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- PDB-7e9b: Structural basis of HLX10 PD-1 receptor recognition, a promising ... -

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Basic information

Entry
Database: PDB / ID: 7e9b
TitleStructural basis of HLX10 PD-1 receptor recognition, a promising anti-PD-1 antibody clinical candidate for cancer immunotherapy
Components
  • Programmed cell death protein 1
  • heavy chain of Fab fragment of HLX10
  • light chain of Fab fragment of HLX10
KeywordsIMMUNE SYSTEM / Antibody / mAb / PD-1 / PD-L-1 / Cancer / T-cell / Immunotherapy / ICI
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 / positive regulation of T cell apoptotic process / B 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 / positive regulation of T cell apoptotic process / B 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 / Potential therapeutics for SARS / adaptive immune response / 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 / molecular replacement / Resolution: 1.78 Å
AuthorsFan, S.L. / Jiang, W.D.
CitationJournal: Plos One / Year: 2021
Title: Structural basis of HLX10 PD-1 receptor recognition, a promising anti-PD-1 antibody clinical candidate for cancer immunotherapy.
Authors: Issafras, H. / Fan, S. / Tseng, C.L. / Cheng, Y. / Lin, P. / Xiao, L. / Huang, Y.J. / Tu, C.H. / Hsiao, Y.C. / Li, M. / Chen, Y.H. / Ho, C.H. / Li, O. / Wang, Y. / Chen, S. / Ji, Z. / Zhang, ...Authors: Issafras, H. / Fan, S. / Tseng, C.L. / Cheng, Y. / Lin, P. / Xiao, L. / Huang, Y.J. / Tu, C.H. / Hsiao, Y.C. / Li, M. / Chen, Y.H. / Ho, C.H. / Li, O. / Wang, Y. / Chen, S. / Ji, Z. / Zhang, E. / Mao, Y.T. / Liu, E. / Yang, S. / Jiang, W.
History
DepositionMar 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author / database_2
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.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 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: heavy chain of Fab fragment of HLX10
L: light chain of Fab fragment of HLX10
C: Programmed cell death protein 1


Theoretical massNumber of molelcules
Total (without water)59,2063
Polymers59,2063
Non-polymers00
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-34 kcal/mol
Surface area23970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.985, 45.014, 80.890
Angle α, β, γ (deg.)93.600, 102.160, 97.340
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody heavy chain of Fab fragment of HLX10


Mass: 22834.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody light chain of Fab fragment of HLX10


Mass: 23455.074 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Programmed cell death protein 1 / Protein PD-1 / hPD-1


Mass: 12916.412 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: Q15116
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 46.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 7.5 containing 23% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9751 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9751 Å / Relative weight: 1
ReflectionResolution: 1.779→31.414 Å / Num. obs: 48174 / % possible obs: 94.63 % / Redundancy: 7.1 % / CC1/2: 0.989 / Net I/σ(I): 28.9
Reflection shellResolution: 1.779→1.84 Å / Num. unique obs: 48174 / CC1/2: 0.989

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.18_3855refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZQK

