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- PDB-7bxa: Crystal structure of PD-1 in complex with tislelizumab Fab -

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Basic information

Entry
Database: PDB / ID: 7bxa
TitleCrystal structure of PD-1 in complex with tislelizumab Fab
Components
  • Programmed cell death protein 1
  • heavy chain
  • light chain
KeywordsIMMUNE SYSTEM / PD-1 / tislelizumab / immune checkpoint / antibody
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / B cell apoptotic process / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / Co-inhibition by PD-1 ...negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / negative regulation of T cell mediated immune response to tumor cell / negative regulation of T cell activation / B cell apoptotic process / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / Co-inhibition by PD-1 / regulation of immune response / signaling receptor activity / adaptive immune response / Potential therapeutics for SARS / external side of plasma membrane / apoptotic process / plasma membrane
Similarity search - Function
Programmed cell death protein 1 / Immunoglobulin V-Type / 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 ...Programmed cell death protein 1 / Immunoglobulin V-Type / 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 protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsHeo, Y.S. / Lee, S.H. / Lim, H. / Lee, H.T. / Kim, Y.J. / Park, E.B.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Crystal structure of PD-1 in complex with an antibody-drug tislelizumab used in tumor immune checkpoint therapy.
Authors: Lee, S.H. / Lee, H.T. / Lim, H. / Kim, Y. / Park, U.B. / Heo, Y.S.
History
DepositionApr 18, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 1.2Nov 13, 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
A: Programmed cell death protein 1
B: heavy chain
C: light chain
P: Programmed cell death protein 1
H: heavy chain
L: light chain


Theoretical massNumber of molelcules
Total (without water)126,0926
Polymers126,0926
Non-polymers00
Water00
1
A: Programmed cell death protein 1
B: heavy chain
C: light chain


Theoretical massNumber of molelcules
Total (without water)63,0463
Polymers63,0463
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-29 kcal/mol
Surface area23650 Å2
MethodPISA
2
P: Programmed cell death protein 1
H: heavy chain
L: light chain


Theoretical massNumber of molelcules
Total (without water)63,0463
Polymers63,0463
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint-29 kcal/mol
Surface area23880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.615, 73.081, 276.388
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Programmed cell death protein 1 / hPD-1


Mass: 14855.473 Da / Num. of mol.: 2 / Mutation: C93S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15116
#2: Antibody heavy chain


Mass: 24641.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody light chain


Mass: 23549.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
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: 2.59 Å3/Da / Density % sol: 52.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 30% w/v polyethylene glycol 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.32→50 Å / Num. obs: 19822 / % possible obs: 99.3 % / Redundancy: 4.5 % / Biso Wilson estimate: 47.94 Å2 / CC1/2: 0.947 / Net I/σ(I): 2
Reflection shellResolution: 3.32→3.41 Å / Num. unique obs: 985 / CC1/2: 0.788

