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- PDB-8u32: Crystal structure of PD-1 in complex with a Fab -

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Basic information

Entry
Database: PDB / ID: 8u32
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 / PD-1 signaling / regulation of immune response / 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 / PD-1 signaling / regulation of immune response / 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: 2.51 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
D: Programmed cell death protein 1
E: Fab light chain
F: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,0148
Polymers126,5726
Non-polymers4422
Water2,612145
1
A: Programmed cell death protein 1
B: Fab light chain
C: Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)63,2863
Polymers63,2863
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Programmed cell death protein 1
E: Fab light chain
F: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7285
Polymers63,2863
Non-polymers4422
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.482, 88.881, 235.859
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 31 through 32 or resid 35...
d_2ens_1(chain "D" and (resid 31 through 32 or resid 35...
d_1ens_2(chain "B" and (resid 1 through 126 or resid 128...
d_2ens_2(chain "E" and (resid 1 through 126 or resid 128...
d_1ens_3(chain "C" and (resid 2 through 43 or resid 45...
d_2ens_3(chain "F" and (resid 2 through 43 or resid 45...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1PROPROTRPTRPAA31 - 3222 - 23
d_12ens_1PROPROSERSERAA35 - 5726 - 48
d_13ens_1SERSERPROPROAA62 - 8353 - 74
d_14ens_1SERSERPHEPHEAA93 - 9584 - 86
d_15ens_1VALVALGLYGLYAA97 - 10388 - 94
d_16ens_1ASPASPVALVALAA105 - 11196 - 102
d_17ens_1ALAALAALAALAAA113104
d_18ens_1ASNASNILEILEAA116 - 134107 - 125
d_19ens_1SERSERVALVALAA137 - 144128 - 135
d_21ens_1PROPROTRPTRPDD31 - 3222 - 23
d_22ens_1PROPROSERSERDD35 - 5726 - 48
d_23ens_1SERSERPROPRODD62 - 8353 - 74
d_24ens_1SERSERPHEPHEDD93 - 9584 - 86
d_25ens_1VALVALGLYGLYDD97 - 10388 - 94
d_26ens_1ASPASPVALVALDD105 - 11196 - 102
d_27ens_1ALAALAALAALADD113104
d_28ens_1ASNASNILEILEDD116 - 134107 - 125
d_29ens_1SERSERVALVALDD137 - 144128 - 135
d_11ens_2ALAALAASPASPBB1 - 1261 - 126
d_12ens_2GLNGLNSERSERBB128 - 172128 - 172
d_13ens_2ASPASPHISHISBB174 - 202174 - 202
d_14ens_2GLYGLYGLUGLUBB204 - 217204 - 217
d_21ens_2ALAALAASPASPEE1 - 1261 - 126
d_22ens_2GLNGLNSERSEREE128 - 172128 - 172
d_23ens_2ASPASPHISHISEE174 - 202174 - 202
d_24ens_2GLYGLYGLUGLUEE204 - 217204 - 217
d_11ens_3GLNGLNGLYGLYCC2 - 432 - 43
d_12ens_3GLYGLYASPASPCC45 - 7545 - 75
d_13ens_3SERSERSERSERCC77 - 14177 - 141
d_14ens_3THRTHRHISHISCC149 - 214149 - 214
d_15ens_3PROPROLYSLYSCC216 - 223216 - 223
d_16ens_3VALVALLYSLYSCC225 - 228225 - 228
d_21ens_3GLNGLNGLYGLYFF2 - 432 - 43
d_22ens_3GLYGLYASPASPFF45 - 7545 - 75
d_23ens_3SERSERSERSERFF77 - 14177 - 141
d_24ens_3THRTHRHISHISFF149 - 214149 - 214
d_25ens_3PROPROLYSLYSFF216 - 223216 - 223
d_26ens_3VALVALLYSLYSFF225 - 228225 - 228

