Mass: 15147.877 Da / Num. of mol.: 1 / Fragment: Extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BTLA / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q7Z6A9
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 23% PEG 10K + 200mM Magnesium Formate + 100mM Sodium Acetate pH 5.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.31→54 Å / Num. obs: 31602 / % possible obs: 99.9 % / Redundancy: 6 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 11.9
Reflection shellResolution: 2.31→2.43 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 4567 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTERv2.11.6refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AW2

2aw2


Resolution: 2.31→54 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2663 --
Rwork0.2152 --
obs0.2177 31602 99.9 %
Refinement stepCycle: LAST / Resolution: 2.31→54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4085 0 0 156 4241
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014206HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.235743HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1371SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes85HARMONIC2
X-RAY DIFFRACTIONt_gen_planes624HARMONIC5
X-RAY DIFFRACTIONt_it4206HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.37
X-RAY DIFFRACTIONt_other_torsion18.97
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion566SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4500SEMIHARMONIC4

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