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- PDB-3bp6: Crystal structure of the mouse PD-1 Mutant and PD-L2 complex -

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Basic information

Entry
Database: PDB / ID: 3bp6
TitleCrystal structure of the mouse PD-1 Mutant and PD-L2 complex
Components
  • Programmed cell death 1 ligand 2
  • Programmed cell death protein 1
KeywordsSIGNALING PROTEIN / PD-1 / PD-L2 / Complex / Costimulation / Glycoprotein / Immunoglobulin domain / Membrane / Transmembrane / Receptor
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / PD-1 signaling / B cell apoptotic process / negative regulation of immune response / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / negative regulation of type II interferon production ...negative regulation of tolerance induction / regulatory T cell apoptotic process / PD-1 signaling / B cell apoptotic process / negative regulation of immune response / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / negative regulation of type II interferon production / regulation of immune response / negative regulation of T cell proliferation / positive regulation of T cell proliferation / T cell costimulation / cellular response to lipopolysaccharide / adaptive immune response / cell surface receptor signaling pathway / immune response / external side of plasma membrane
Similarity search - Function
Programmed cell death protein 1 / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...Programmed cell death protein 1 / CD80-like, immunoglobulin C2-set / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Programmed cell death protein 1 / Programmed cell death 1 ligand 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsYan, Q. / Lazar-Molnar, E. / Cao, E. / Ramagopal, U.A. / Toro, R. / Nathenson, S.G. / Almo, S.C.
CitationJournal: To be published
Title: Crystal structure of the mouse PD-1 A99L and PD-L2 complex
Authors: Yan, Q. / Lazar-Molnar, E. / Cao, E. / Ramagopal, U.A. / Toro, R. / Nathenson, S.G. / Almo, S.C.
History
DepositionDec 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Dec 27, 2023Group: Derived calculations / Category: struct_conn / struct_conn_type

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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
B: Programmed cell death 1 ligand 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3846
Polymers36,0162
Non-polymers3684
Water5,008278
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.747, 84.335, 52.281
Angle α, β, γ (deg.)90.00, 108.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Programmed cell death protein 1 / Protein PD-1 / mPD-1 / CD279 antigen


Mass: 13218.794 Da / Num. of mol.: 1 / Fragment: Extrocellular domain / Mutation: C50S, A99L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pdcd1, Pd1 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q02242
#2: Protein Programmed cell death 1 ligand 2 / Programmed death ligand 2 / PD-L2 / PD-1-ligand 2 / PDCD1 ligand 2 / Butyrophilin B7-DC / B7-DC / ...Programmed death ligand 2 / PD-L2 / PD-1-ligand 2 / PDCD1 ligand 2 / Butyrophilin B7-DC / B7-DC / CD273 antigen


Mass: 22797.139 Da / Num. of mol.: 1 / Fragment: Extrocellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pdcd1lg2, B7dc, Btdc, Cd273, Pdl2 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q9WUL5
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 291 K / Method: sitting drop / pH: 8.5
Details: 20% PEG 6000, 0.1 M Tris pH 8.5, Sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 21, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 47813 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 16
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.6-1.664.40.405199.5
1.66-1.724.50.333199.6
1.72-1.84.80.259199.6
1.8-1.950.183199.7
1.9-2.025.30.128199.7
2.02-2.175.60.097199.9
2.17-2.395.70.0751100
2.39-2.745.70.059199.9
2.74-3.455.90.043199.9
3.45-306.20.033199.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.3.0034refinement
PDB_EXTRACT3.004data extraction
CBASSdata collection
HKL-2000data reduction
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BP5

3bp5


Resolution: 1.6→23.98 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.684 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21833 2405 5 %RANDOM
Rwork0.18407 ---
obs0.18583 45379 99.59 %-
all-47784 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.773 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→23.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 24 278 2649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222553
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.9633494
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9795326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19324110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00615425
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0551517
X-RAY DIFFRACTIONr_chiral_restr0.0860.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021947
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1780.31033
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.51717
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.5458
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.355
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.532
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.19821617
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.32632592
X-RAY DIFFRACTIONr_scbond_it3.30631053
X-RAY DIFFRACTIONr_scangle_it5.1795897
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.637 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 169 -
Rwork0.249 3280 -
obs--97.4 %

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