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- PDB-9nmu: TCR156 bound to HLA A*02:01-PAP -

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Basic information

Entry
Database: PDB / ID: 9nmu
TitleTCR156 bound to HLA A*02:01-PAP
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A alpha chain
  • Prostatic acid phosphatase
  • TCR156 alpha chain
  • TCR156 beta chain
KeywordsIMMUNE SYSTEM / complex / TCR
Function / homology
Function and homology information


thiamine phosphate phosphatase activity / positive regulation of adenosine receptor signaling pathway / thiamine metabolic process / Golgi cisterna / adenosine metabolic process / acid phosphatase / regulation of sensory perception of pain / acid phosphatase activity / lysophosphatidic acid phosphatase activity / 5'-nucleotidase ...thiamine phosphate phosphatase activity / positive regulation of adenosine receptor signaling pathway / thiamine metabolic process / Golgi cisterna / adenosine metabolic process / acid phosphatase / regulation of sensory perception of pain / acid phosphatase activity / lysophosphatidic acid phosphatase activity / 5'-nucleotidase / 5'-nucleotidase activity / choline binding / nucleotide metabolic process / vesicle membrane / azurophil granule membrane / purine nucleobase metabolic process / phosphatase activity / antigen processing and presentation of peptide antigen via MHC class I / multivesicular body / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / filopodium / lipid metabolic process / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / cellular response to iron(III) ion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / multicellular organismal-level iron ion homeostasis / positive regulation of T cell mediated cytotoxicity / specific granule lumen / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / negative regulation of epithelial cell proliferation / positive regulation of T cell activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / apical part of cell / Modulation by Mtb of host immune system / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / T cell differentiation in thymus / late endosome membrane / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / molecular adaptor activity / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / : / extracellular exosome / extracellular region / membrane / identical protein binding / nucleus
Similarity search - Function
Histidine acid phosphatases active site signature. / : / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin ...Histidine acid phosphatases active site signature. / : / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
MHC class I antigen / Prostatic acid phosphatase / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJude, K.M. / Chen, X. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5 R01 AI103867 08 United States
CitationJournal: To Be Published
Title: T cell receptor catch bond engineering enhances T cell function and killing of prostate cancer
Authors: Chen, X. / Jude, K.M. / Garcia, K.C.
History
DepositionMar 4, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: Prostatic acid phosphatase
D: TCR156 alpha chain
E: TCR156 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,16115
Polymers107,8535
Non-polymers1,30810
Water4,792266
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)225.107, 47.349, 90.730
Angle α, β, γ (deg.)90.000, 95.827, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 4 types, 4 molecules ABDE

#1: Protein HLA class I histocompatibility antigen, A alpha chain / HLA A*02:01


Mass: 32256.670 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A / Production host: Escherichia coli (E. coli) / References: UniProt: A5I8L1
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#4: Protein TCR156 alpha chain


Mass: 28261.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Protein TCR156 beta chain


Mass: 34474.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)

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Protein/peptide / Sugars , 2 types, 4 molecules C

#3: Protein/peptide Prostatic acid phosphatase / PAP / 5'-nucleotidase / 5'-NT / Acid phosphatase 3 / Ecto-5'-nucleotidase / Protein tyrosine ...PAP / 5'-nucleotidase / 5'-NT / Acid phosphatase 3 / Ecto-5'-nucleotidase / Protein tyrosine phosphatase ACP3 / Thiamine monophosphatase / TMPase


Mass: 981.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ACP3, ACPP / Production host: synthetic construct (others)
References: UniProt: P15309, acid phosphatase, 5'-nucleotidase, protein-tyrosine-phosphatase
#7: 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.: 3 / Source method: obtained synthetically / 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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Non-polymers , 2 types, 273 molecules

#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.23 Å3/Da / Density % sol: 44.84 %
Crystal growTemperature: 295 K / Method: vapor diffusion
Details: 0.2 M Sodium malonate, 0.1 M bis Tris-propane pH 7.5, 17% PEG 3500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Apr 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→46.32 Å / Num. obs: 55350 / % possible obs: 98.39 % / Redundancy: 3.2 % / Biso Wilson estimate: 42.06 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.09938 / Rpim(I) all: 0.06568 / Rrim(I) all: 0.1197 / Net I/σ(I): 7.03
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.9876 / Mean I/σ(I) obs: 1.01 / Num. unique obs: 4641 / CC1/2: 0.583 / Rpim(I) all: 0.6305 / Rrim(I) all: 1.176 / % possible all: 99.38

