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- PDB-8f6l: anti-BTLA monoclonal antibody h25F7 in complex with BTLA -

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Basic information

Entry
Database: PDB / ID: 8f6l
Titleanti-BTLA monoclonal antibody h25F7 in complex with BTLA
Components
  • B- and T-lymphocyte attenuator
  • h25F7 Fab heavy chain
  • h25F7 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: 1.85 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: h25F7 Fab heavy chain
B: h25F7 Fab light chain
C: B- and T-lymphocyte attenuator


Theoretical massNumber of molelcules
Total (without water)63,6953
Polymers63,6953
Non-polymers00
Water7,638424
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)48.961, 68.600, 187.321
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: Antibody h25F7 Fab heavy chain


Mass: 25036.982 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 h25F7 Fab light chain


Mass: 23509.982 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.: 424 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop
Details: 18% PEG 5000 MME + 200mM Magnesium Formate dihydrate + 100mM Sodium Acetate pH 4.6

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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: Nov 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.85→64 Å / Num. obs: 54860 / % possible obs: 99.8 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 15.7
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.672 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 7911 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMACv5.8refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AW2

2aw2


Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.632 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.136 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24006 2689 4.9 %RANDOM
Rwork0.19805 ---
obs0.20016 52084 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.162 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0 Å20 Å2
2--0.21 Å2-0 Å2
3---0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4063 0 0 424 4487
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.024227
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3491.9435778
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9365555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81324.793169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83215664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6811514
X-RAY DIFFRACTIONr_chiral_restr0.0880.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213181
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_it3.9937.7472166
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.2411.5062706
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.518.5562061
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.51436.716581
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: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 197 -
Rwork0.287 3795 -
obs--99.45 %

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