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- PDB-7sjq: Ex silico engineering of cystine-dense peptides yielding a potent... -

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Basic information

Entry
Database: PDB / ID: 7sjq
TitleEx silico engineering of cystine-dense peptides yielding a potent bispecific T-cell engager
Components
  • Cystine-dense peptide
  • Programmed cell death 1 ligand 1
KeywordsANTITUMOR PROTEIN / PDL1 binder
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
Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRupert, P.B. / Strong, R.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Sci Transl Med / Year: 2022
Title: Ex silico engineering of cystine-dense peptides yielding a potent bispecific T cell engager.
Authors: Crook, Z.R. / Girard, E.J. / Sevilla, G.P. / Brusniak, M.Y. / Rupert, P.B. / Friend, D.J. / Gewe, M.M. / Clarke, M. / Lin, I. / Ruff, R. / Pakiam, F. / Phi, T.D. / Bandaranayake, A. / ...Authors: Crook, Z.R. / Girard, E.J. / Sevilla, G.P. / Brusniak, M.Y. / Rupert, P.B. / Friend, D.J. / Gewe, M.M. / Clarke, M. / Lin, I. / Ruff, R. / Pakiam, F. / Phi, T.D. / Bandaranayake, A. / Correnti, C.E. / Mhyre, A.J. / Nairn, N.W. / Strong, R.K. / Olson, J.M.
History
DepositionOct 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Programmed cell death 1 ligand 1
D: Cystine-dense peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6426
Polymers19,2102
Non-polymers4324
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-13 kcal/mol
Surface area8430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.040, 65.330, 99.912
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-203-

SO4

21A-301-

HOH

31A-372-

HOH

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Components

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Protein , 2 types, 2 molecules AD

#1: Protein Programmed cell death 1 ligand 1 / PD-L1 / PDCD1 ligand 1 / Programmed death ligand 1 / hPD-L1 / B7 homolog 1 / B7-H1


Mass: 13538.503 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 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q9NZQ7
#2: Protein Cystine-dense peptide


Mass: 5671.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Sugars , 1 types, 1 molecules

#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 80 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.38 Å3/Da / Density % sol: 48.32 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: Sodium Citrate pH 7, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU HyPix-6000HE / Detector: PIXEL / Date: Sep 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→99.91 Å / Num. obs: 12762 / % possible obs: 99.8 % / Redundancy: 4.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Net I/σ(I): 32.45
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 8.26 / Num. unique obs: 1278 / CC1/2: 0.968

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5C3T

5c3t


Resolution: 2→28.04 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.907 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.232 593 4.7 %RANDOM
Rwork0.1909 ---
obs0.1928 12119 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.16 Å2 / Biso mean: 22.768 Å2 / Biso min: 9.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å2-0 Å2
2--0.21 Å2-0 Å2
3----0.92 Å2
Refinement stepCycle: final / Resolution: 2→28.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1166 0 26 77 1269
Biso mean--39.29 28.31 -
Num. residues----150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131241
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171154
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.6541692
X-RAY DIFFRACTIONr_angle_other_deg1.2951.6022656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5595156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32123.3959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.17815204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.978155
X-RAY DIFFRACTIONr_chiral_restr0.0670.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021396
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02272
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 52 -
Rwork0.219 878 -
all-930 -
obs--99.36 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.79360.3244-0.21280.5686-0.28950.49970.031-0.0253-0.0280.043-0.0188-0.0010.02420.0314-0.01220.0869-0.0205-0.00360.05060.00440.11272.738226.005110.9258
23.6335-0.5807-1.79192.1651-0.56652.4340.0244-0.2228-0.49170.2055-0.2384-0.76510.09360.23460.21390.0545-0.0128-0.14890.16270.13940.52618.822724.070819.4423
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 134
2X-RAY DIFFRACTION2D2 - 51

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