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- PDB-6j15: Complex structure of GY-5 Fab and PD-1 -

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Basic information

Entry
Database: PDB / ID: 6j15
TitleComplex structure of GY-5 Fab and PD-1
Components
  • GY-5 heavy chain Fab
  • GY-5 light chain Fab
  • Programmed cell death protein 1
KeywordsIMMUNE SYSTEM / Tumor immunotherapy / complex structure / FG loop
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / B cell apoptotic process / negative regulation of immune response / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / PD-1 signaling / regulation of immune response / Potential therapeutics for SARS ...negative regulation of tolerance induction / regulatory T cell apoptotic process / B cell apoptotic process / negative regulation of immune response / positive regulation of T cell apoptotic process / negative regulation of B cell apoptotic process / humoral immune response / PD-1 signaling / regulation of immune response / 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 / Immunoglobulins ...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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Programmed cell death protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsChen, D. / Tan, S. / Zhang, H. / Wang, H. / Chai, Y. / Qi, J. / Yan, J. / Gao, G.F.
CitationJournal: Iscience / Year: 2019
Title: The FG Loop of PD-1 Serves as a "Hotspot" for Therapeutic Monoclonal Antibodies in Tumor Immune Checkpoint Therapy.
Authors: Chen, D. / Tan, S. / Zhang, H. / Wang, H. / He, W. / Shi, R. / Tong, Z. / Zhu, J. / Cheng, H. / Gao, S. / Chai, Y. / Qi, J. / Xiao, M. / Yan, J. / Gao, G.F.
History
DepositionDec 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Programmed cell death protein 1
D: Programmed cell death protein 1
H: GY-5 heavy chain Fab
L: GY-5 light chain Fab
A: GY-5 heavy chain Fab
B: GY-5 light chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,29610
Polymers122,5506
Non-polymers1,7464
Water0
1
C: Programmed cell death protein 1
A: GY-5 heavy chain Fab
B: GY-5 light chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2886
Polymers61,2753
Non-polymers1,0133
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Programmed cell death protein 1
H: GY-5 heavy chain Fab
L: GY-5 light chain Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0084
Polymers61,2753
Non-polymers7331
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.595, 64.347, 151.481
Angle α, β, γ (deg.)90.00, 98.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules CD

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


Mass: 13487.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q15116

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Antibody , 2 types, 4 molecules HALB

#2: Antibody GY-5 heavy chain Fab


Mass: 23941.707 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody GY-5 light chain Fab


Mass: 23846.482 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Sugars , 3 types, 4 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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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: 2.51 Å3/Da / Density % sol: 50.9 %
Crystal growTemperature: 277 K / Method: evaporation
Details: 0.1 M citrate (pH 5.0), 20% w/v polyethylene glycol 6000, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 29, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 33831 / % possible obs: 92.2 % / Redundancy: 6.2 % / Net I/σ(I): 3.17
Reflection shellResolution: 2.6→2.69 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RRQ, 3EYQ

