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- PDB-5xxy: Crystal structure of PD-L1 complexed with atezolizumab fab at 2.9A -

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Basic information

Entry
Database: PDB / ID: 5xxy
TitleCrystal structure of PD-L1 complexed with atezolizumab fab at 2.9A
Components
  • Programmed cell death 1 ligand 1
  • heavy chain of atezolizumab fab
  • light chain of atezolizumab fab
KeywordsIMMUNE SYSTEM / PD-L1 / ATEZOLIZUMAB
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 / Immunoglobulins ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Programmed cell death 1 ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZhou, A. / Zhang, F.
CitationJournal: Oncotarget / Year: 2017
Title: Structural basis of the therapeutic anti-PD-L1 antibody atezolizumab.
Authors: Zhang, F. / Qi, X. / Wang, X. / Wei, D. / Wu, J. / Feng, L. / Cai, H. / Wang, Y. / Zeng, N. / Xu, T. / Zhou, A. / Zheng, Y.
History
DepositionJul 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _struct.title
Revision 1.2Apr 11, 2018Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: heavy chain of atezolizumab fab
L: light chain of atezolizumab fab
A: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)63,2693
Polymers63,2693
Non-polymers00
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-30 kcal/mol
Surface area22750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.220, 72.710, 63.800
Angle α, β, γ (deg.)90.00, 104.44, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody heavy chain of atezolizumab fab


Mass: 25677.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293S / Production host: Homo sapiens (human)
#2: Antibody light chain of atezolizumab fab


Mass: 23386.951 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293S / Production host: Homo sapiens (human)
#3: Protein Programmed cell death 1 ligand 1 / Programmed death ligand 1 / B7 homolog 1 / B7-H1


Mass: 14204.211 Da / Num. of mol.: 1 / Fragment: IgV domain,UNP residues 18-133
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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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: 2.26 Å3/Da / Density % sol: 45.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2M ammonium sulfate, 0.1M Tris PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→61.72 Å / Num. obs: 11768 / % possible obs: 91 % / Redundancy: 3 % / Net I/σ(I): 4.4
Reflection shellResolution: 2.9→3.08 Å / Rmerge(I) obs: 0.573 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.612 / % possible all: 95.3

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JDS,5GGT

5jds

5ggt


Resolution: 2.9→61.601 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2948 545 4.64 %
Rwork0.2361 --
obs0.2389 11744 92.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→61.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3977 0 0 2 3979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044075
X-RAY DIFFRACTIONf_angle_d0.8455535
X-RAY DIFFRACTIONf_dihedral_angle_d14.5891440
X-RAY DIFFRACTIONf_chiral_restr0.05624
X-RAY DIFFRACTIONf_plane_restr0.003701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9001-3.19190.32741290.28312845X-RAY DIFFRACTION94
3.1919-3.65380.28821150.24612828X-RAY DIFFRACTION94
3.6538-4.60310.29971580.20922785X-RAY DIFFRACTION93
4.6031-61.61440.27551430.22862741X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: 0.0589 Å / Origin y: -32.9488 Å / Origin z: 17.5613 Å
111213212223313233
T0.2159 Å20.0147 Å20.0049 Å2-0.3107 Å20.0298 Å2--0.1529 Å2
L1.5134 °20.7764 °20.3527 °2-0.8863 °20.1793 °2--0.2139 °2
S-0.0575 Å °-0.0457 Å °-0.0052 Å °-0.0772 Å °0.0259 Å °0.0143 Å °-0.0509 Å °-0.0481 Å °0.0348 Å °
Refinement TLS groupSelection details: all

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