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- PDB-5grj: Crystal structure of human PD-L1 with monoclonal antibody avelumab -

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Basic information

Entry
Database: PDB / ID: 5grj
TitleCrystal structure of human PD-L1 with monoclonal antibody avelumab
Components
  • Programmed cell death 1 ligand 1
  • avelumab H chain
  • avelumab L chain
KeywordsIMMUNE SYSTEM / PD-L1 / avelumab / monoclonal antibody / tumor immunothepapy
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 ...: / 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 / Immunoglobulins / 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: 3.206 Å
AuthorsLiu, K. / Tan, S. / Chai, Y. / Chen, D. / Song, H. / Zhang, C.W.-H. / Shi, Y. / Liu, J. / Tan, W. / Lyu, J. ...Liu, K. / Tan, S. / Chai, Y. / Chen, D. / Song, H. / Zhang, C.W.-H. / Shi, Y. / Liu, J. / Tan, W. / Lyu, J. / Gao, S. / Yan, J. / Qi, J. / Gao, G.F.
Funding support China, 2items
OrganizationGrant numberCountry
the Ministry of Science and Technology of China2013CB531502, 2014CB542503 China
Grand S&T project of China Health and Family Planning Commission013ZX10004608-002, 2016ZX10004201-009 China
CitationJournal: Cell Res. / Year: 2017
Title: Structural basis of anti-PD-L1 monoclonal antibody avelumab for tumor therapy.
Authors: Liu, K. / Tan, S. / Chai, Y. / Chen, D. / Song, H. / Zhang, C.W. / Shi, Y. / Liu, J. / Tan, W. / Lyu, J. / Gao, S. / Yan, J. / Qi, J. / Gao, G.F.
History
DepositionAug 11, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Nov 8, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: avelumab H chain
L: avelumab L chain
A: Programmed cell death 1 ligand 1


Theoretical massNumber of molelcules
Total (without water)49,8283
Polymers49,8283
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-17 kcal/mol
Surface area20600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.870, 98.151, 62.036
Angle α, β, γ (deg.)90.00, 108.43, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody avelumab H chain


Mass: 13047.749 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)
#2: Antibody avelumab L chain


Mass: 11484.462 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: Protein Programmed cell death 1 ligand 1 / human PD-L1


Mass: 25295.676 Da / Num. of mol.: 1 / Fragment: UNP residues 18-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDL1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NZQ7
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: 3.5 Å3/Da / Density % sol: 64.89 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 7.5
Details: 0.2 M magnesium chloride hexahydrate, 0.1 M HEPES-Na, 30%(v/v) iso-Propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 11319 / % possible obs: 99.3 % / Redundancy: 6.6 % / Net I/σ(I): 10.5
Reflection shellResolution: 3.2→3.31 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BIK and 4NKI

