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- PDB-3rnq: Crystal structure of the complex between the extracellular domain... -

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Basic information

Entry
Database: PDB / ID: 3rnq
TitleCrystal structure of the complex between the extracellular domains of mouse PD-1 mutant and PD-L2
Components
  • Programmed cell death 1 ligand 2
  • Programmed cell death protein 1
KeywordsIMMUNE SYSTEM / PD-1-mutant / PD-L2 / B7-DC / Programmed death-1 Ligand 2 / complex / costimulatory
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / PD-1 signaling / negative regulation of T cell activation / B cell apoptotic process / positive regulation of T cell apoptotic process / negative regulation of immune response / negative regulation of B cell apoptotic process / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation ...negative regulation of tolerance induction / regulatory T cell apoptotic process / PD-1 signaling / negative regulation of T cell activation / B cell apoptotic process / positive regulation of T cell apoptotic process / negative regulation of immune response / 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 / signaling receptor activity / 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 / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / : / CD80-like C2-set immunoglobulin domain / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. ...Programmed cell death protein 1 / : / Butyrophilin subfamily 3 member A2-like, Ig-C domain / : / 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
AuthorsLazar-Molnar, E. / Ramagopal, U.A. / Nathenson, S.G. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of the complex between the extracellular domains of mouse PD-1 mutant and PD-L2
Authors: Lazar-Molnar, E. / Ramagopal, U.A. / Nathenson, S.G. / Almo, S.C.
History
DepositionApr 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Programmed cell death 1 ligand 2
A: Programmed cell death protein 1


Theoretical massNumber of molelcules
Total (without water)35,8872
Polymers35,8872
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-5 kcal/mol
Surface area15530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.516, 79.716, 51.693
Angle α, β, γ (deg.)90.000, 105.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Programmed cell death 1 ligand 2 / PD-1 ligand 2 / PD-L2 / PDCD1 ligand 2 / Programmed death ligand 2 / Butyrophilin B7-DC / B7-DC


Mass: 22665.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B7dc, Btdc, Cd273, Murine, Pdcd1lg2, Pdl2 / Plasmid: pET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q9WUL5
#2: Protein Programmed cell death protein 1 / Protein PD-1 / mPD-1


Mass: 13220.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pd1, Pdcd1 / Plasmid: PET-3a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: Q02242
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.02 Å3/Da / Density % sol: 39.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M Tris pH 8, 17.5% PEG 6000, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.071 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 7, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.071 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 36039 / % possible obs: 96.1 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.046 / Χ2: 1.147 / Net I/σ(I): 16.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.662.30.19628280.845174.7
1.66-1.722.60.16332910.994188.5
1.72-1.83.40.13236611.063198.8
1.8-1.93.80.09937411.167199.9
1.9-2.023.80.07237291.205199.9
2.02-2.173.80.0637371.2471100
2.17-2.393.80.0537411.2271100
2.39-2.743.80.04337551.0641100
2.74-3.453.80.04337701.2661100
3.45-503.70.0437861.113199.1

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NPU,3BP6

1npu

3bp6


Resolution: 1.6→49.81 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / WRfactor Rfree: 0.2286 / WRfactor Rwork: 0.1967 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.8738 / SU B: 1.581 / SU ML: 0.057 / SU R Cruickshank DPI: 0.0994 / SU Rfree: 0.0939 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2068 1809 5 %RANDOM
Rwork0.1827 ---
obs0.184 36008 96.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 49.8 Å2 / Biso mean: 22.0941 Å2 / Biso min: 10.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å2-0.6 Å2
2--0.16 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.6→49.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2331 0 0 218 2549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222429
X-RAY DIFFRACTIONr_angle_refined_deg1.4351.9533314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5255307
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40623.604111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12115411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6551520
X-RAY DIFFRACTIONr_chiral_restr0.1040.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211846
X-RAY DIFFRACTIONr_mcbond_it0.9341.51503
X-RAY DIFFRACTIONr_mcangle_it1.71122446
X-RAY DIFFRACTIONr_scbond_it2.5343926
X-RAY DIFFRACTIONr_scangle_it4.1714.5862
LS refinement shellResolution: 1.602→1.644 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 99 -
Rwork0.208 1895 -
all-1994 -
obs--72.06 %

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