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.32 Å / SU ML: 0.2721 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6072
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2265 1703 3.08 %
Rwork0.1933 53621 -
obs0.1943 55324 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.39 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6597 0 84 266 6947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00366875
X-RAY DIFFRACTIONf_angle_d0.61369326
X-RAY DIFFRACTIONf_chiral_restr0.0422984
X-RAY DIFFRACTIONf_plane_restr0.0051219
X-RAY DIFFRACTIONf_dihedral_angle_d14.31692560
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.36071430.3224493X-RAY DIFFRACTION99.38
2.16-2.230.33031410.29034446X-RAY DIFFRACTION98.92
2.23-2.310.28841400.27544410X-RAY DIFFRACTION98.81
2.31-2.40.26411420.25654474X-RAY DIFFRACTION98.86
2.4-2.510.27421420.24344436X-RAY DIFFRACTION98.07
2.51-2.650.32441340.25874217X-RAY DIFFRACTION93.63
2.65-2.810.29211430.22974503X-RAY DIFFRACTION99.57
2.81-3.030.24781440.2114517X-RAY DIFFRACTION99.62
3.03-3.330.23711430.20344498X-RAY DIFFRACTION99.66
3.33-3.820.1961440.16674539X-RAY DIFFRACTION99.38
3.82-4.810.1741420.14484527X-RAY DIFFRACTION98.15
4.81-46.320.19231450.1664561X-RAY DIFFRACTION96.71
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)
12.69001409658-0.6772480686470.002630983438742.41494986506-0.1693125788073.931231254370.02377022944930.158787900087-0.0764775060408-0.163759367623-0.05674234111610.05258831385670.332421503966-0.1278093377030.06268324383890.267126334124-0.0199087302468-0.01501090200410.274723211696-0.01621282172330.315408410797-41.3032204302-6.31341492745-6.24196391583
22.98595690317-0.633474982660.09347274190462.597843992161.002400429012.939100017070.03397412699120.07296100939570.427267659655-0.209584442873-0.107893017047-0.306471725138-0.1659754615860.197748767210.02894518393010.2707316673770.005323840859120.01716515025450.2491817300330.06315507737420.404210405753-34.99005238966.97646541646-3.19902521357
32.028788691960.6712980618830.9398671503173.35873770839-0.356394417284.46289332149-0.08522175906140.9825191074020.829836983779-0.5959844154830.1924470119150.474324790819-0.862298193643-0.0532201914314-0.05576039308890.7469823753250.03684561104730.07136879597730.7711708870110.3354730665980.587055868421-51.246636403213.5067161118-34.0914590229
43.887598445770.22209547255-0.5823746972274.02230693011-0.2151704870634.04096300841-0.01161346231460.5500370974560.175683673912-0.5983800981690.131814532253-0.1648185760640.141225509973-0.0699148067864-0.02206440612460.3022635158210.0233153102945-0.07302928489450.4207369387760.02217607201620.323849436533-58.06543945272.18258020658-22.6209025807
52.684199241090.001132667000311.952487228342.602622368870.8209123802275.815857588730.1247839407530.0898280850398-0.193256455904-0.09671967221190.01354747158330.03299116313210.477099004481-0.350278336224-0.1293760228120.3379056855970.00857757072642-0.0009794390535410.366124738360.04046285051830.339668092831-57.1865348698-2.98014344124-17.3186888968
65.504033029320.6666958423931.574576165338.607059772430.7906600125085.796772373970.4973731352111.40683285593-0.548676875468-0.8135860496610.04080285228780.942487769679-0.0691995642429-1.25298224383-0.4408915237390.955605197997-0.0309415162241-0.2710102376841.1293591983-2.52426910102E-50.601415178236-70.4553687208-5.70512701719-33.8078689597
73.112764500260.1472013047020.794005542863.063119759841.674834637886.5525724365-0.2218470871390.4866727688580.275625855027-0.395641236368-0.1542770319090.344529311559-0.164936748506-1.285667108450.240737248050.4104873040860.030136226468-0.09494055298450.6473251487790.09730590945030.45709034672-66.03761187212.14886176815-19.3983794838
82.90065039066-1.08422061602-2.12161899590.8821022516670.5299971509375.033168186420.100516182962-0.03822927569040.760177483542-0.1084043210410.197038232226-0.20822819489-0.4182848775140.641400493482-0.182171614230.252348065359-0.004105024600760.01337492098350.354326932875-0.01035043249430.505276663899-33.7853570425-1.180331080550.561974106439
