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- PDB-6hig: hPD-1/NBO1a Fab complex -

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Basic information

Entry
Database: PDB / ID: 6hig
TitlehPD-1/NBO1a Fab complex
Components
  • Heavy Chain
  • Light Chain
  • Programmed cell death protein 1
KeywordsIMMUNE SYSTEM / Non-blocking antibody / PD-1/PD-L1 pathway / anti-PD-1 antibody / tumor clearance
Function / homology
Function and homology information


negative regulation of tolerance induction / regulatory T cell apoptotic process / negative regulation of immune response / B cell apoptotic process / 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 / negative regulation of immune response / B cell apoptotic process / 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 speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLoredo-Varela, J.L. / Fenwick, C. / Pantaleo, G. / Weissenhorn, W.
CitationJournal: J.Exp.Med. / Year: 2019
Title: Tumor suppression of novel anti-PD-1 antibodies mediated through CD28 costimulatory pathway.
Authors: Fenwick, C. / Loredo-Varela, J.L. / Joo, V. / Pellaton, C. / Farina, A. / Rajah, N. / Esteves-Leuenberger, L. / Decaillon, T. / Suffiotti, M. / Noto, A. / Ohmiti, K. / Gottardo, R. / ...Authors: Fenwick, C. / Loredo-Varela, J.L. / Joo, V. / Pellaton, C. / Farina, A. / Rajah, N. / Esteves-Leuenberger, L. / Decaillon, T. / Suffiotti, M. / Noto, A. / Ohmiti, K. / Gottardo, R. / Weissenhorn, W. / Pantaleo, G.
History
DepositionAug 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Heavy Chain
L: Light Chain
B: Programmed cell death protein 1


Theoretical massNumber of molelcules
Total (without water)61,7323
Polymers61,7323
Non-polymers00
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-33 kcal/mol
Surface area22590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.514, 63.049, 68.297
Angle α, β, γ (deg.)90.00, 106.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Heavy Chain


Mass: 25238.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#2: Antibody Light Chain /


Mass: 23264.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Protein Programmed cell death protein 1 / / hPD-1


Mass: 13228.716 Da / Num. of mol.: 1 / 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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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: 2.16 Å3/Da / Density % sol: 42.98 %
Crystal growTemperature: 293 K / Method: evaporation / Details: 0.2 M NH4I 20 % PEG 3.35 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.2→65.49 Å / Num. obs: 26237 / % possible obs: 97.59 % / Redundancy: 2.9 % / Biso Wilson estimate: 33.88 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.0696 / Rrim(I) all: 0.08456 / Net I/σ(I): 10.77
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.5201 / Mean I/σ(I) obs: 2.16 / Num. unique obs: 2261 / CC1/2: 0.711 / Rrim(I) all: 0.6447 / % possible all: 98.28