3rrq

3eyq


Resolution: 2.6→41.624 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.37
RfactorNum. reflection% reflection
Rfree0.2767 1698 5.02 %
Rwork0.2116 --
obs0.2148 33831 92.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.6→41.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8342 0 0 0 8342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018560
X-RAY DIFFRACTIONf_angle_d1.24811660
X-RAY DIFFRACTIONf_dihedral_angle_d19.983121
X-RAY DIFFRACTIONf_chiral_restr0.071329
X-RAY DIFFRACTIONf_plane_restr0.0071465
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5955-2.67180.3673920.27291655X-RAY DIFFRACTION57
2.6718-2.7580.31811340.25752057X-RAY DIFFRACTION73
2.758-2.85660.33831160.27122434X-RAY DIFFRACTION84
2.8566-2.97090.351430.27212787X-RAY DIFFRACTION96
2.9709-3.10610.36361370.26822873X-RAY DIFFRACTION99
3.1061-3.26980.31151420.24642865X-RAY DIFFRACTION99
3.2698-3.47460.35851520.23042868X-RAY DIFFRACTION99
3.4746-3.74270.27681480.20952891X-RAY DIFFRACTION100
3.7427-4.1190.26771520.19442891X-RAY DIFFRACTION100
4.119-4.71430.22911510.15612918X-RAY DIFFRACTION100
4.7143-5.93680.22981530.16892923X-RAY DIFFRACTION100
5.9368-41.62940.22171780.21342971X-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)
10.18570.30530.61851.87110.98292.0863-0.0859-0.5069-0.2664-0.30410.1859-0.0457-0.51390.1062-0.16560.1104-0.13910.05280.42370.03460.326259.54212.601241.1234
27.40463.0816-3.50414.4827-1.12634.40050.0967-0.3516-0.3935-0.41450.1610.3562-0.2948-0.9033-0.17250.18160.0372-0.12130.4450.01560.281437.34814.265133.0474
33.86320.90131.83680.98110.67983.91470.0945-0.0009-0.2149-0.04060.02830.0189-0.43380.0103-0.10840.1738-0.05620.07160.2042-0.01220.218951.276413.204848.1166
40.93430.073-0.31542.1429-2.8284.4275-0.5038-0.41740.51950.0883-0.0966-0.0312-1.1073-0.19380.52990.51-0.0136-0.15180.358-0.21140.524945.894322.857248.7082
53.2417-2.23972.61481.8083-1.61382.18780.3333-1.1651-0.79770.4610.59540.89250.0806-1.0228-0.23840.23530.01310.09640.57880.22810.426540.567210.542449.6284
61.26121.51640.88593.14730.44346.50440.160.05140.03420.01150.2267-0.0432-0.2072-0.227-0.32240.1603-0.04030.06780.2934-0.03520.267744.71813.256443.2873
75.31651.40190.95422.7212-0.24675.0923-0.17321.01670.12080.3080.28230.7959-1.06280.87480.23030.33-0.17820.01720.32540.04240.337759.176418.006150.5911
86.2143.8996-1.39195.95080.99691.9632-0.30420.45381.2144-0.9798-0.02860.6084-0.536-1.4903-0.24840.17690.11950.00290.5274-0.02650.274737.906419.368731.6631
93.36820.06922.74540.35890.2622.34670.05320.35830.5187-0.3104-0.54470.2526-0.00740.56440.05780.20450.054-0.01790.4523-0.03420.377854.217812.752630.576
105.4003-0.5781-0.85143.62160.4640.26940.30440.4947-0.20570.2061-0.3433-0.3230.57780.9232-0.04980.30550.120.01970.6876-0.01150.344874.40669.377336.0061
112.12410.26972.09920.4681-0.46192.9301-0.0411.4566-0.2804-0.03060.2888-0.3674-0.46041.66390.01410.18510.03990.02970.65450.09780.397765.667213.385521.5267
123.66762.77782.26756.13760.93451.55460.5835-0.3243-0.3717-0.9079-0.2913-1.50060.04791.4375-0.25120.3710.22980.07891.1832-0.0840.551675.02097.67123.2683
136.0359-0.94581.16832.3434-1.413.86280.3030.57270.1805-0.2225-0.3481-0.57410.69541.4039-0.16220.10960.07840.08411.1130.03550.546673.24538.538329.9316
142.50831.28172.45336.04281.76663.41690.6663-0.0026-0.04470.5187-0.1816-1.4664-0.37511.20910.02510.3847-0.1054-0.00070.58910.08420.410766.323316.946926.1767
152.709-1.90311.61031.4836-0.07929.9186-0.75-0.3040.10780.17340.0037-0.3415-0.65551.37760.37020.18360.01540.0230.3627-0.01190.337457.681818.051621.7109
166.0736-6.06232.77346.0636-3.11155.07630.566-0.87220.88730.5136-0.5489-0.6586-0.18920.5922-0.02950.1223-0.20080.03921.00450.03610.537278.738314.717240.6534
175.59810.89261.40928.69131.05186.2957-0.07740.3238-0.0905-1.21290.3972-0.8271-0.98451.1634-0.15580.3490.01520.15240.4463-0.01420.251654.076514.4422-14.0309
184.3011-0.4846-0.81094.1653-0.51664.80790.0520.0877-0.0618-0.3777-0.1087-0.26950.14390.76750.0260.26380.050.07370.2771-0.04160.180954.826214.2074-0.095
193.4631-2.26360.45854.46632.8777.25620.18540.2432-0.4079-1.00920.1625-0.1825-0.80750.4241-0.08540.2398-0.02570.1180.19680.05010.235549.580613.5591-5.1617
200.1393-0.54720.59730.308-0.79472.93730.17980.0542-0.0126-0.1423-0.05270.09240.23070.1436-0.13170.26730.01480.0010.11420.00140.240836.415220.43-20.3619
