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- PDB-8u31: Crystal structure of PD-1 in complex with a Fab -

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Basic information

Entry
Database: PDB / ID: 8u31
TitleCrystal structure of PD-1 in complex with a Fab
Components
  • Fab heavy chain
  • Fab light chain
  • Programmed cell death protein 1
KeywordsSTRUCTURAL PROTEIN/IMMUNE SYSTEM / PD-1 / Fab / STRUCTURAL PROTEIN / STRUCTURAL PROTEIN-IMMUNE SYSTEM complex
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 / regulation of immune response / PD-1 signaling / adaptive immune response ...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 / regulation of immune response / PD-1 signaling / 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
Similarity search - Domain/homology
Programmed cell death protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsSun, D. / Masureel, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Mabs / Year: 2024
Title: Structure- and machine learning-guided engineering demonstrate that a non-canonical disulfide in an anti-PD-1 rabbit antibody does not impede antibody developability.
Authors: Liang, W.C. / Xi, H. / Sun, D. / D'Ascenzo, L. / Zarzar, J. / Stephens, N. / Cook, R. / Li, Y. / Ye, Z. / Matsumoto, M. / Payandeh, J. / Masureel, M. / Wu, Y.
History
DepositionSep 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Programmed cell death protein 1
B: Fab light chain
C: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3984
Polymers63,3063
Non-polymers921
Water79344
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.069, 104.069, 143.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Programmed cell death protein 1


Mass: 15765.327 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDCD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15116
#2: Antibody Fab light chain


Mass: 23509.783 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: Antibody Fab heavy chain


Mass: 24030.955 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)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 1% w/v Tryptone, 0.001 M Sodium azide, 0.05 M HEPES sodium pH 7.0, 20% w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.73→42.13 Å / Num. obs: 80752 / % possible obs: 88.7 % / Redundancy: 5 % / Biso Wilson estimate: 59.23 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.094 / Net I/σ(I): 12.05
Reflection shellResolution: 2.73→2.83 Å / Rmerge(I) obs: 0.658 / Num. unique obs: 8206 / CC1/2: 0.794