3bik

4nki


Resolution: 3.206→42.173 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.61
RfactorNum. reflection% reflection
Rfree0.2384 498 5.11 %
Rwork0.2035 --
obs0.2053 9745 85.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.206→42.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3398 0 0 0 3398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113469
X-RAY DIFFRACTIONf_angle_d1.2784714
X-RAY DIFFRACTIONf_dihedral_angle_d17.8121260
X-RAY DIFFRACTIONf_chiral_restr0.074540
X-RAY DIFFRACTIONf_plane_restr0.009598
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2062-3.52870.2951750.25731542X-RAY DIFFRACTION57
3.5287-4.03890.2641270.24292303X-RAY DIFFRACTION86
4.0389-5.08730.2311560.18292674X-RAY DIFFRACTION99
5.0873-42.17670.21791400.18822728X-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)
17.1473-2.64061.56115.04892.10872.10750.0347-1.38631.28011.2381-0.0662-0.13360.34690.2068-0.350.6732-0.09360.08741.0668-0.35630.570424.8552-63.838736.9333
21.92341.81330.88522.1360.48480.6978-0.48860.0621.2633-0.42370.3339-0.44080.14140.4643-0.05390.88420.38930.31140.66880.14571.72629.1713-48.187219.5086
35.5422-0.5125-0.75593.23251.09952.79590.6823-0.64352.0960.6849-0.3937-0.7472-1.03430.40290.14430.4559-0.02550.16290.7367-0.38151.488331.3097-59.536228.7253
41.9331-0.77521.97183.3265-4.48156.52060.4759-0.6240.76381.225-0.58430.39130.0674-0.1379-0.20470.5088-0.13760.00240.8148-0.15740.237328.9008-75.551434.0292
54.8457-1.76465.06412.6391-3.17319.23940.1036-1.53412.21410.1110.01770.5913-0.678-1.2160.04980.41760.06290.09380.6282-0.05820.990419.3285-61.769522.2881
65.10250.6098-6.29033.45240.57228.27090.24030.45771.1588-0.59520.48131.2813-0.206-0.6408-0.28420.4719-0.1196-0.20.35360.08370.493222.797-67.308219.6888
74.8636-1.0422-2.88812.49320.57682.4609-0.1862-0.06211.3656-0.85330.41230.07020.3413-0.6757-0.23620.3778-0.0903-0.01880.39360.12820.411830.06-71.432517.9397
84.82452.2458-2.95258.6816-0.2322.99390.4298-0.0232.2784-0.32010.18540.1359-0.09230.089-0.43210.28540.0210.11690.5586-0.10290.835233.6243-64.417723.8958
91.88720.9865-3.63968.7991-2.64527.08780.811.07520.9871-0.60690.68691.3486-0.3491-1.7905-0.62710.86720.3416-0.10710.85730.25041.019624.6022-54.205814.0083
105.1406-4.30724.8436.5789-0.54678.69910.211-0.6591-0.0120.99960.43490.3459-0.4844-1.6157-0.81670.34320.2865-0.04660.82780.00160.414221.8623-63.748327.4216
110.65430.1146-2.42083.5195-0.19679.3633-0.4137-0.9269-0.05381.11410.55270.2612-0.102-0.29140.20930.6251-0.22760.14651.20190.0362-0.014820.0888-77.039527.8864
125.65880.7337-0.72671.33552.00863.6630.97250.46390.25330.7909-0.36210.4161-0.3296-0.4365-0.65120.49960.08430.11810.88230.0291.172821.1531-58.88128.2495
133.5417-1.1863-1.65483.49721.36851.74721.2589-0.14261.0433-0.1289-0.24150.905-0.5833-1.2483-0.33010.30790.22020.17971.4650.31011.1941-1.3979-65.445624.4379
141.3495-0.8265-0.60893.36081.42452.2281-0.0540.67690.3218-0.5016-0.21121.0917-0.5606-0.5975-0.16890.4143-0.0402-0.14110.97640.28010.70696.4683-76.370617.7326
157.52475.24814.21855.71141.54226.27780.6054-1.38642.3596-0.0441-0.21090.2221-1.0139-0.5183-0.26090.4687-0.10310.20710.9302-0.30120.951410.1676-67.303330.7795
164.3633-2.7833-2.58053.6895-0.594.2037-0.2878-1.59140.70060.69760.83290.79640.73430.48110.39380.5739-0.41450.30021.1705-0.10810.58036.767-77.746834.1375
177.7875-1.6084-4.5634.4445-0.67134.78260.4745-0.63790.79280.41520.02780.0654-0.3943-1.1723-0.22380.3995-0.03760.03991.4594-0.02610.43010.2147-71.383929.0617