95.341467140350.03312326960250.7038130784211.33293408912-0.3343218952362.884159282240.08010137058030.0823379084530.1942257936440.0678077455304-0.0284144076474-0.02006842817690.006990115611530.153450418784-0.05041417268240.227619642940.007749847368190.01483549436410.251881850869-0.01798637376450.305328136235-11.425672664-6.536912734664.12545670249
104.14398200915-0.7416300821093.133882257711.9860902856-1.367289604996.25460570933-0.519592989371-0.279931125132-0.1657983072220.306619525425-0.0254904445789-0.589909532687-0.01469451552710.9834499379520.4195285621390.4141088724050.1740418060770.04186960917140.6994002957240.07900266954350.4933039462168.25636293035-16.736529606825.473996311
114.078776037990.9970263598950.07495308389414.030186693150.6650082294823.71308478094-0.112737818696-0.255735864959-0.743497250496-0.820653358335-0.0753337334815-0.725454123570.2239135451980.6947215853570.218430232620.6498750735670.09507482328810.1704016129710.6142700264520.1290053442660.52986381276311.7751480812-21.302559909124.4427445872
124.09633433294-3.107675234671.229891932776.85000176839-2.638966300934.008607784510.150186576926-0.619232197931-0.1661544017480.204553220857-0.005874735110640.2975463329670.27799466682-0.0235617395486-0.07984546021450.352342963661-0.0746849242277-0.002395494798760.344945059212-0.01622301663350.272759791537-27.6112826078-17.08187838122.9877194448
133.48930398918-1.165963027591.265322938272.57159993395-1.077112264553.654992069030.164262410194-0.0767097479145-0.1314167892230.0383033619673-0.01767076861370.08720434067270.3610662828690.0152936033207-0.1541108125690.325179268514-0.05085749961250.01010222569550.267460788422-0.02320685483920.340772006318-28.2302795731-16.898222694213.7389498227
144.298985793540.4652335251883.252171841720.06202456301840.4591839126453.556437384360.362734466583-0.718805537568-0.8059655147980.058681732296-0.141851904723-0.069768153970.8219568118880.181633504705-0.147238039690.745111492024-0.0690189742921-0.07737601626530.4440629470320.1548567584250.517515672458-16.5911407674-29.672780373727.888077863
153.95806566521.14641839258-0.6661514480653.37442658631-0.8609750837822.81916491424-0.149165405819-0.289462674761-0.36968509959-0.265993975744-0.0651860136138-0.343230230326-0.04931574857440.6748522052080.1976765805770.5008337635410.0589159936302-0.03371805262690.574351257380.09486258228840.3201080595471.8920799231-18.078803885232.2480682251
166.871786770723.367368370831.582896662224.691026548351.499186185453.106250609030.382400313755-0.687324966836-0.003292587688230.522127256692-0.3653856649670.1353847684970.2753196045250.11958496731-0.02341531131430.614824501084-0.0386396622937-0.05293733305350.6626594724460.1325409474410.26197796143-8.3473225283-21.083332788440.2694549453
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 84 )AA1 - 841 - 84
22chain 'A' and (resid 85 through 174 )AA85 - 17485 - 174
33chain 'A' and (resid 175 through 276 )AA175 - 276175 - 276
44chain 'B' and (resid 1 through 20 )BE1 - 201 - 20
55chain 'B' and (resid 21 through 72 )BE21 - 7221 - 72
66chain 'B' and (resid 73 through 78 )BE73 - 7873 - 78
77chain 'B' and (resid 79 through 100 )BE79 - 10079 - 100
88chain 'C' and (resid 1 through 9 )CH1 - 91 - 9
99chain 'D' and (resid 2 through 98 )DI2 - 981 - 97
1010chain 'D' and (resid 99 through 128 )DI99 - 12898 - 127
1111chain 'D' and (resid 129 through 198 )DI129 - 198128 - 197
1212chain 'E' and (resid 3 through 30 )EL3 - 301 - 28
1313chain 'E' and (resid 31 through 106 )EL31 - 10629 - 104
1414chain 'E' and (resid 107 through 121 )EL107 - 121105 - 119
1515chain 'E' and (resid 122 through 200 )EL122 - 200120 - 198
1616chain 'E' and (resid 201 through 242 )EL201 - 242199 - 240

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