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KY1

4ky1


Resolution: 3.32→48.407 Å / SU ML: 0.55 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 29.67
RfactorNum. reflection% reflection
Rfree0.2986 1014 5.12 %
Rwork0.2427 --
obs0.2456 19790 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.43 Å2 / Biso mean: 35.2836 Å2 / Biso min: 16.05 Å2
Refinement stepCycle: final / Resolution: 3.32→48.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8095 0 0 0 8095
Num. residues----1053
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.3202-3.49510.39281490.3037239891
3.4951-3.71410.36121400.27672679100
3.7141-4.00070.32441460.25992686100
4.0007-4.40310.27611490.22532685100
4.4031-5.03960.23191310.206271699
5.0396-6.34710.27051330.2261274499
6.3471-48.40.29241660.2427286899
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)
10.64551.75010.72545.54281.15691.616-0.1038-0.7849-0.12390.8485-0.1346-0.46130.2287-0.2972-0.02390.36060.15830.05560.43160.16250.1850.006-33.069339.9107
28.19853.20191.51481.6673-0.60883.76580.36110.9234-0.9350.4067-0.3003-1.11580.53380.75880.02160.67640.1679-0.12340.28690.09410.40669.1769-41.264329.1687
35.4767-0.04161.70814.7497-3.10921.99910.0003-0.7803-0.74021.1723-0.02270.799-0.1577-1.1729-0.28910.4183-0.16660.09810.3045-0.00220.3975-12.0352-34.760941.1623
43.6953-3.068-0.43082.55520.16531.9995-0.0759-0.2819-0.9788-0.0623-0.61870.1031-0.06630.5718-0.7160.51990.0398-0.0995-0.3180.3784-0.054-4.3896-31.403529.9153
55.989-2.2519-2.64314.22951.56135.3296-0.3525-0.846-0.55750.6367-0.7608-0.60470.07070.77850.42810.8476-0.2684-0.36110.40840.28410.71144.3436-20.839625.219
62.4645-1.3568-0.27331.17720.95811.55440.5150.05530.5254-0.3645-0.3433-0.1174-0.06660.1585-0.10120.24290.00960.14710.4234-0.02940.1033-5.1591-32.26525.9869
74.31210.4767-2.58150.1139-0.15813.8156-0.02290.1434-1.4754-0.608-0.38610.47160.5654-0.04530.02520.5108-0.0306-0.24080.2760.0170.6078-7.4228-40.032125.0798
88.71521.3991-1.00624.949-0.13454.5881-1.14280.1752-0.91190.19150.17640.02230.62170.27640.69290.39110.0137-0.03380.21290.02070.275-4.4415-42.525236.388
90.50280.54640.46071.4892-0.03330.6687-0.16860.2887-0.0867-0.67140.4117-0.5605-0.0942-0.2632-0.0660.4841-0.03070.58720.40410.04420.23323.6115-34.320226.0719
103.00730.29590.79510.89940.26210.2589-0.07090.32380.70250.20010.11490.0614-0.41110.12050.11850.1691-0.27010.16490.13250.01651.0435-5.858-26.347636.9544
112.72041.7075-1.00496.81842.76799.4962-0.73910.1373-0.16920.21970.2642-0.97531.14281.0783-0.05660.69580.11720.02840.31210.06680.234212.719-34.955329.3698
123.4856-1.74030.34931.7562-0.87990.5373-0.3471-0.07550.5310.01030.0765-0.28270.0163-0.0360.14540.266-0.0096-0.01350.1134-0.03510.1537-6.7997-16.41393.1364
131.5093-1.26221.08041.02440.07744.25390.18640.1283-0.30250.02880.23050.08840.14950.2793-0.23140.3203-0.02370.10750.20120.03830.3025-8.0338-21.66053.9942
141.90891.7419-0.32662.4020.50021.12370.094-0.12850.08740.1490.0186-0.12-0.1788-0.2096-0.07590.15740.0519-0.02640.2134-0.00240.2502-8.98497.4272.2217
152.3477-2.0245-1.09675.72350.81120.50270.19050.01891.22650.67940.016-0.94980.0326-0.2027-0.20230.24220.07820.09690.5702-0.09030.2722-1.891415.946211.4331
163.3322-0.77491.28955.28991.32424.0172-0.19260.25460.23610.21750.5171-0.34030.02940.4589-0.26310.17050.1164-0.04130.2593-0.0290.29190.00111.2780.749
171.9403-0.10880.45174.33841.00012.5157-0.0785-0.06260.13430.23130.16790.28320.1201-0.1723-0.08750.2515-0.00430.05940.26430.03050.1866-15.0096-15.111423.3569
181.39060.581-1.14423.9856-1.50783.85060.0871-0.01570.2063-0.14020.03480.0024-0.08390.055-0.09360.16130.0429-0.04750.1821-0.02420.262-17.734519.335210.3052
194.25820.6685-1.73984.90151.43915.96220.17690.30870.1932-0.9680.0670.1917-1.34470.6607-0.39950.4694-0.16630.02370.4606-0.06180.39715.6493-15.274227.5566
203.3419-0.29161.01814.72591.25661.66960.014-0.18430.1231-0.83450.007-0.13040.14560.7755-0.15660.2567-0.0074-0.09960.5583-0.0740.267418.4134-15.334935.104
218.15172.3544-3.93065.4188-2.07123.9487-0.12531.17010.0852-0.19920.3761.09020.1862-0.8652-0.14640.71610.1285-0.17310.4025-0.01690.253310.0284-10.331940.7139