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.920933275438, 0.270580089267, 0.280478729109), (0.183470411321, -0.333939018252, 0.924566568863), (0.343832096175, 0.90292366642, 0.257892113603)-18.5921904016, -76.0092613261, 61.4333048192
2given(-0.948097711802, 0.242211369554, 0.20602034204), (0.138235573976, -0.269520554615, 0.953021299199), (0.286359310942, 0.932036653302, 0.22204959342)-18.2760581886, -76.3364824466, 61.8067083638
3given(-0.937282641878, 0.263093132276, 0.228655314792), (0.141656261, -0.3118703506, 0.93950539548), (0.318488230478, 0.912972556086, 0.255041876721)-18.5097277423, -76.6710804127, 61.0985525539

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Components

#1: Protein Programmed cell death protein 1


Mass: 15765.327 Da / Num. of mol.: 2 / Mutation: C93S
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.: 2
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: 24010.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 3.17 Å3/Da / Density % sol: 61.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 20 %w/v PEG 3350, 0.2 M Na2 Malon, 0.1 M BIS-TRIS prop pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.51→84.17 Å / Num. obs: 52262 / % possible obs: 93 % / Redundancy: 6.7 % / Biso Wilson estimate: 48.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Net I/σ(I): 16.7
Reflection shellResolution: 2.51→2.6 Å / Rmerge(I) obs: 0.6855 / Num. unique obs: 5506 / CC1/2: 0.884 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874_finalrefinement
autoPROCdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→34.96 Å / SU ML: 0.3163 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6325
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2304 2663 5.1 %
Rwork0.1954 49552 -
obs0.1972 52215 93.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.37 Å2
Refinement stepCycle: LAST / Resolution: 2.51→34.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8366 0 28 145 8539
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098585
X-RAY DIFFRACTIONf_angle_d1.22211678
X-RAY DIFFRACTIONf_chiral_restr0.06751320
X-RAY DIFFRACTIONf_plane_restr0.00831502
X-RAY DIFFRACTIONf_dihedral_angle_d34.16591194
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.835179540219
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS1.06956829943
ens_3d_2CCX-RAY DIFFRACTIONTorsion NCS0.714262952636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.550.35521390.29632779X-RAY DIFFRACTION99.39
2.55-2.60.32491340.26792755X-RAY DIFFRACTION99.9
2.6-2.650.3211290.26922575X-RAY DIFFRACTION97.37
2.69-2.710.2675610.26071184X-RAY DIFFRACTION97.11
2.71-2.770.3041540.24632752X-RAY DIFFRACTION99.79
2.77-2.840.27041630.24182745X-RAY DIFFRACTION99.35
2.84-2.920.26481630.23972735X-RAY DIFFRACTION99.93
2.92-3.010.30991510.24182778X-RAY DIFFRACTION99.97
3.01-3.10.27561550.24422772X-RAY DIFFRACTION99.93
3.1-3.210.27011470.2412727X-RAY DIFFRACTION97.82
3.21-3.340.26291440.23492729X-RAY DIFFRACTION97.75
3.34-3.50.2962620.23051193X-RAY DIFFRACTION42.86
3.5-3.680.26751550.21442793X-RAY DIFFRACTION99.76
3.68-3.910.20441530.18982796X-RAY DIFFRACTION99.66
3.91-4.210.22671470.17232831X-RAY DIFFRACTION99.73
4.21-4.630.16361400.13952803X-RAY DIFFRACTION99.76
4.63-5.30.15991550.14462765X-RAY DIFFRACTION97.24
5.3-6.670.22941530.17422873X-RAY DIFFRACTION99.64
6.67-34.960.18361580.16762967X-RAY DIFFRACTION97.93
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)
