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- PDB-8f60: anti-BTLA monoclonal antibody r23C8 in complex with BTLA -

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Basic information

Entry
Database: PDB / ID: 8f60
Titleanti-BTLA monoclonal antibody r23C8 in complex with BTLA
Components
  • B- and T-lymphocyte attenuator
  • r23C8 Fab heavy chain
  • r23C8 Fab light chain
KeywordsIMMUNE SYSTEM / monoclonal antibody
Function / homology
Function and homology information


immune response-regulating cell surface receptor signaling pathway / Co-inhibition by BTLA / negative regulation of T cell proliferation / signaling receptor activity / adaptive immune response / plasma membrane
Similarity search - Function
B- and T-lymphocyte attenuator / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / B- and T-lymphocyte attenuator
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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 15, 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
Revision 1.4Nov 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
A: r23C8 Fab heavy chain
B: r23C8 Fab light chain
C: B- and T-lymphocyte attenuator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6645
Polymers60,8573
Non-polymers8082
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-21 kcal/mol
Surface area24110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.464, 79.661, 74.692
Angle α, β, γ (deg.)90.00, 102.85, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 2 types, 2 molecules AB

#1: Antibody r23C8 Fab heavy chain


Mass: 23285.057 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody r23C8 Fab light chain


Mass: 23035.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Production host: Cricetulus griseus (Chinese hamster)

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Protein / Sugars , 2 types, 2 molecules C

#3: Protein B- and T-lymphocyte attenuator / B- and T-lymphocyte-associated protein


Mass: 14536.262 Da / Num. of mol.: 1
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: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 477 molecules

#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 3.73 Å3/Da / Density % sol: 67.01 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 4K + 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: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.64→60 Å / Num. obs: 108178 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 8.3
Reflection shellResolution: 1.64→1.73 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 15736 / % possible all: 95.5

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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: 1.64→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.6 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20546 5400 5 %RANDOM
Rwork0.18149 ---
obs0.18272 102757 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.634 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20.93 Å2
2--0.01 Å2-0 Å2
3----0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.64→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3959 0 54 476 4489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.024230
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.9675835
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2575567
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19324.706153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.05715626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6631513
X-RAY DIFFRACTIONr_chiral_restr0.0840.2698
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213178
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_it3.0647.8642165
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.14211.7112708
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.4228.6342065
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.02938.4476530
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: 1.643→1.686 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 380 -
Rwork0.297 7563 -
obs--99.56 %

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