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- PDB-7uxo: Structure of PDL1 in complex with FP30790, a Helicon Polypeptide -

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Basic information

Entry
Database: PDB / ID: 7uxo
TitleStructure of PDL1 in complex with FP30790, a Helicon Polypeptide
Components
  • FP30790
  • Programmed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / Complex / stapled
Function / homology
Function and homology information


positive regulation of tolerance induction to tumor cell / negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production ...positive regulation of tolerance induction to tumor cell / negative regulation of tumor necrosis factor superfamily cytokine production / positive regulation of activated CD8-positive, alpha-beta T cell apoptotic process / negative regulation of CD8-positive, alpha-beta T cell activation / TRIF-dependent toll-like receptor signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / STAT3 nuclear events downstream of ALK signaling / negative regulation of interleukin-10 production / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production / negative regulation of type II interferon production / PD-1 signaling / positive regulation of T cell proliferation / T cell costimulation / response to cytokine / recycling endosome membrane / actin cytoskeleton / early endosome membrane / cellular response to lipopolysaccharide / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / positive regulation of cell migration / immune response / external side of plasma membrane / signal transduction / extracellular exosome / nucleoplasm / plasma membrane
Similarity search - Function
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 / Immunoglobulin-like fold
Similarity search - Domain/homology
AMINO GROUP / N,N'-(1,4-phenylene)diacetamide / Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLi, K. / Agarwal, S. / Tokareva, O. / Thomson, T. / Travaline, T. / Tattersfield, H. / Wahl, S. / Verdine, G. / McGee, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: De novo mapping of alpha-helix recognition sites on protein surfaces using unbiased libraries.
Authors: Li, K. / Tokareva, O.S. / Thomson, T.M. / Wahl, S.C.T. / Travaline, T.L. / Ramirez, J.D. / Choudary, S.K. / Agarwal, S. / Walkup 4th, W.G. / Olsen, T.J. / Brennan, M.J. / Verdine, G.L. / McGee, J.H.
History
DepositionMay 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Programmed cell death 1 ligand 1
B: FP30790
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9434
Polymers16,7352
Non-polymers2082
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-6 kcal/mol
Surface area7300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.410, 62.980, 83.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Programmed cell death 1 ligand 1 / hPD-L1 / B7 homolog 1 / B7-H1


Mass: 14809.955 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD274, B7H1, PDCD1L1, PDCD1LG1, PDL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZQ7
#2: Protein/peptide FP30790


Mass: 1925.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Stapled peptide / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-NH2 / AMINO GROUP


Mass: 16.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NH2
#4: Chemical ChemComp-WHL / N,N'-(1,4-phenylene)diacetamide


Mass: 192.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Sodium acetate pH 4.6, 2.0 M Sodium formate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→43.22 Å / Num. obs: 7385 / % possible obs: 95.69 % / Redundancy: 6 % / Biso Wilson estimate: 28.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Net I/σ(I): 22.2
Reflection shellResolution: 2.25→2.33 Å / Num. unique obs: 572 / CC1/2: 0.978

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZQK

4zqk


Resolution: 2.25→43.22 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 29.0268
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2499 340 4.6 %
Rwork0.2185 7045 -
obs0.22 7385 95.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.63 Å2
Refinement stepCycle: LAST / Resolution: 2.25→43.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1065 0 15 27 1107
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00781099
X-RAY DIFFRACTIONf_angle_d0.9431486
X-RAY DIFFRACTIONf_chiral_restr0.0524165
X-RAY DIFFRACTIONf_plane_restr0.0058188
X-RAY DIFFRACTIONf_dihedral_angle_d18.7029396
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.830.33011550.26323367X-RAY DIFFRACTION93.15
2.83-43.220.2231850.2023678X-RAY DIFFRACTION98.12

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