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- PDB-8gad: Crystal structure of a high affinity PD-L1 binder -

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Basic information

Entry
Database: PDB / ID: 8gad
TitleCrystal structure of a high affinity PD-L1 binder
ComponentsPD-L1 binder
KeywordsPROTEIN BINDING / De novo protein design / high affinity binder / PD-L1
Function / homologyINDOLE
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsYang, W. / Almo, S.C. / Baker, D. / Ghosh, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10 OD020068 United States
CitationJournal: Biorxiv / Year: 2024
Title: Design of High Affinity Binders to Convex Protein Target Sites.
Authors: Yang, W. / Hicks, D.R. / Ghosh, A. / Schwartze, T.A. / Conventry, B. / Goreshnik, I. / Allen, A. / Halabiya, S.F. / Kim, C.J. / Hinck, C.S. / Lee, D.S. / Bera, A.K. / Li, Z. / Wang, Y. / ...Authors: Yang, W. / Hicks, D.R. / Ghosh, A. / Schwartze, T.A. / Conventry, B. / Goreshnik, I. / Allen, A. / Halabiya, S.F. / Kim, C.J. / Hinck, C.S. / Lee, D.S. / Bera, A.K. / Li, Z. / Wang, Y. / Schlichthaerle, T. / Cao, L. / Huang, B. / Garrett, S. / Gerben, S.R. / Rettie, S. / Heine, P. / Murray, A. / Edman, N. / Carter, L. / Stewart, L. / Almo, S. / Hinck, A.P. / Baker, D.
History
DepositionFeb 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2024Group: Structure summary / Category: audit_author / pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Oct 23, 2024Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID / _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PD-L1 binder
B: PD-L1 binder
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5303
Polymers23,4132
Non-polymers1171
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Superdex S200
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
ΔGint-9 kcal/mol
Surface area10680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.242, 67.242, 101.902
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-340-

HOH

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Components

#1: Protein PD-L1 binder


Mass: 11706.420 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET29 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-IND / INDOLE


Mass: 117.148 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7N
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.47 Å3/Da / Density % sol: 50.18 % / Description: Hexagonal rods
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 22.5% (w/v) PEG 3350, 0.08 M Bis-Tris and 2% (v/v) Ethylene glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.88→19.62 Å / Num. obs: 19563 / % possible obs: 99.8 % / Redundancy: 14.4 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.014 / Rrim(I) all: 0.052 / Χ2: 1.01 / Net I/σ(I): 27.9 / Num. measured all: 282139
Reflection shellResolution: 1.88→1.93 Å / % possible obs: 98.8 % / Redundancy: 14.6 % / Rmerge(I) obs: 0.794 / Num. measured all: 17768 / Num. unique obs: 1218 / CC1/2: 0.871 / Rpim(I) all: 0.212 / Rrim(I) all: 0.823 / Χ2: 1.06 / Net I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
autoPROCdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→19.62 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2116 984 5.04 %
Rwork0.1884 --
obs0.1896 19507 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→19.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1632 0 9 103 1744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.881
X-RAY DIFFRACTIONf_dihedral_angle_d4.185235
X-RAY DIFFRACTIONf_chiral_restr0.047267
X-RAY DIFFRACTIONf_plane_restr0.009287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.980.28861460.24422573X-RAY DIFFRACTION99
1.98-2.110.25631390.21482593X-RAY DIFFRACTION100
2.11-2.270.28191400.19772592X-RAY DIFFRACTION100
2.27-2.50.23081420.19872624X-RAY DIFFRACTION100
2.5-2.860.22681190.20842646X-RAY DIFFRACTION100
2.86-3.60.23551460.19492671X-RAY DIFFRACTION100
3.6-19.620.17021520.16812824X-RAY DIFFRACTION100
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)
16.49272.69430.05675.2652-0.0013.1563-0.0399-0.3058-0.1032-0.10220.1647-0.1416-0.03060.0703-0.17620.2838-0.0227-0.02450.283-0.0520.204-21.3672-4.83922.2876
26.81990.8377-1.10842.85630.31984.16570.0641-0.118-0.0107-0.1447-0.033-0.34350.19950.2761-0.06610.2625-0.0178-0.03910.21270.00970.3018-28.6395-7.9859-2.6006
35.45383.7603-5.61266.1908-3.70087.8275-0.4313-0.4664-1.8239-0.2513-0.1836-0.290.82040.18270.50.38760.0387-0.02780.30280.08290.4331-32.9071-17.9943-0.721
47.78820.8731-5.80352.6529-1.43829.3166-0.44640.297-0.5238-0.24370.062-0.05680.7067-0.10460.31810.3202-0.009-0.02130.2744-0.00310.3497-38.6607-12.5223-6.7918
57.99481.82820.7847.8890.94328.9467-0.0148-0.2852-0.0090.5531-0.1926-0.13530.9944-0.08560.18940.2314-0.02850.06250.34240.01330.2904-58.5249-12.7585-1.6133
67.51374.20881.52554.0033-0.15082.3004-0.08660.0470.6511-0.08010.08370.5148-0.1044-0.31570.01430.27050.01480.010.25680.04590.2956-55.0288-3.7991-3.3891
75.52945.1024.28156.49934.34323.5232-0.61620.73541.4448-0.7490.39590.7792-0.92730.25110.21790.3940.05520.00730.36210.09280.3904-46.42094.608-6.3455
87.24093.19251.39197.29661.88789.0819-0.47920.77710.2688-0.86120.39280.1011-0.48150.0937-0.0950.297-0.01560.05110.29290.02840.3021-39.8702-2.5119-8.3333
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 63 )
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 104 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 20 )
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 63 )
7X-RAY DIFFRACTION7chain 'B' and (resid 64 through 84 )
8X-RAY DIFFRACTION8chain 'B' and (resid 85 through 104 )

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