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- PDB-5wt9: Complex structure of PD-1 and nivolumab-Fab -

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Basic information

Entry
Database: PDB / ID: 5wt9
TitleComplex structure of PD-1 and nivolumab-Fab
Components
  • Heavy Chain of Nivolumab
  • Light Chain of Nivolumab
  • Programmed cell death protein 1
KeywordsIMMUNE SYSTEM / PD-1 / Nivolumab
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: 2.401 Å
AuthorsTan, S. / Zhang, H. / Chai, Y. / Song, H. / Tong, Z. / Wang, Q. / Qi, J. / Wong, G. / Zhu, X. / Liu, W.J. ...Tan, S. / Zhang, H. / Chai, Y. / Song, H. / Tong, Z. / Wang, Q. / Qi, J. / Wong, G. / Zhu, X. / Liu, W.J. / Gao, S. / Wang, Z. / Shi, Y. / Yang, F. / Gao, G.F. / Yan, J.
Funding support China, 6items
OrganizationGrant numberCountry
Scientific Research and Development of China2016YFC1200300 China
National Natural Science Foundation of China31390432 China
National Natural Science Foundation of China31500722 China
Chinese Academy of Sciences153211KYSB20160001 China
China National Grand S&T Special Project2013ZX10004608-002 China
National Natural Science Foundation of China81321063 China
CitationJournal: Nat Commun / Year: 2017
Title: An unexpected N-terminal loop in PD-1 dominates binding by nivolumab.
Authors: Tan, S. / Zhang, H. / Chai, Y. / Song, H. / Tong, Z. / Wang, Q. / Qi, J. / Wong, G. / Zhu, X. / Liu, W.J. / Gao, S. / Wang, Z. / Shi, Y. / Yang, F. / Gao, G.F. / Yan, J.
History
DepositionDec 10, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
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 / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 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: Heavy Chain of Nivolumab
L: Light Chain of Nivolumab
G: Programmed cell death protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5374
Polymers66,9673
Non-polymers5711
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-7 kcal/mol
Surface area25140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.527, 108.527, 145.423
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Antibody Heavy Chain of Nivolumab


Mass: 23679.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#2: Antibody Light Chain of Nivolumab


Mass: 23641.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293T / Production host: Homo sapiens (human)
#3: Protein Programmed cell death protein 1 / hPD-1


Mass: 19646.043 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-167
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1, PD1 / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: Q15116
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 3.2 Å3/Da / Density % sol: 61.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Ammonium acetate, 0.1 M BIS-TRIS pH5.5, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97907 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 34630 / % possible obs: 100 % / Redundancy: 21.7 % / Net I/σ(I): 32.1
Reflection shellResolution: 2.4→2.49 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: 3EYQ

