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- PDB-8eq6: PD1 signaling receptor bound to FAB Complex -

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Basic information

Entry
Database: PDB / ID: 8eq6
TitlePD1 signaling receptor bound to FAB Complex
Components
  • Antibody FAB heavy chain
  • Antibody FAB light chain
  • Programmed cell death protein 1
KeywordsSIGNALING PROTEIN/Immune System / Immune signaling receptor FAB complex / SIGNALING PROTEIN / SIGNALING PROTEIN-Immune System complex
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / B cell apoptotic process / negative regulation of immune response / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / PD-1 signaling / regulation of immune response / adaptive immune response ...negative regulation of tolerance induction / regulatory T cell apoptotic process / B cell apoptotic process / negative regulation of immune response / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / PD-1 signaling / regulation of immune response / adaptive immune response / Potential therapeutics for SARS / external side of plasma membrane / apoptotic process / plasma membrane
Similarity search - Function
Programmed cell death protein 1 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Programmed cell death protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBjorkelid, C. / Paluch, C. / Robertson, N.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Not fundedna United Kingdom
CitationJournal: Immunity / Year: 2024
Title: Antibody agonists trigger immune receptor signaling through local exclusion of receptor-type protein tyrosine phosphatases.
Authors: Lippert, A.H. / Paluch, C. / Gaglioni, M. / Vuong, M.T. / McColl, J. / Jenkins, E. / Fellermeyer, M. / Clarke, J. / Sharma, S. / Moreira da Silva, S. / Akkaya, B. / Anzilotti, C. / Morgan, S. ...Authors: Lippert, A.H. / Paluch, C. / Gaglioni, M. / Vuong, M.T. / McColl, J. / Jenkins, E. / Fellermeyer, M. / Clarke, J. / Sharma, S. / Moreira da Silva, S. / Akkaya, B. / Anzilotti, C. / Morgan, S.H. / Jessup, C.F. / Korbel, M. / Gileadi, U. / Leitner, J. / Knox, R. / Chirifu, M. / Huo, J. / Yu, S. / Ashman, N. / Lui, Y. / Wilkinson, I. / Attfield, K.E. / Fugger, L. / Robertson, N.J. / Lynch, C.J. / Murray, L. / Steinberger, P. / Santos, A.M. / Lee, S.F. / Cornall, R.J. / Klenerman, D. / Davis, S.J.
History
DepositionOct 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Programmed cell death protein 1
L: Antibody FAB light chain
H: Antibody FAB heavy chain


Theoretical massNumber of molelcules
Total (without water)62,3023
Polymers62,3023
Non-polymers00
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.744, 78.510, 102.021
Angle α, β, γ (deg.)90.000, 106.423, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Programmed cell death protein 1 / Protein PD-1 / hPD-1


Mass: 14365.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Production host: Expression vector pcDNA-inf (others) / References: UniProt: Q15116
#2: Antibody Antibody FAB light chain


Mass: 23442.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Expression vector pcDNA-inf (others)
#3: Antibody Antibody FAB heavy chain


Mass: 24493.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Expression vector pcDNA-inf (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.06 Å3/Da / Density % sol: 40.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 20.5% PEG 3350, 0.4M MgCl2, 0.1M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→49.62 Å / Num. obs: 60066 / % possible obs: 98.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 15.86 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.156 / Rpim(I) all: 0.066 / Rrim(I) all: 0.169 / Net I/av σ(I): 5.6 / Net I/σ(I): 4.86
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 4.1 % / Rmerge(I) obs: 2.329 / Mean I/σ(I) obs: 0.2 / Num. unique obs: 10635 / CC1/2: 0.338 / Rpim(I) all: 1.246 / Rrim(I) all: 2.657 / % possible all: 86.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6k0y

6k0y


Resolution: 1.65→49.616 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.196 / SU B: 5.284 / SU ML: 0.15 / Average fsc free: 0.919 / Average fsc work: 0.933 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.119
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2642 3020 5.029 %RANDOM
Rwork0.2278 57032 --
all0.23 ---
obs-60052 98.926 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 25.019 Å2
Baniso -1Baniso -2Baniso -3
1-0.359 Å20 Å20.404 Å2
2--0.601 Å20 Å2
3----1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.65→49.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3877 0 0 183 4060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123985
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163532
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.6535421
X-RAY DIFFRACTIONr_angle_other_deg0.541.5588272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0775502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.661520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1610639
X-RAY DIFFRACTIONr_dihedral_angle_6_deg17.29810163
X-RAY DIFFRACTIONr_chiral_restr0.0750.2610
X-RAY DIFFRACTIONr_chiral_restr_other0.0030.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024494
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02794
X-RAY DIFFRACTIONr_nbd_refined0.2120.2595
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.23300
X-RAY DIFFRACTIONr_nbtor_refined0.1810.21891
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0920.22257
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2209
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.110.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2420.239
X-RAY DIFFRACTIONr_nbd_other0.1950.2166
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1410.227
X-RAY DIFFRACTIONr_mcbond_it2.3062.4992011
X-RAY DIFFRACTIONr_mcbond_other2.3062.4982011
X-RAY DIFFRACTIONr_mcangle_it3.3293.7352503
X-RAY DIFFRACTIONr_mcangle_other3.3293.7362504
X-RAY DIFFRACTIONr_scbond_it3.1262.7881974
X-RAY DIFFRACTIONr_scbond_other3.1252.7881975
X-RAY DIFFRACTIONr_scangle_it4.6054.0472915
X-RAY DIFFRACTIONr_scangle_other4.6044.0472916
X-RAY DIFFRACTIONr_lrange_it5.89436.0234232
X-RAY DIFFRACTIONr_lrange_other5.8835.5764211
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.65-1.6930.3951990.3937120.3944230.7780.79788.42410.392
1.693-1.740.4192150.37840770.3843770.870.88998.0580.38
1.74-1.790.3772530.34640000.34842530.8910.9031000.347
1.79-1.8450.3612130.34539070.34641200.8980.9051000.346
1.845-1.9050.3252030.32537760.32539800.9240.91499.97490.328
1.905-1.9720.3511880.33436740.33438650.8630.89499.92240.341
1.972-2.0460.2881850.26635150.26737020.9410.94999.9460.264
2.046-2.130.31820.27534040.27635910.9350.94299.86080.275
2.13-2.2240.2831520.21533210.21834740.9470.96899.97120.204
2.224-2.3330.3241460.27431260.27632740.9080.93299.93890.265
2.333-2.4590.2471630.19829720.231370.9620.97699.93620.176
2.459-2.6070.2591590.19727830.20129430.9570.97799.9660.176
2.607-2.7870.2931200.20526730.20927940.9460.97399.96420.177
2.787-3.0090.251300.19224870.19426180.9630.97799.96180.166
3.009-3.2950.2271320.18322470.18623790.9670.9791000.162
3.295-3.6820.221980.19320870.19421890.9720.97899.81730.173
3.682-4.2480.182880.1718200.17119160.9790.98399.58250.157
4.248-5.1930.166990.1515310.15116300.9820.9881000.142
5.193-7.3040.23550.18912280.19112830.9750.981000.181
7.304-49.6160.252400.26900.2027310.9670.97599.86320.202

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