186.19590.0561-2.7444.7285-1.97246.24410.5986-0.38431.7673-0.2073-0.00070.43370.051-1.5579-0.28850.2029-0.0912-0.03171.0111-0.05460.826210.3947-70.066522.2977
197.23430.7672-3.47324.1824-1.00581.7651-0.2508-0.0374-0.3964-0.7961-0.1482-0.838-0.083-1.0141-0.1660.61580-0.17540.40160.15260.275917.0604-73.75416.8143
200.05050.07480.16150.10120.23330.5139-0.35150.58060.57980.2129-0.6823-0.5709-0.2241-0.19060.43140.6862-0.01280.27670.76610.31571.34421.7772-61.375625.8295
214.08012.52680.64531.53860.42570.11610.2143-0.0166-1.1416-0.26670.18290.2680.3909-0.0907-0.11790.6244-0.2127-0.05120.40320.04870.787828.0754-94.980712.6471
229.35622.78720.69922.84624.42969.211-0.0410.1873-0.8760.36550.809-0.89170.17450.84060.05360.3489-0.1148-0.16630.290.07461.085646.2881-87.988520.0038
231.5797-0.33312.42872.18960.27754.0590.019-1.542-1.5630.1487-0.3258-0.08650.6905-1.0101-1.20970.5335-0.3016-0.03930.70170.55710.752428.1704-88.984226.6076
241.5793-0.20581.27360.7405-0.10653.10190.3648-0.6921-1.12930.54850.1552-0.62540.5072-0.78910.14050.5486-0.4413-0.12690.34970.21570.782428.8493-92.195618.9372
257.92798.06750.49518.40480.68590.16990.2780.14450.329-0.78340.05340.12160.1562-0.17080.22320.5253-0.2099-0.09840.3119-0.0890.245525.4964-88.189412.0712
266.70684.82011.09754.66890.07381.44050.1854-0.32220.16370.0711-0.3263-0.0703-0.17430.34020.09050.3121-0.10490.04070.3948-0.00710.2476-4.5721-112.949513.3682
277.09920.91270.50774.8735-1.41771.13050.19-0.03010.92990.2724-0.2360.4678-0.5898-0.1427-0.05370.4469-0.16320.07670.4037-0.04630.4445-4.7834-108.366411.1371
283.7550.38150.16054.16251.19432.2767-0.13130.6376-0.3498-0.1782-0.03580.7739-0.1230.3186-0.21150.6681-0.1268-0.2290.4347-0.1460.2567-3.3558-118.15547.6601
293.69435.0868-3.91627.8949-5.07846.0888-0.01340.5232-0.76810.2322-0.5828-0.9839-0.31680.68340.06740.422-0.24480.02760.658-0.04540.5058-0.8991-116.433311.8878
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 7 )
2X-RAY DIFFRACTION2chain 'H' and (resid 8 through 16 )
3X-RAY DIFFRACTION3chain 'H' and (resid 17 through 25 )
4X-RAY DIFFRACTION4chain 'H' and (resid 26 through 33 )
5X-RAY DIFFRACTION5chain 'H' and (resid 34 through 44 )
6X-RAY DIFFRACTION6chain 'H' and (resid 45 through 51 )
7X-RAY DIFFRACTION7chain 'H' and (resid 52 through 64 )
8X-RAY DIFFRACTION8chain 'H' and (resid 65 through 84 )
9X-RAY DIFFRACTION9chain 'H' and (resid 85 through 92 )
10X-RAY DIFFRACTION10chain 'H' and (resid 93 through 98 )
11X-RAY DIFFRACTION11chain 'H' and (resid 99 through 108 )
12X-RAY DIFFRACTION12chain 'H' and (resid 109 through 118 )
13X-RAY DIFFRACTION13chain 'L' and (resid 2 through 17 )
14X-RAY DIFFRACTION14chain 'L' and (resid 18 through 34 )
15X-RAY DIFFRACTION15chain 'L' and (resid 35 through 50 )
16X-RAY DIFFRACTION16chain 'L' and (resid 51 through 63 )
17X-RAY DIFFRACTION17chain 'L' and (resid 64 through 86 )
18X-RAY DIFFRACTION18chain 'L' and (resid 87 through 94 )
19X-RAY DIFFRACTION19chain 'L' and (resid 95 through 101 )
20X-RAY DIFFRACTION20chain 'L' and (resid 102 through 109 )
21X-RAY DIFFRACTION21chain 'A' and (resid 18 through 41 )
22X-RAY DIFFRACTION22chain 'A' and (resid 42 through 53 )
23X-RAY DIFFRACTION23chain 'A' and (resid 54 through 90 )
24X-RAY DIFFRACTION24chain 'A' and (resid 91 through 119 )
25X-RAY DIFFRACTION25chain 'A' and (resid 120 through 131 )
26X-RAY DIFFRACTION26chain 'A' and (resid 132 through 169 )
27X-RAY DIFFRACTION27chain 'A' and (resid 170 through 200 )
28X-RAY DIFFRACTION28chain 'A' and (resid 201 through 213 )
29X-RAY DIFFRACTION29chain 'A' and (resid 214 through 233 )

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