14.04269176096-1.08918249741-0.8064197064620.719174740395-0.9071095114195.49255699943-0.09314319481480.326943536176-0.375168403707-0.5202280095520.0666123478640.01988379239580.351821766705-0.2414534656580.01273166439760.4609988546490.0205774931396-0.03013554325680.381027971792-0.03589196662030.360337942118-22.1797842575-30.12785337468.98377461887
22.982507962460.9357189009530.1788833175521.69236934215-1.153875844333.4866852396-0.0805601350220.00926153230210.040106722117-0.2647799592510.04709564408870.403547738973-0.0156690941433-0.0777400453730.04255400806730.4075457551950.0595694157132-0.04068855936150.359566409213-0.05112744032040.369479674994-25.0165840615-23.658397105410.2030569181
31.652435761870.629012563662-0.177274457010.210196799729-0.01438833258390.843314715835-0.148078596703-0.0187390299954-0.113765401214-0.07474984843410.131727307666-0.1397594469880.006667278898610.1502508959550.01471634351290.5158613377380.02799284319570.009260254849620.36925187406-0.03497756753470.3864589298693.2374782093-10.915278123213.8932995158
44.92367141767-0.3982608914823.975754985251.06831560641-0.04876456688318.01191319663-0.05144166701650.4566354591470.130742776264-0.200680374050.137588599304-0.2795662929950.3534629021520.913165047565-0.1764648845120.404838856285-0.006412596547930.06842240148990.341978459303-0.04611216144910.45250204915114.4124176064-10.654967052313.8389016016
55.379562641731.678136668840.4034902296327.19310488127-2.74130892437.659882919580.002306606910970.0610672876964-0.112563008691-0.4936204360450.206543737887-0.2101398816070.378337345502-0.342752082162-0.2053971188370.344343830114-0.05296630771550.08530477195670.382993684420.003848535903090.4294934328129.38420517068-47.170161291310.7596486347
63.0622041004-1.058033847185.126356083571.85434078929-2.065516832868.640073720820.6772203207960.220522332817-1.364973741840.003020354818510.6723100638570.3808295193071.02202072426-0.957441743214-1.373394615931.07598467768-0.366497877987-0.1194879566740.769681163073-0.095785161690.9196106679855.10708029634-58.71847040424.64417310694
74.056634314140.797759690318-0.9584659789926.01104035709-3.62807684087.47182612684-0.03559218902910.8358315831150.0280927413525-0.8113330873390.224134943225-0.02482906658540.556721729893-0.0856912897766-0.09163008874410.459349288991-0.1208704038840.08941726335420.534143220926-0.06148486215370.4925233865159.46045781607-49.55042313734.45900671922
80.4876317302810.727413773532-1.119890309162.69392001973-2.139026154513.64561145024-0.1042527730080.05770766787340.02785355438910.1820885827650.3661831342960.22648130587-0.532131215281-0.437540733105-0.1908240047620.3499205335540.001159852989780.001303111903250.4390027501850.06390681453950.5649844158678.46286862699-45.030673358112.2455711853
96.18294065669-3.44080116702-2.358321985445.190144600362.768781766972.96976358321-0.236358808443-0.267736925983-0.001245945625610.6546816311870.331997401202-0.3654079716180.1075763810480.298170102584-0.1099168506390.467715639772-0.0182560447622-0.1088250025630.3068393525120.03103569807440.3457379637482.86446231465-44.266072202641.5679487422
102.065782308380.46799467339-1.045601724044.75619177681-1.72632291555.869449953580.0524758739257-0.0603709450295-0.178057024545-0.453134703786-0.06077339987270.1514571568780.483450284901-0.395848660745-0.02065881443390.415003458069-0.00971974829808-0.06366874108440.4170517490330.02668438793770.369761031558-17.3642421913-53.392382081870.6724420178
115.76932684862.33563117027-1.813858540262.911131128130.257904390345.344990416040.18056163288-0.352707089554-0.5434642091850.8731849976790.2138378317621.088912585760.669397252264-0.767020745048-0.4826153722730.695896037405-0.104095221180.07643973539640.287072478814-0.06133360183360.580114001877-9.74528332584-67.64379617236.9624374423