213.2842-2.62291.92092.052-1.63842.9982-0.00910.61670.9339-0.5109-0.2337-0.3099-0.1774-0.01140.10510.3879-0.014-0.02370.2028-0.01310.266529.837725.898-36.3824
227.7276-5.78985.25244.6236-4.41495.1430.2455-0.3586-0.6079-0.53950.22490.7541-0.0773-0.4271-0.35930.2262-0.028-0.00930.21890.02590.291727.917121.31054.1846
233.0686-0.2180.961.344-1.1143.88860.0345-0.0882-0.0149-0.0117-0.08440.1324-0.0078-0.01550.01540.20770.00570.04440.0853-0.0360.195638.708121.20799.2482
242.3734-0.01961.7263-0.0355-0.26392.7383-0.2326-0.24460.2807-0.0932-0.00220.0898-0.5128-0.33720.18290.29240.0657-0.010.1704-0.04650.231633.212925.48446.0572
251.87420.0281-0.35192.19070.45852.0405-0.17820.0980.0177-0.06590.12850.14280.4071-0.2030.01140.4331-0.048-0.08520.16390.05160.265819.445712.3033-23.8715
263.0590.91580.57841.91460.88538.474-0.0178-0.08470.2120.19940.06720.2199-0.4854-0.6322-0.04740.23680.02770.01540.21110.05320.305962.986316.396373.5822
272.89370.15220.57870.33110.21752.82980.1221-0.16770.06280.0094-0.0098-0.01080.26040.1421-0.14540.3660.0979-0.010.1894-0.01250.239984.944820.6712101.7357
284.49410.53252.83751.00721.72343.8486-0.01610.7175-0.6792-0.56430.4501-1.2368-0.6181.7903-0.08620.3811-0.2212-0.00840.6905-0.0250.420589.254116.28367.9394
291.74191.46921.2892.17832.4172.7321-0.15370.13460.2337-0.0285-0.01480.0391-0.40750.56180.13030.3098-0.19430.00480.42480.09170.350978.466517.895862.8362
303.17811.45472.41011.4320.98531.8657-0.38970.83981.0006-0.07990.4654-0.5037-1.18131.2470.09060.8839-0.5575-0.1910.5010.15170.624280.001728.043458.8008
311.5655-0.00111.50690.94281.45483.093-0.73550.74590.5598-0.30460.61480.1083-0.76691.34440.13510.3389-0.228-0.03560.65060.04610.380486.060719.593767.4448
321.07290.0179-0.93173.6701-1.13492.7350.29390.2352-0.1840.3310.3401-0.26530.94330.5385-0.21550.42170.2624-0.16510.4709-0.16640.299795.389811.324397.8676
332.3324-0.0286-0.80621.8257-1.03923.2922-0.02620.031-0.29850.39610.32260.21610.49390.1891-0.23840.56450.2079-0.11420.3779-0.18120.435292.78599.111895.5638
341.3333-0.1072-0.18383.1844-1.57193.6250.1714-0.41730.04460.2016-0.0043-0.74380.31271.45670.2080.69930.3407-0.05780.7996-0.20170.6372103.68497.11796.9239
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 30 through 40 )
2X-RAY DIFFRACTION2chain 'C' and (resid 41 through 49 )
3X-RAY DIFFRACTION3chain 'C' and (resid 50 through 71 )
4X-RAY DIFFRACTION4chain 'C' and (resid 72 through 82 )
5X-RAY DIFFRACTION5chain 'C' and (resid 83 through 99 )
6X-RAY DIFFRACTION6chain 'C' and (resid 100 through 127 )
7X-RAY DIFFRACTION7chain 'C' and (resid 128 through 139 )
8X-RAY DIFFRACTION8chain 'C' and (resid 140 through 147 )
9X-RAY DIFFRACTION9chain 'D' and (resid 28 through 40 )
10X-RAY DIFFRACTION10chain 'D' and (resid 41 through 55 )
11X-RAY DIFFRACTION11chain 'D' and (resid 56 through 82 )
12X-RAY DIFFRACTION12chain 'D' and (resid 83 through 99 )
13X-RAY DIFFRACTION13chain 'D' and (resid 100 through 118 )
14X-RAY DIFFRACTION14chain 'D' and (resid 119 through 127 )
15X-RAY DIFFRACTION15chain 'D' and (resid 128 through 139 )
16X-RAY DIFFRACTION16chain 'D' and (resid 140 through 147 )
17X-RAY DIFFRACTION17chain 'H' and (resid 2 through 15 )
18X-RAY DIFFRACTION18chain 'H' and (resid 16 through 81 )
19X-RAY DIFFRACTION19chain 'H' and (resid 82 through 98 )
20X-RAY DIFFRACTION20chain 'H' and (resid 99 through 189 )
21X-RAY DIFFRACTION21chain 'H' and (resid 190 through 217 )
22X-RAY DIFFRACTION22chain 'L' and (resid 1 through 18 )
23X-RAY DIFFRACTION23chain 'L' and (resid 19 through 53 )
24X-RAY DIFFRACTION24chain 'L' and (resid 54 through 118 )
25X-RAY DIFFRACTION25chain 'L' and (resid 119 through 216 )
26X-RAY DIFFRACTION26chain 'A' and (resid 2 through 111 )
27X-RAY DIFFRACTION27chain 'A' and (resid 112 through 217 )
28X-RAY DIFFRACTION28chain 'B' and (resid 1 through 18 )
29X-RAY DIFFRACTION29chain 'B' and (resid 19 through 53 )
30X-RAY DIFFRACTION30chain 'B' and (resid 54 through 66 )
31X-RAY DIFFRACTION31chain 'B' and (resid 67 through 118 )
32X-RAY DIFFRACTION32chain 'B' and (resid 119 through 155 )
33X-RAY DIFFRACTION33chain 'B' and (resid 156 through 193 )
34X-RAY DIFFRACTION34chain 'B' and (resid 194 through 216 )

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