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZQK, 4Q9Q

4zqk

4q9q


Resolution: 2.2→65.489 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.83
RfactorNum. reflection% reflection
Rfree0.2697 1265 4.82 %
Rwork0.2148 --
obs0.2174 26236 97.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→65.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3787 0 0 155 3942
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023875
X-RAY DIFFRACTIONf_angle_d0.4795270
X-RAY DIFFRACTIONf_dihedral_angle_d12.5272306
X-RAY DIFFRACTIONf_chiral_restr0.041603
X-RAY DIFFRACTIONf_plane_restr0.004665
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.28810.35941570.28392769X-RAY DIFFRACTION98
2.2881-2.39230.30971260.27222799X-RAY DIFFRACTION99
2.3923-2.51840.32951480.25682806X-RAY DIFFRACTION99
2.5184-2.67620.31131370.24862758X-RAY DIFFRACTION98
2.6762-2.88280.32761450.24192740X-RAY DIFFRACTION97
2.8828-3.17290.29761360.22782812X-RAY DIFFRACTION98
3.1729-3.6320.29421280.20572755X-RAY DIFFRACTION97
3.632-4.57580.21161360.17792786X-RAY DIFFRACTION97
4.5758-65.51760.22661520.19282746X-RAY DIFFRACTION95
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)
13.0718-0.64660.07021.6787-0.49462.9325-0.06220.65210.4873-0.9381-0.31850.7166-0.7338-0.69570.40430.32930.1245-0.2750.4643-0.21350.6255-19.8813-11.4614-28.8662
22.0649-0.1462-2.05064.04781.4434.05170.21150.27710.181-0.7898-0.31930.2735-0.7408-0.07940.0830.61370.012-0.08020.4896-0.07020.2984-9.9823-17.2229-33.5151
35.1003-3.4407-5.45626.32925.46968.9583-0.1054-0.53850.06230.67670.03080.80180.2866-0.77520.21640.40480.04910.1350.5596-0.11120.3862-14.1152-23.4845-21.7579
44.6151.8797-6.40061.9269-2.94439.0206-0.16440.5714-1.2786-0.2389-1.13030.3722-0.2724-0.66350.86780.5453-0.080.02950.5306-0.25290.5881-13.1789-28.5119-34.4553
54.04712.9138-0.61224.8216-1.083.7102-0.27470.58640.8212-2.3782-0.59711.23960.1975-0.71630.1240.80020.0858-0.44720.4643-0.42880.7166-18.0701-20.1238-36.2322
64.05841.20340.35114.00791.5414.6738-0.21390.11680.3484-0.3328-0.30.4464-0.0816-0.3620.57910.41120.0216-0.04120.2903-0.07450.2607-12.7883-19.1925-26.555
75.9469-2.8475-0.99544.52361.97293.14610.2260.182-0.9354-0.4128-0.0310.2802-0.3711-0.0886-0.17310.41950.0472-0.09150.4161-0.14890.4104-29.6999-8.9038-19.4667
84.76851.52923.60138.7312.94077.5161-0.2417-0.11580.26980.1735-0.0156-0.07310.02820.09820.24040.2290.04420.02140.2468-0.01370.1782-27.40830.57610.7056
94.17720.7522.24733.98840.82374.74450.2020.14550.20610.1638-0.26760.06530.24690.09910.07820.18660.04290.0790.26550.02280.2127-21.7593-0.7168-5.0131
108.86332.66886.53618.8354.94865.6052-0.51150.25530.673-0.3063-0.13550.3516-0.99350.20710.73670.35870.0911-0.01840.23550.0360.3314-26.12137.8445-6.0156
113.1137-0.41890.24563.33190.97721.7845-0.0145-0.2985-0.3770.3509-0.12790.2580.2392-0.06810.16170.38380.0520.12280.2950.05210.2597-0.2473-25.5257-11.0169
122.62421.63060.56311.7759-1.09723.6766-0.16280.06720.0937-0.3928-0.0886-0.46870.05310.39150.23010.28770.070.05510.2775-0.02420.1974.3383-21.4368-17.7646
130.8196-1.4745-2.34622.14964.17417.8394-0.0567-0.1661-0.11650.1866-0.24550.0640.5122-0.02550.27040.2790.03650.02920.31970.03850.2066-2.701-18.4288-8.8097
148.17820.43955.45412.532-0.21267.6622-0.18230.44850.9534-0.1647-0.15660.3053-0.4935-0.49230.18770.26350.04170.01120.2656-0.02420.238-32.6811-1.42754.7719
152.7691-0.4534-0.24861.3336-0.21932.0075-0.29620.51350.2902-0.07280.0506-0.01550.4009-0.13480.35760.2831-0.00920.03490.2585-0.02120.2176-21.7594-11.72866.1029
169.80112.403-5.61262.1493-2.89594.974-0.17290.0999-0.069-0.0210.1583-0.0820.42460.03230.21420.4020.0335-0.00550.1725-0.05070.1987-29.734-16.11594.7314
174.9505-0.45070.52280.3392-0.22561.5769-0.0929-0.037-0.110.00290.09610.04130.0635-0.119-0.05990.29670.03280.01470.1653-0.00720.1964-24.7586-9.84317.8226
188.5246-0.2449-2.74845.8449-2.23432.35140.2956-0.0496-0.46560.0402-0.4496-0.5118-0.31960.14720.13860.45520.03350.0050.4520.01840.24647.7627-26.0644-41.6573
193.11982.8759-1.33669.5854-3.24115.6877-0.4604-0.4413-0.5022-0.72390.2774-0.57210.66770.38180.21910.40360.07560.050.58780.1580.445515.7396-24.8488-43.1937
205.19391.5627-0.93135.5928-1.05180.5154-0.2752-0.1087-0.1928-0.0035-0.0072-0.07590.27310.070.32360.46790.02670.02590.4660.00660.25019.9477-28.0449-39.8675
218.48460.45210.87214.19924.98825.9892-0.46510.7036-0.99170.36820.06440.79121.12460.7540.32430.5359-0.0320.02310.3824-0.10360.5541-0.4444-34.7081-44.5505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'H' and (resid 18 through 39 )
3X-RAY DIFFRACTION3chain 'H' and (resid 40 through 51 )
4X-RAY DIFFRACTION4chain 'H' and (resid 52 through 64 )
5X-RAY DIFFRACTION5chain 'H' and (resid 65 through 83 )
6X-RAY DIFFRACTION6chain 'H' and (resid 84 through 110 )
7X-RAY DIFFRACTION7chain 'H' and (resid 111 through 123 )
8X-RAY DIFFRACTION8chain 'H' and (resid 124 through 149 )
9X-RAY DIFFRACTION9chain 'H' and (resid 150 through 192 )
10X-RAY DIFFRACTION10chain 'H' and (resid 193 through 217 )
11X-RAY DIFFRACTION11chain 'L' and (resid 2 through 38 )
12X-RAY DIFFRACTION12chain 'L' and (resid 39 through 75 )
13X-RAY DIFFRACTION13chain 'L' and (resid 76 through 113 )
14X-RAY DIFFRACTION14chain 'L' and (resid 114 through 128 )
15X-RAY DIFFRACTION15chain 'L' and (resid 129 through 150 )
16X-RAY DIFFRACTION16chain 'L' and (resid 151 through 163 )
17X-RAY DIFFRACTION17chain 'L' and (resid 164 through 211 )
18X-RAY DIFFRACTION18chain 'B' and (resid 33 through 69 )
19X-RAY DIFFRACTION19chain 'B' and (resid 75 through 104 )
20X-RAY DIFFRACTION20chain 'B' and (resid 105 through 139 )
21X-RAY DIFFRACTION21chain 'B' and (resid 140 through 147 )

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