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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-Immune System complex
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / positive regulation of T cell apoptotic process / B cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / Co-inhibition by PD-1 ...negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / positive regulation of T cell apoptotic process / B cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / Co-inhibition by PD-1 / regulation of immune response / signaling receptor activity / Potential therapeutics for SARS / adaptive immune response / 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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 2.0Jan 22, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / cell ...atom_site / cell / entity / pdbx_contact_author / pdbx_database_related / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / software / struct_conn / struct_keywords / struct_mon_prot_cis
Item: _cell.angle_alpha / _cell.angle_gamma ..._cell.angle_alpha / _cell.angle_gamma / _entity.pdbx_number_of_molecules / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine.pdbx_overall_ESU_R_Free / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.R_factor_all / _refine_ls_shell.number_reflns_R_work / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_fsc_free / _refine_ls_shell.pdbx_fsc_work / _refine_ls_shell.percent_reflns_obs / _refine_ls_shell.wR_factor_R_work / _reflns.d_resolution_high / _reflns.number_obs / _software.version / _struct_conn.pdbx_dist_value / _struct_keywords.text / _struct_mon_prot_cis.pdbx_omega_angle
Description: Model orientation/position
Details: Corrected symmetry components to show the interaction between the FAB and PD1
Provider: author / Type: Coordinate replacement

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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
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-30 kcal/mol
Surface area22650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.744, 78.51, 102.021
Angle α, β, γ (deg.)90, 106.423, 90
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.: 229 / Source method: isolated from a natural source / Formula: H2O
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: 2.06 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: 1.62→49.62 Å / Num. obs: 62817 / % 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
REFMAC5.8.0430 (refmacat 0.4.88)refinement
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: 0.938 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.195 / SU B: 4.703 / SU ML: 0.137 / Average fsc free: 0.9276 / Average fsc work: 0.9397 / Cross valid method: THROUGHOUT / ESU R: 0.121 / ESU R Free: 0.116 / Details: Hydrogens have not been used
RfactorNum. reflection% reflectionSelection details
Rfree0.2568 3020 5.029 %RANDOM
Rwork0.226 57032 --
all0.227 ---
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: 26.485 Å2
Baniso -1Baniso -2Baniso -3
1-0.398 Å20 Å20.418 Å2
2--0.592 Å20 Å2
3----1.053 Å2
Refinement stepCycle: LAST / Resolution: 1.65→49.616 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3877 0 0 229 4106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0123985
X-RAY DIFFRACTIONr_angle_refined_deg1.9221.8115421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8435502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.693520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.81810639
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.96510163
X-RAY DIFFRACTIONr_chiral_restr0.1270.2610
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023020
X-RAY DIFFRACTIONr_nbd_refined0.2230.21739
X-RAY DIFFRACTIONr_nbtor_refined0.310.22696
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2307
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2060.293
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1590.218
X-RAY DIFFRACTIONr_mcbond_it2.4682.4442011
X-RAY DIFFRACTIONr_mcangle_it3.5694.3712503
X-RAY DIFFRACTIONr_scbond_it3.7912.7341974
X-RAY DIFFRACTIONr_scangle_it5.4614.8432915
X-RAY DIFFRACTIONr_lrange_it6.85929.7036074
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
1.65-1.6930.3861990.37237120.37344230.8830.88988.42410.375
1.693-1.740.4082150.36840770.3743770.8750.89498.0580.371
1.74-1.790.3852530.35140000.35342530.8940.9031000.351
1.79-1.8450.3712130.34739070.34841200.8950.9051000.348
1.845-1.9050.3262030.3237760.3239800.9230.91699.97490.324
1.905-1.9720.3561880.33236740.33338650.8590.89599.92240.339
1.972-2.0460.2831850.26335150.26437020.9430.95199.9460.262
2.046-2.130.2931820.27634040.27735910.9360.94299.86080.278
2.13-2.2240.2471520.21233210.21334740.9560.96999.97120.2
2.224-2.3330.3221460.27531260.27732740.9130.93399.93890.266
2.333-2.4590.2461630.19429720.19631370.9620.97699.93620.173
2.459-2.6070.2451590.19527840.19829440.9580.97799.9660.173
2.607-2.7870.2771200.20726730.21127940.950.97299.96420.18
2.787-3.0090.2431300.19424870.19726180.9670.97799.96180.169
3.009-3.2950.2111320.18222470.18423790.970.981000.161
3.295-3.6820.219980.18420870.18521890.9730.9899.81730.166
3.682-4.2480.17880.16518200.16519160.9840.98499.58250.152
4.248-5.1930.167990.14915310.1516300.9820.9881000.141
5.193-7.3040.211550.20212280.20312830.9740.9761000.192
7.304-49.6160.24400.1946910.1977320.9690.97499.86340.201

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