4zqk


Resolution: 1.78→31.41 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 22.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2098 1999 4.15 %
Rwork0.1699 46175 -
obs0.1716 48174 94.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.89 Å2 / Biso mean: 32.7236 Å2 / Biso min: 14.05 Å2
Refinement stepCycle: final / Resolution: 1.78→31.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4099 0 0 486 4585
Biso mean---41.03 -
Num. residues----536
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.78-1.820.30961330.22873074320790
1.82-1.870.2211470.20093421356896
1.87-1.930.22321430.18423311345496
1.93-1.990.23281460.17293347349396
1.99-2.060.23981410.17573278341993
2.06-2.140.21841460.17613351349797
2.14-2.240.22171440.17693329347396
2.24-2.360.21081440.1763349349396
2.36-2.510.24131390.18133209334892
2.51-2.70.24721450.18073357350297
2.7-2.970.2421470.18383351349896
2.97-3.40.19931380.16983215335392
3.4-4.280.17921460.15193367351396
4.28-31.410.18641400.15683216335692
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)
11.20750.68990.60653.38041.17962.1077-0.05350.08230.1496-0.1320.0057-0.0611-0.15260.0540.05940.14610.01350.02180.1710.0440.171-12.209712.9926-25.8674
22.2725-0.44851.10531.02420.10082.0664-0.0841-0.14120.03350.17820.0051-0.0976-0.00010.05830.05510.232-0.0127-0.00080.18930.03930.20974.167419.30521.1502
35.8987-1.51140.98155.5599-2.75624.6410.0603-0.14480.3610.2054-0.3239-0.92650.09060.550.27190.28360.0207-0.04180.2292-0.01750.344911.6216.95774.9688
48.696-5.76494.88697.4003-3.32294.43770.041-0.1827-0.07770.34040.01050.24810.036-0.5038-0.08570.2589-0.01530.06480.3271-0.03440.1956-21.1878-0.4636-4.4121
50.49140.0070.4472.1162-0.61032.56460.0196-0.0302-0.01440.1187-0.01780.07040.0456-0.2025-0.00050.1198-0.00110.0310.19850.01170.1796-20.1464-2.3948-13.8483
62.87960.48374.67310.16851.09328.99660.0994-0.10150.00770.3095-0.12740.1607-0.06880.2935-0.09490.3329-0.05310.02030.22890.02170.186-10.4161-0.72136.6746
71.94971.6404-0.63422.1266-1.19712.68330.00680.0669-0.05670.06370.046-0.6651-0.03980.4445-0.15110.3757-0.0141-0.0150.3153-0.04940.30254.432725.208513.1476
80.96321.1013-0.47747.77230.39190.9412-0.29090.0328-0.026-0.06330.2480.2276-0.0031-0.1856-00.44-0.0294-0.08430.27460.03530.1986-7.159615.148512.726
90.868-0.25170.10465.43281.15214.08320.0459-0.03860.0217-0.35920.0457-0.22070.0757-0.15120.00670.1689-0.0288-0.05920.22460.03190.1726-7.01913.46978.8288
101.41061.7923-0.25037.32320.17263.75130.1327-0.05250.12620.1453-0.08020.2043-0.2739-0.1784-0.0760.31340.019-0.02410.2592-0.02390.1929-5.281422.806218.1043
114.0602-0.1223-0.15552.93242.39864.25360.167-0.35110.1840.0601-0.2270.32260.1283-0.24680.05550.2262-0.015-0.00430.25340.03340.1927-27.736-12.9152-39.2596
121.91262.57561.02556.37765.32615.6214-0.041-0.0604-0.19240.0340.3069-0.37240.25790.2098-0.27810.25250.02570.04910.23550.030.2393-19.0277-10.2177-40.9943
131.67290.4850.62825.13932.49773.22940.0151-0.1164-0.26440.2127-0.15830.38560.395-0.18010.1690.2075-0.01980.00580.2360.05490.209-28.2641-16.5747-37.7879
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 112 )H1 - 112
2X-RAY DIFFRACTION2chain 'H' and (resid 113 through 178 )H113 - 178
3X-RAY DIFFRACTION3chain 'H' and (resid 179 through 215 )H179 - 215
4X-RAY DIFFRACTION4chain 'L' and (resid 1 through 18 )L1 - 18
5X-RAY DIFFRACTION5chain 'L' and (resid 19 through 101 )L19 - 101
6X-RAY DIFFRACTION6chain 'L' and (resid 102 through 113 )L102 - 113
7X-RAY DIFFRACTION7chain 'L' and (resid 114 through 128 )L114 - 128
8X-RAY DIFFRACTION8chain 'L' and (resid 129 through 150 )L129 - 150
9X-RAY DIFFRACTION9chain 'L' and (resid 151 through 174 )L151 - 174
10X-RAY DIFFRACTION10chain 'L' and (resid 175 through 212 )L175 - 212
11X-RAY DIFFRACTION11chain 'C' and (resid 32 through 82 )C32 - 82
12X-RAY DIFFRACTION12chain 'C' and (resid 83 through 110 )C83 - 110
13X-RAY DIFFRACTION13chain 'C' and (resid 111 through 146 )C111 - 146

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