220.45220.0628-0.891.08-0.58041.924-0.2272-0.44740.67340.4792-0.58210.1925-0.0865-0.2420.24070.5445-0.1165-0.19940.5662-0.23660.844523.0499-7.870445.6797
231.8558-0.02970.07882.64610.56650.2629-0.181-0.2360.56030.32030.35630.01780.60050.36770.14660.48950.1509-0.06530.7173-0.14980.526926.8743-14.747935.064
243.865-0.1441.19475.2244-1.07442.5625-0.1427-0.8819-0.53370.85210.137-0.6008-0.5761-0.94970.11820.3886-0.0082-0.03350.5184-0.01780.304516.1513-17.880640.6648
252.7942-0.62740.4032.5697-1.29212.7034-0.17020.2332-0.18450.14810.21180.7452-0.3239-0.392-0.10590.25220.07390.01390.38550.00450.372610.3428-17.701634.7843
261.67690.6196-0.43944.11910.93953.36650.082-0.512-0.0890.2274-0.12130.14660.0660.43960.04920.194-0.0112-0.03280.39460.02390.18025.35961.81562.2314
271.2646-1.1282-0.25361.89471.11261.3138-0.1261-0.1883-0.0570.17510.125-0.4238-0.134-0.38750.15690.273-0.0227-0.0060.39710.04730.25854.55481.402465.6052
282.616-1.3895-0.63291.62910.61671.30210.2251-0.1211-0.20480.1226-0.08410.04010.13670.1221-0.09750.3601-0.04860.00050.27090.03780.291-6.94347.80459.5938
293.1691-0.4380.97572.47550.87873.73520.0642-0.311-0.79170.1750.27750.38120.2805-0.6759-0.24030.2961-0.0806-0.04440.41810.06890.2791-22.561713.535959.6827
302.4903-0.75541.06931.14340.49421.8434-0.1428-0.17550.1699-0.84620.1115-0.3659-0.1154-0.50060.06480.4801-0.17080.00730.31560.05590.36054.115315.907439.1609
312.4476-0.7014-0.77053.08270.07752.073-0.21010.0487-0.225-0.2142-0.1042-0.1498-0.03080.28170.36350.3502-0.0799-0.00180.26370.05290.19823.99686.065840.3689
322.1579-0.1136-1.59410.13380.18281.255-0.21070.7049-0.13410.20820.035-0.1988-0.58520.46360.15020.3281-0.0066-0.07380.4084-0.11450.27692.876313.251944.2959
332.7508-0.8554-0.62782.2827-0.83652.6217-0.1089-0.26650.10290.34790.30110.17-0.0265-0.5043-0.21030.2991-0.03040.04690.41070.05510.282-24.140529.436354.2928
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 40 )A33 - 40
2X-RAY DIFFRACTION2chain 'A' and (resid 41 through 53 )A41 - 53
3X-RAY DIFFRACTION3chain 'A' and (resid 54 through 62 )A54 - 62
4X-RAY DIFFRACTION4chain 'A' and (resid 63 through 70 )A63 - 70
5X-RAY DIFFRACTION5chain 'A' and (resid 71 through 75 )A71 - 75
6X-RAY DIFFRACTION6chain 'A' and (resid 76 through 82 )A76 - 82
7X-RAY DIFFRACTION7chain 'A' and (resid 83 through 99 )A83 - 99
8X-RAY DIFFRACTION8chain 'A' and (resid 100 through 110 )A100 - 110
9X-RAY DIFFRACTION9chain 'A' and (resid 111 through 127 )A111 - 127
10X-RAY DIFFRACTION10chain 'A' and (resid 128 through 139 )A128 - 139
11X-RAY DIFFRACTION11chain 'A' and (resid 140 through 145 )A140 - 145
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 51 )B1 - 51
13X-RAY DIFFRACTION13chain 'B' and (resid 52 through 111 )B52 - 111
14X-RAY DIFFRACTION14chain 'B' and (resid 112 through 180 )B112 - 180
15X-RAY DIFFRACTION15chain 'B' and (resid 181 through 199 )B181 - 199
16X-RAY DIFFRACTION16chain 'B' and (resid 200 through 220 )B200 - 220
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 101 )C1 - 101
18X-RAY DIFFRACTION18chain 'C' and (resid 102 through 213 )C102 - 213
19X-RAY DIFFRACTION19chain 'P' and (resid 33 through 40 )P33 - 40
20X-RAY DIFFRACTION20chain 'P' and (resid 41 through 70 )P41 - 70
21X-RAY DIFFRACTION21chain 'P' and (resid 71 through 82 )P71 - 82
22X-RAY DIFFRACTION22chain 'P' and (resid 83 through 94 )P83 - 94
23X-RAY DIFFRACTION23chain 'P' and (resid 95 through 104 )P95 - 104
24X-RAY DIFFRACTION24chain 'P' and (resid 105 through 126 )P105 - 126
25X-RAY DIFFRACTION25chain 'P' and (resid 133 through 146 )P133 - 146
26X-RAY DIFFRACTION26chain 'H' and (resid 1 through 66 )H1 - 66
27X-RAY DIFFRACTION27chain 'H' and (resid 67 through 98 )H67 - 98
28X-RAY DIFFRACTION28chain 'H' and (resid 99 through 141 )H99 - 141
29X-RAY DIFFRACTION29chain 'H' and (resid 142 through 219 )H142 - 219
30X-RAY DIFFRACTION30chain 'L' and (resid 1 through 18 )L1 - 18
31X-RAY DIFFRACTION31chain 'L' and (resid 19 through 90 )L19 - 90
32X-RAY DIFFRACTION32chain 'L' and (resid 91 through 110 )L91 - 110
33X-RAY DIFFRACTION33chain 'L' and (resid 111 through 211 )L111 - 211

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