122.41728562440.753963613199-1.113590798594.845503331270.1944343075773.38491725205-0.202002132908-0.0581381460708-0.1291120980530.5249891521910.1114874088350.1222311848190.460759790937-0.01518359633380.09301733685620.426831290182-0.00317681130524-0.003166476052660.284331554850.01846170612650.438146341741-1.00944402943-62.654877678933.279289187
132.69513732906-1.50967208821-0.09008188849874.94119434033-0.3859170789222.238505248210.2536060382680.342291255383-0.271481253756-1.26486307456-0.3118305215770.9452124686810.461142993946-0.939803330890.1104328668470.932495440368-0.104646669649-0.319086324470.7741625528960.0228191035880.67016463453-26.8601431928-59.865247892858.6006965007
144.54131802192.97146373254-2.091635142816.65859995480.9329999567597.687826655170.132144689848-0.341286959009-1.235405611560.356729143121-0.245235123077-0.6326294226550.984471429986-0.318430583619-0.004671738900170.637652401043-0.14021918401-0.1570200401110.6065167568160.1645229689660.977340646102-38.0711043535-48.606660956821.1227299243
153.890134733292.579309511341.234167148444.05810375548-0.2056236657114.903649934650.4184715763890.0497677380319-1.504067885530.2478559419620.0259047099251-0.2914752959471.32312817363-0.440634836522-0.4499323086780.690285684977-0.0901700603963-0.1119142410950.6435854136140.08170801970590.914033667512-38.995080065-49.672640463318.4364701985
167.69776045731-0.3771753681662.79125605891.406883093530.1444025828273.468197602990.0298521298471-0.1055742508550.06393144038530.1335469958490.009008289058130.153280260751-0.244489278766-0.39665746103-0.05975460143460.3689719468450.05386894853160.05223021014430.3220695190260.01900719261410.275501631785-21.2798897339-22.435707985230.4592198737
171.53083314831.18402516254-0.3186027639144.77104430063-2.067483066393.82537667861-0.0626456154110.0506883335910.1623775377040.02828141989830.113849071201-0.160491614174-0.2550448679860.0868969309207-0.04827295869620.335833789792-0.02169357839160.00345698038080.312791443316-0.03471444554960.3660692084434.878842468512.399189453323.9540862051
184.522290274883.2452325689-2.944404309444.7519947716-5.169480514396.341965760520.02833050529410.293920116684-0.247397538018-1.94481492104-0.274517086204-0.8043176498931.303407059720.6141891434210.2069644584770.5140507451840.005706145102-0.09655591416010.452233785678-0.1164852571570.246962723331-14.6984838544-22.69322031734.20654655962
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 18 through 40 )CC18 - 4018 - 40
22chain 'C' and (resid 41 through 113 )CC41 - 11341 - 113
33chain 'C' and (resid 114 through 189 )CC114 - 189114 - 189
44chain 'C' and (resid 190 through 229 )CC190 - 229190 - 229
55chain 'D' and (resid 29 through 81 )DD29 - 811 - 53
66chain 'D' and (resid 82 through 94 )DD82 - 9454 - 60
77chain 'D' and (resid 95 through 127 )DD95 - 12761 - 93
88chain 'D' and (resid 128 through 147 )DD128 - 14794 - 113
99chain 'E' and (resid 1 through 110 )EG1 - 1101 - 110
1010chain 'E' and (resid 111 through 217 )EG111 - 217111 - 217
1111chain 'F' and (resid 1 through 17 )FH1 - 171 - 17
1212chain 'F' and (resid 18 through 125 )FH18 - 12518 - 125
1313chain 'F' and (resid 126 through 228 )FH126 - 228126 - 222
1414chain 'A' and (resid 31 through 81 )AA31 - 811 - 51
1515chain 'A' and (resid 82 through 144 )AA82 - 14452 - 106
1616chain 'B' and (resid 1 through 110 )BB1 - 1101 - 110
1717chain 'B' and (resid 111 through 218 )BB111 - 218111 - 218
1818chain 'C' and (resid 1 through 17 )CC1 - 171 - 17

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