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874_finalrefinement
autoPROCdata reduction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→42.13 Å / SU ML: 0.4094 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0691
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2375 1460 4.85 %
Rwork0.199 28625 -
obs0.2008 30085 88.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.43 Å2
Refinement stepCycle: LAST / Resolution: 2.73→42.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4085 0 6 44 4135
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00764195
X-RAY DIFFRACTIONf_angle_d0.93875716
X-RAY DIFFRACTIONf_chiral_restr0.0545645
X-RAY DIFFRACTIONf_plane_restr0.0062736
X-RAY DIFFRACTIONf_dihedral_angle_d9.2764584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.830.37741610.32862895X-RAY DIFFRACTION91.44
2.83-2.940.35811640.29822969X-RAY DIFFRACTION91.08
2.94-3.070.32511460.27592870X-RAY DIFFRACTION90.38
3.07-3.230.34141270.24532879X-RAY DIFFRACTION88.02
3.23-3.440.25821470.23992900X-RAY DIFFRACTION89.64
3.44-3.70.28741670.21172892X-RAY DIFFRACTION90.21
3.7-4.070.22111510.18852864X-RAY DIFFRACTION89.12
4.08-4.660.16321220.15092830X-RAY DIFFRACTION87.03
4.66-5.870.19681680.15072751X-RAY DIFFRACTION86.36
5.87-42.130.18031070.17842775X-RAY DIFFRACTION84.47
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)
14.505070666871.2563439304-0.5289392047734.55513523052-1.777714869013.5882252747-0.3302914541060.594875516648-0.455241176693-0.9510044743370.267170091-1.94454610347-0.437529791650.161719584776-0.01708632813540.986488808091-0.1448234715550.2653811925180.743578775233-0.1132926032260.850518381245-2.2466027383398.2769813067-11.0929131833
24.320088733664.992260646951.144077342665.797110138141.118849594051.02362998742-0.7586870779480.8756411202360.890496671762-0.3205692887760.4516943230070.383666203036-0.2760541172720.07771817397780.1851022236360.800364907898-0.1384831369220.08045339022080.8880803380820.0663005358330.40019898727-10.539223102199.1725074385-2.27418133878
35.807383944733.01174312904-3.226029323711.81169501495-1.034269889183.431566617570.523861567417-0.218908809449-1.357459074930.708123688937-0.668976964449-0.349225970509-0.1667437148381.569711006750.05665475156930.873163702706-0.0415746618443-0.02081132350910.922422709978-0.009748387434820.8489449495612.6057135600199.69389284212.46369755401
42.842659898740.634568257734-1.693237504721.87909447235-1.779506847852.293491541280.0346103378050.3175207138480.662491670644-0.4932452653930.108544893241-0.248584465548-0.2559716157570.268429341927-0.04609909827410.73144504258-0.1145579578060.06851756770550.622018686853-0.006690440093050.637352096314-5.07596705095101.908960678-5.59382987469
57.465474613270.425743218793-1.643969428323.83351352619-0.2463884518635.251633214880.123155805014-0.6884857087881.647509456350.6522661515050.251412478513-0.296256845493-0.3343379970140.335849020828-0.3782856287170.5202756076070.0691215847774-0.1032431341510.3416996402730.03065594849380.614863260345-14.328216336294.633345776731.6312351068
60.734527526503-1.29300245535-0.4757982793343.177072125360.05274918388854.95979817796-0.0899919012188-0.06404035512320.02990467844650.01540811310340.177609080480.0863671076335-0.1725939410270.0137149348961-0.177921094860.269736225242-0.0364795497514-0.006087229770220.362675856289-0.04553219199470.351735373146-15.705156707493.031386822621.1403368263
72.58616664003-0.106506422595-0.5940258284172.70466700031-0.5884401099282.76027245340.263041875260.0188316850840.4180477921810.783881722412-0.389838415219-0.49545353753-0.7392886698790.2839224489270.2270198703590.629975412011-0.0970632933061-0.04307574242810.5063730401450.01236973122560.434231883224-8.5069820218478.456227391250.1821312977
82.292303692470.01278894394410.5222670378282.55928731880.3521359145513.816929841160.46169265146-0.262592441297-0.3830767116650.555413133294-0.423117510716-0.497288578493-0.3097278077260.6684993370910.0903828394720.428487524444-0.130066472063-0.1061850120860.5553739102770.1382620375690.571248878831-3.7628408375172.013169453548.4962369314
92.07633217247-1.167952970620.6822589110613.51020999909-1.50538281133.245249658080.554094858664-0.2269765699820.07003037820061.12253464077-0.146873218286-0.40297412447-0.8724640238840.581832947824-0.1837591443270.938902965021-0.241257530115-0.05686720165090.66310658435-0.008671452614150.776822990214-2.8651029003780.86478901553.9816476358
101.929446119351.275789988211.479714468192.86625062103-0.8213913811653.794984173140.1284011651190.310789570481-0.870696328157-0.7549121833320.1105303813840.394821244020.5025107463620.124676165766-0.1185701977810.5519612738410.0172772903240.04170079336670.403367986726-0.02473403245560.637632734437-10.822645290767.171357060817.6566340404
113.349573920730.7127324447240.4782118770213.415565376080.5609634298843.17700220092-0.1702693090410.264883491641-0.808062921666-0.5545589533630.277598154513-0.2483022931630.0244212418488-0.162639780358-0.0340592730890.431233678657-0.08738135791210.05557606111450.517461543126-0.005578240750090.456932976098-14.323707075276.187021927310.2796231561
121.62032136334-1.6107126533-0.1772720122854.73375262815-1.201207657250.624924671361-0.1650872342730.06234602478760.3498447247420.1634804154810.265573200453-0.1180880123770.0565761326491.11085033425-0.09970092841740.449647922834-0.05783927702660.005469103796670.510694950498-0.01417695134060.570100474038-4.8836238558881.019444363319.6399794193
130.949716500968-0.3278173024472.181871213860.876584644612-0.2654152366555.43649764277-0.559307999743-0.4221056576810.398144102141-0.1553525781410.00768833051463-1.27496609966-0.6175217931610.9621701103740.0547332460220.676760608582-0.06597381153150.1981981770950.839664920341-0.08401535382830.740370675652-0.43392488921479.84770827048.92732797175
140.9193518677590.325038981516-0.1673890604411.8097232629-1.467496506682.09428241074-0.1182434930550.181723118008-0.202025768341-0.199888742456-0.173395819396-0.05222415443690.4348042043790.3880341895690.2465015347280.4297750726360.03405239200760.04536360211160.467163715622-0.0401269999370.415491953557-9.0446121264272.015315956417.1907143961
153.273446551031.11182354821-2.259895561222.22837843268-2.40012318394.665376757890.0882474002921-0.14169547149-0.3036037273930.251339159352-0.300997033726-0.0895786321836-0.4130235241390.09365234012930.1928644761850.4162494157980.0738805709335-0.04527450839450.4412013970810.03752013052690.458739498514-11.967811867663.866750798149.3670666973
161.612091489760.00894137830421-1.586745666331.67051629617-1.082152617154.041079946710.2927464529890.1750825642110.239473714760.0799845855334-0.0768328748555-0.0356355042728-0.05626040684670.08009306625440.002055590124580.435491728954-0.00676845203422-0.08834735812670.4432118921310.01018326220060.515177309658-11.362303756464.235183792141.5739424111
172.33099763841-0.0999054723877-0.9853492687362.37242099768-1.35587514244.343612239770.02561319532140.0517619285802-0.01179816453980.429899281567-0.243253072342-0.1700843143020.01330530645-0.3825261022620.2484169705040.458869958925-0.0251972000673-0.00244983845410.4704991529940.04362168391070.512015313982-15.909212879759.106521493152.7581138463
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 30 through 55 )AA30 - 551 - 28
22chain 'A' and (resid 56 through 70 )AA56 - 7029 - 43
33chain 'A' and (resid 71 through 81 )AA71 - 8144 - 54
44chain 'A' and (resid 82 through 143 )AA82 - 14355 - 110
55chain 'C' and (resid 1 through 17 )CC1 - 171 - 17
66chain 'C' and (resid 18 through 125 )CC18 - 12518 - 125
77chain 'C' and (resid 126 through 171 )CC126 - 171126 - 163
88chain 'C' and (resid 172 through 207 )CC172 - 207164 - 199
99chain 'C' and (resid 208 through 228 )CC208 - 228200 - 220
1010chain 'B' and (resid 1 through 18 )BB1 - 181 - 18
1111chain 'B' and (resid 19 through 40 )BB19 - 4019 - 40
1212chain 'B' and (resid 41 through 51 )BB41 - 5141 - 51
1313chain 'B' and (resid 52 through 63 )BB52 - 6352 - 63
1414chain 'B' and (resid 64 through 117 )BB64 - 11764 - 117
1515chain 'B' and (resid 118 through 154 )BB118 - 154118 - 154
1616chain 'B' and (resid 155 through 178 )BB155 - 178155 - 178
1717chain 'B' and (resid 179 through 216 )BB179 - 216179 - 216

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