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- PDB-7uxq: Structure of PDL1 in complex with FP28135, a Helicon Polypeptide -

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Basic information

Entry
Database: PDB / ID: 7uxq
TitleStructure of PDL1 in complex with FP28135, a Helicon Polypeptide
Components
  • FP28135
  • Programmed cell death 1 ligand 1
KeywordsIMMUNE SYSTEM / Complex / stapled
Function / homology
Function and homology information


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 / negative regulation of T cell mediated immune response to tumor cell / 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 / negative regulation of type II interferon production ...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 / negative regulation of T cell mediated immune response to tumor cell / 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 / negative regulation of type II interferon production / positive regulation of interleukin-10 production / Co-inhibition by PD-1 / negative regulation of T cell proliferation / T cell costimulation / positive regulation of T cell proliferation / response to cytokine / recycling endosome membrane / actin cytoskeleton / cellular response to lipopolysaccharide / early endosome membrane / adaptive immune response / transcription coactivator activity / cell surface receptor signaling pathway / immune response / receptor ligand activity / 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
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: 2.89 Å
AuthorsLi, K. / Agarwal, S. / Tokareva, O. / Thomson, T. / Travaline, T. / 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
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: Programmed cell death 1 ligand 1
C: FP28135
D: FP28135
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,65616
Polymers33,6514
Non-polymers1,00512
Water21612
1
A: Programmed cell death 1 ligand 1
C: FP28135
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2667
Polymers16,8252
Non-polymers4405
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-8 kcal/mol
Surface area8380 Å2
MethodPISA
2
B: Programmed cell death 1 ligand 1
D: FP28135
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3909
Polymers16,8252
Non-polymers5657
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-8 kcal/mol
Surface area8160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)236.990, 236.990, 236.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132
Space group name HallF4d23
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+1/4
#3: x+1/4,z+1/4,-y+1/4
#4: z+1/4,y+1/4,-x+1/4
#5: -z+1/4,y+1/4,x+1/4
#6: -y+1/4,x+1/4,z+1/4
#7: y+1/4,-x+1/4,z+1/4
#8: z,x,y
#9: y,z,x
#10: -y,-z,x
#11: z,-x,-y
#12: -y,z,-x
#13: -z,-x,y
#14: -z,x,-y
#15: y,-z,-x
#16: x,-y,-z
#17: -x,y,-z
#18: -x,-y,z
#19: y+1/4,x+1/4,-z+1/4
#20: -y+1/4,-x+1/4,-z+1/4
#21: z+1/4,-y+1/4,x+1/4
#22: -z+1/4,-y+1/4,-x+1/4
#23: -x+1/4,z+1/4,y+1/4
#24: -x+1/4,-z+1/4,-y+1/4
#25: x,y+1/2,z+1/2
#26: x+1/4,-z+3/4,y+3/4
#27: x+1/4,z+3/4,-y+3/4
#28: z+1/4,y+3/4,-x+3/4
#29: -z+1/4,y+3/4,x+3/4
#30: -y+1/4,x+3/4,z+3/4
#31: y+1/4,-x+3/4,z+3/4
#32: z,x+1/2,y+1/2
#33: y,z+1/2,x+1/2
#34: -y,-z+1/2,x+1/2
#35: z,-x+1/2,-y+1/2
#36: -y,z+1/2,-x+1/2
#37: -z,-x+1/2,y+1/2
#38: -z,x+1/2,-y+1/2
#39: y,-z+1/2,-x+1/2
#40: x,-y+1/2,-z+1/2
#41: -x,y+1/2,-z+1/2
#42: -x,-y+1/2,z+1/2
#43: y+1/4,x+3/4,-z+3/4
#44: -y+1/4,-x+3/4,-z+3/4
#45: z+1/4,-y+3/4,x+3/4
#46: -z+1/4,-y+3/4,-x+3/4
#47: -x+1/4,z+3/4,y+3/4
#48: -x+1/4,-z+3/4,-y+3/4
#49: x+1/2,y,z+1/2
#50: x+3/4,-z+1/4,y+3/4
#51: x+3/4,z+1/4,-y+3/4
#52: z+3/4,y+1/4,-x+3/4
#53: -z+3/4,y+1/4,x+3/4
#54: -y+3/4,x+1/4,z+3/4
#55: y+3/4,-x+1/4,z+3/4
#56: z+1/2,x,y+1/2
#57: y+1/2,z,x+1/2
#58: -y+1/2,-z,x+1/2
#59: z+1/2,-x,-y+1/2
#60: -y+1/2,z,-x+1/2
#61: -z+1/2,-x,y+1/2
#62: -z+1/2,x,-y+1/2
#63: y+1/2,-z,-x+1/2
#64: x+1/2,-y,-z+1/2
#65: -x+1/2,y,-z+1/2
#66: -x+1/2,-y,z+1/2
#67: y+3/4,x+1/4,-z+3/4
#68: -y+3/4,-x+1/4,-z+3/4
#69: z+3/4,-y+1/4,x+3/4
#70: -z+3/4,-y+1/4,-x+3/4
#71: -x+3/4,z+1/4,y+3/4
#72: -x+3/4,-z+1/4,-y+3/4
#73: x+1/2,y+1/2,z
#74: x+3/4,-z+3/4,y+1/4
#75: x+3/4,z+3/4,-y+1/4
#76: z+3/4,y+3/4,-x+1/4
#77: -z+3/4,y+3/4,x+1/4
#78: -y+3/4,x+3/4,z+1/4
#79: y+3/4,-x+3/4,z+1/4
#80: z+1/2,x+1/2,y
#81: y+1/2,z+1/2,x
#82: -y+1/2,-z+1/2,x
#83: z+1/2,-x+1/2,-y
#84: -y+1/2,z+1/2,-x
#85: -z+1/2,-x+1/2,y
#86: -z+1/2,x+1/2,-y
#87: y+1/2,-z+1/2,-x
#88: x+1/2,-y+1/2,-z
#89: -x+1/2,y+1/2,-z
#90: -x+1/2,-y+1/2,z
#91: y+3/4,x+3/4,-z+1/4
#92: -y+3/4,-x+3/4,-z+1/4
#93: z+3/4,-y+3/4,x+1/4
#94: -z+3/4,-y+3/4,-x+1/4
#95: -x+3/4,z+3/4,y+1/4
#96: -x+3/4,-z+3/4,-y+1/4

