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- PDB-5xj4: Complex structure of durvalumab-scFv/PD-L1 -

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Basic information

Entry
Database: PDB / ID: 5xj4
TitleComplex structure of durvalumab-scFv/PD-L1
Components
  • Programmed cell death 1 ligand 1
  • durvalumab-VH
  • durvalumab-VL
KeywordsIMMUNE SYSTEM / durvalumab / PD-L1 / complex structure
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: 2.3 Å
AuthorsTan, S. / Liu, K. / Chai, Y. / Gao, G.F. / Qi, J.
CitationJournal: Protein Cell / Year: 2018
Title: Distinct PD-L1 binding characteristics of therapeutic monoclonal antibody durvalumab
Authors: Tan, S. / Liu, K. / Chai, Y. / Zhang, C.W. / Gao, S. / Gao, G.F. / Qi, J.
History
DepositionApr 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 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
A: Programmed cell death 1 ligand 1
H: durvalumab-VH
L: durvalumab-VL


Theoretical massNumber of molelcules
Total (without water)51,0923
Polymers51,0923
Non-polymers00
Water3,045169
1
A: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)25,3561
Polymers25,3561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: durvalumab-VH


Theoretical massNumber of molelcules
Total (without water)13,4231
Polymers13,4231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
L: durvalumab-VL


Theoretical massNumber of molelcules
Total (without water)12,3141
Polymers12,3141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.890, 133.890, 133.890
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23

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Components

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


Mass: 25355.795 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: Antibody durvalumab-VH


Mass: 13422.940 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody durvalumab-VL


Mass: 12313.643 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 3.91 Å3/Da / Density % sol: 68.58 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7 / Details: 3.5 M sodium formate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 36086 / % possible obs: 100 % / Redundancy: 21.3 % / Net I/σ(I): 32
Reflection shellResolution: 2.3→2.38 Å / % possible obs: 100 % / Redundancy: 17.8 % / Rmerge(I) obs: 4.415 / Rsym value: 4.415

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RRQ, 3EYQ

3rrq

3eyq


Resolution: 2.3→42.34 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.98
RfactorNum. reflection% reflection
Rfree0.2403 1743 4.99 %
Rwork0.2158 --
obs0.217 34942 96.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→42.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3457 0 0 169 3626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043532
X-RAY DIFFRACTIONf_angle_d0.9464778
X-RAY DIFFRACTIONf_dihedral_angle_d14.9221283
X-RAY DIFFRACTIONf_chiral_restr0.075526
X-RAY DIFFRACTIONf_plane_restr0.005612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2935-2.3610.5165890.45651972X-RAY DIFFRACTION69
2.361-2.43720.40041250.34282618X-RAY DIFFRACTION93
2.4372-2.52430.2811580.26992825X-RAY DIFFRACTION100
2.5243-2.62530.31131660.26762839X-RAY DIFFRACTION100
2.6253-2.74480.32561410.26532805X-RAY DIFFRACTION100
2.7448-2.88950.28471550.24992818X-RAY DIFFRACTION100
2.8895-3.07050.27441400.24112857X-RAY DIFFRACTION100
3.0705-3.30740.23551490.22892849X-RAY DIFFRACTION100
3.3074-3.64010.23721420.20342883X-RAY DIFFRACTION100
3.6401-4.16650.18431530.17642872X-RAY DIFFRACTION100
4.1665-5.24770.18861640.15042873X-RAY DIFFRACTION100
5.2477-42.34690.18371610.18062988X-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)
10.0371-0.03390.00690.02210.04610.08410.0619-0.14380.13660.0190.0103-0.0018-0.23640.0192-0.00530.44730.07420.20150.3425-0.02260.16691.078832.300178.5407
20.0282-0.01470.0380.0093-0.02520.06390.1237-0.0390.069-0.03510.0039-0.03030.05580.15970.1010.26150.09720.1210.2664-0.0370.157731.297116.010759.4606
30.0064-0.0060.00230.01070.00040.00480.0410.01510.078-0.060.0196-0.0274-0.081-0.01390.02040.26590.08060.20190.19110.10380.145916.353127.38347.6247
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain H
3X-RAY DIFFRACTION3chain L

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