3eyq


Resolution: 2.401→37.1 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.12
RfactorNum. reflection% reflection
Rfree0.2278 1698 4.91 %
Rwork0.187 --
obs0.189 34560 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.401→37.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4128 0 0 263 4391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114229
X-RAY DIFFRACTIONf_angle_d1.2185754
X-RAY DIFFRACTIONf_dihedral_angle_d21.2251546
X-RAY DIFFRACTIONf_chiral_restr0.087652
X-RAY DIFFRACTIONf_plane_restr0.007737
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4007-2.47140.27921390.21592662X-RAY DIFFRACTION99
2.4714-2.55110.22471420.20812681X-RAY DIFFRACTION100
2.5511-2.64230.22971450.20212704X-RAY DIFFRACTION100
2.6423-2.7480.28511480.20572676X-RAY DIFFRACTION100
2.748-2.87310.28561250.2062708X-RAY DIFFRACTION100
2.8731-3.02450.27811540.21792703X-RAY DIFFRACTION100
3.0245-3.21390.26941440.20422719X-RAY DIFFRACTION100
3.2139-3.46180.25091270.19472739X-RAY DIFFRACTION100
3.4618-3.80990.24351370.18832737X-RAY DIFFRACTION100
3.8099-4.36050.18871340.15742787X-RAY DIFFRACTION100
4.3605-5.49090.1651620.14122786X-RAY DIFFRACTION100
5.4909-37.10480.22141410.20372960X-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)
13.2448-0.2319-0.13130.6980.43430.90740.0497-0.22180.40680.220.0217-0.1534-0.18880.1421-0.09010.3355-0.02640.02010.2829-0.00370.210326.8545-38.9943-25.8441
21.3226-0.3202-0.27451.5297-0.30930.7153-0.06280.0617-0.09310.07050.05540.0321-0.0643-0.0367-0.00250.2067-0.02290.00070.20970.03110.196924.6971-44.2394-32.5502
31.3332-0.3008-0.43040.06630.04481.52930.31150.07530.27230.35140.00440.2028-0.4489-0.2998-0.29670.39680.04920.08890.24930.05430.3574-1.2068-41.0947-13.9857
40.74690.69310.12690.95620.05510.97020.1564-0.02190.1770.1222-0.0699-0.0059-0.0384-0.1291-0.07780.30680.04240.08030.29380.01970.31770.6839-46.4069-9.3938
51.1520.7654-0.59821.8928-1.56723.1170.2365-0.11050.20810.2276-0.21360.068-0.2444-0.0261-0.05580.47520.00490.11530.29910.00270.3745-0.6111-39.3057-3.0052
61.17950.2893-0.46041.2938-0.82454.0594-0.11030.1098-0.1802-0.17640.05940.0690.4053-0.12830.09050.2227-0.00910.02580.19150.01310.21916.633-67.5996-29.2087
71.26270.3150.33341.2212-0.34340.6538-0.0345-0.1059-0.17520.08630.01080.0198-0.07840.28040.00820.27440.03180.0270.23760.03690.263926.713-62.3318-25.5094
81.24610.0702-0.99551.2053-0.91041.5361-0.1148-0.1745-0.12940.1047-0.0012-0.01670.12410.27970.12750.27160.01260.03490.21090.0380.220521.9866-67.3206-23.8623
91.33320.6653-0.79980.6791-1.01751.5296-0.10920.1518-0.13220.0095-0.038-0.1374-0.1059-0.15930.16310.26660.00790.00520.206-0.00280.247613.9748-62.6532-25.5827
101.1316-0.57210.72524.009-0.80751.64220.1695-0.48210.45580.3303-0.0021-0.0958-0.1132-0.2666-0.130.31990.07040.18420.3988-0.00070.4555-13.2548-43.8884-10.9381
111.926-2.10380.67222.955-0.95990.59430.1140.17580.12030.07490.02590.0616-0.071-0.2683-0.18120.29360.03980.07050.38750.06420.3125-7.9323-56.8288-17.2948
121.891-0.69261.21720.8086-0.18170.90760.0133-0.0469-0.10980.17820.15760.2527-0.072-0.4899-0.21720.31630.04630.01590.5020.0930.2803-12.5066-51.9689-23.7759
131.4432-0.65010.32562.5873-0.46640.88470.12040.05550.18820.11590.01020.3621-0.0929-0.3813-0.08720.31550.06880.07310.43850.07560.3069-11.8231-54.4707-15.5146
140.2068-0.4931-0.66713.20451.65842.1606-0.040.1253-0.6919-0.6011-0.0567-0.72750.67450.37660.26330.33330.0583-0.03750.33320.05640.48443.6009-53.7782-33.7665
151.3628-0.3462-0.37171.1820.02081.6-0.1921-0.2473-0.1476-0.0387-0.0031-1.1560.18440.43320.12150.44880.0483-0.08350.63620.13261.113858.3602-63.3791-21.1575
160.97150.8786-0.34862.94980.25621.5922-0.2489-0.4862-0.22330.7498-0.1324-1.44230.42130.36480.34480.76490.129-0.23730.6390.04370.990554.5268-64.8893-16.815
170.5887-1.3824-0.32823.3820.67490.2505-0.265-0.4468-0.13460.3725-0.1959-0.34750.39880.63680.43270.82510.2357-0.30130.89160.17221.641562.6502-69.501-15.2166
183.2936-1.4038-0.67781.0827-0.09330.9576-0.32330.2269-0.7329-0.07750.0267-0.33160.4080.17990.12020.33040.0397-0.00450.35230.03680.735849.9884-64.5827-25.2781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 33 )
2X-RAY DIFFRACTION2chain 'H' and (resid 34 through 106 )
3X-RAY DIFFRACTION3chain 'H' and (resid 107 through 145 )
4X-RAY DIFFRACTION4chain 'H' and (resid 146 through 190 )
5X-RAY DIFFRACTION5chain 'H' and (resid 191 through 214 )
6X-RAY DIFFRACTION6chain 'L' and (resid -2 through 25 )
7X-RAY DIFFRACTION7chain 'L' and (resid 26 through 61 )
8X-RAY DIFFRACTION8chain 'L' and (resid 62 through 90 )
9X-RAY DIFFRACTION9chain 'L' and (resid 91 through 113 )
10X-RAY DIFFRACTION10chain 'L' and (resid 114 through 128 )
11X-RAY DIFFRACTION11chain 'L' and (resid 129 through 150 )
12X-RAY DIFFRACTION12chain 'L' and (resid 151 through 163 )
13X-RAY DIFFRACTION13chain 'L' and (resid 164 through 213 )
14X-RAY DIFFRACTION14chain 'G' and (resid 25 through 35 )
15X-RAY DIFFRACTION15chain 'G' and (resid 36 through 70 )
16X-RAY DIFFRACTION16chain 'G' and (resid 71 through 104 )
17X-RAY DIFFRACTION17chain 'G' and (resid 105 through 118 )
18X-RAY DIFFRACTION18chain 'G' and (resid 119 through 142 )

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