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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.: 2
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 FP28135


Mass: 2015.338 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-WHL / N,N'-(1,4-phenylene)diacetamide


Mass: 192.214 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 4.12 Å3/Da / Density % sol: 70.15 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 1.1 M Sodium Malonate pH 7.0, 0.1 M HEPES pH 7.0, 0.5% v/v Jeffamine ED-2001 Reagent pH 7.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.89→48.38 Å / Num. obs: 13300 / % possible obs: 99.91 % / Redundancy: 83.4 % / Biso Wilson estimate: 76.94 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.382 / Net I/σ(I): 26.6
Reflection shellResolution: 2.89→2.99 Å / Num. unique obs: 1294 / CC1/2: 0.776

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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: 2.89→48.38 Å / SU ML: 0.3366 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.6943
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2279 670 5.04 %
Rwork0.1998 12625 -
obs0.2012 13295 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.23 Å2
Refinement stepCycle: LAST / Resolution: 2.89→48.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2284 0 68 12 2364
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092390
X-RAY DIFFRACTIONf_angle_d1.18693212
X-RAY DIFFRACTIONf_chiral_restr0.0658348
X-RAY DIFFRACTIONf_plane_restr0.0079408
X-RAY DIFFRACTIONf_dihedral_angle_d28.1178862
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-3.110.31381260.29952463X-RAY DIFFRACTION100
3.11-3.430.31591400.24342445X-RAY DIFFRACTION100
3.43-3.920.23821430.20212480X-RAY DIFFRACTION99.92
3.92-4.940.18521220.1622537X-RAY DIFFRACTION100
4.94-48.380.20861390.19692700X-RAY DIFFRACTION99.89

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