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- PDB-9pbh: AS19.2 TCR complex with PSG5-HLA B*27:05 -

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Basic information

Entry
Database: PDB / ID: 9pbh
TitleAS19.2 TCR complex with PSG5-HLA B*27:05
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Pregnancy-specific beta-1-glycoprotein 5
  • TCR 19.2 beta chain
  • TCR19.2 alpha chain
KeywordsIMMUNE SYSTEM / TCR / complex
Function / homology
Function and homology information


heterophilic cell-cell adhesion / antigen processing and presentation of peptide antigen via MHC class I / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Cell surface interactions at the vascular wall / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane ...heterophilic cell-cell adhesion / antigen processing and presentation of peptide antigen via MHC class I / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / Cell surface interactions at the vascular wall / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / female pregnancy / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / 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 epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / positive regulation of immune response / specific granule lumen / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / sensory perception of smell / Modulation by Mtb of host immune system / tertiary granule lumen / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / late endosome membrane / ER-Phagosome pathway / early endosome membrane / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / Golgi membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / : / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane
Similarity search - Function
: / Immunoglobulin domain / Immunoglobulin domain / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like ...: / Immunoglobulin domain / Immunoglobulin domain / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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 / Beta-2-microglobulin / Pregnancy-specific beta-1-glycoprotein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsJude, K.M. / Wang, N. / Garcia, K.C.
Funding support United States, United Kingdom, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)OT2CA297242 United States
Cancer Research UKCGCATF-2023/100006 United Kingdom
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI103867 08 United States
CitationJournal: Nat.Biotechnol. / Year: 2026
Title: Deep peptide recognition profiling decodes TCR specificity and enables disease-associated antigen discovery.
Authors: Wang, N. / Yeh, H. / Lai, B. / Perera, J. / Jude, K.M. / Risch, I. / Um, J. / Chen, X. / Xiang, X. / Wang, C. / Liu, L.D. / Yang, X. / Paley, M.A. / Khan, A.A. / Garcia, K.C.
History
DepositionJun 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2026Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: Pregnancy-specific beta-1-glycoprotein 5
D: TCR19.2 alpha chain
E: TCR 19.2 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9629
Polymers95,3365
Non-polymers6274
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11690 Å2
ΔGint-44 kcal/mol
Surface area38320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.079, 52.719, 100.317
Angle α, β, γ (deg.)90.000, 96.346, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 4 types, 4 molecules ABDE

#1: Protein MHC class I antigen


Mass: 32217.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B / Production host: Escherichia coli (E. coli) / References: UniProt: A3F718
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
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 TCR19.2 alpha chain


Mass: 22716.121 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)
#5: Protein TCR 19.2 beta chain


Mass: 27529.416 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, 3 molecules C

#3: Protein/peptide Pregnancy-specific beta-1-glycoprotein 5 / PS-beta-G-5 / PSBG-5 / Pregnancy-specific glycoprotein 5 / Fetal liver non-specific cross-reactive ...PS-beta-G-5 / PSBG-5 / Pregnancy-specific glycoprotein 5 / Fetal liver non-specific cross-reactive antigen 3 / FL-NCA-3


Mass: 993.224 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15238
#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.: 2 / 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, 142 molecules

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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.32 Å3/Da / Density % sol: 46.93 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium formate; 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 27, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.13→49.85 Å / Num. obs: 47977 / % possible obs: 97.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 39.03 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.091 / Rrim(I) all: 0.169 / Χ2: 0.99 / Net I/σ(I): 7.3
Reflection shellResolution: 2.13→2.19 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.283 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3933 / CC1/2: 0.37 / Rpim(I) all: 0.807 / Rrim(I) all: 1.522 / Χ2: 0.94 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→44.59 Å / SU ML: 0.3626 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.1289
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2465 1436 2.99 %
Rwork0.2097 46513 -
obs0.2107 47949 97.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.89 Å2
Refinement stepCycle: LAST / Resolution: 2.13→44.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6645 0 40 140 6825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00336855
X-RAY DIFFRACTIONf_angle_d0.58059319
X-RAY DIFFRACTIONf_chiral_restr0.0432999
X-RAY DIFFRACTIONf_plane_restr0.00451227
X-RAY DIFFRACTIONf_dihedral_angle_d12.07572550
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.210.38871460.32564676X-RAY DIFFRACTION97.73
2.21-2.290.36591450.30574609X-RAY DIFFRACTION97.78
2.29-2.40.31591420.34656X-RAY DIFFRACTION97.84
2.4-2.530.32221360.27854460X-RAY DIFFRACTION94.16
2.53-2.680.32861450.26444689X-RAY DIFFRACTION98.11
2.68-2.890.26331470.24974697X-RAY DIFFRACTION98.88
2.89-3.180.24721440.22154700X-RAY DIFFRACTION98.72
3.18-3.640.26591370.20064602X-RAY DIFFRACTION95.45
3.64-4.590.20221460.16194678X-RAY DIFFRACTION97.2
4.59-44.590.18471480.16684746X-RAY DIFFRACTION95.81
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)
13.57486509283-0.8742172428453.801649163582.25689249015-0.6470993474756.426807648240.1566815856850.0143349344426-0.3499790935-0.187966086275-0.002651345222630.3372285794050.156580215245-0.0186086701493-0.1442093317710.3004556944670.01327847747020.02337431912540.266837061204-0.02521275834140.346693578673-0.43110.847-29.51
24.16587571830.218172911429-0.1871369210054.07224288160.9890732663723.277482341570.04077970663930.708796378798-0.585546261354-0.9601552076760.160506339090.821337740949-0.1210238490330.328753745609-0.2004375148640.8578829433060.0584122285124-0.4247255887990.693085363339-0.1398512383411.01463361453-20.10519.503-56.275
31.778680515420.3698753259840.04036360939794.19803206353-3.259578229175.628244066010.0331726921221-0.03139512928290.148093635840.343555309021-0.151532567789-0.111179878836-0.5093621547150.2424649543540.1233572248120.342108222974-0.01792421312740.01046298672160.256877150551-0.03158742503630.2685700694634.10933.28-24.887
43.726967860530.9212634219010.5376687982683.464596370670.3384524366141.079837163370.01103044093740.148944858238-0.213591131067-0.4574635290180.006978260783990.941126531197-0.0593430905557-0.135990407978-0.01603408430110.5297748135090.0553821693107-0.1805932317430.3919774736420.02414890824870.603802067352-17.73433.498-46.147
52.21379703614-0.685037634317-0.5404682690532.32410610110.8168137836361.696356802110.1027118816620.1714944524040.0768953618791-0.2400349340310.00523574384259-0.436440126176-0.1559928170180.215728109629-0.1186120231810.242034022711-0.03595692162840.06416927232270.3675458022810.02554508731230.35262507010822.84815.225-5.107
63.57973849465-0.4225770666360.1030050809052.03320121270.6009741280831.37291306372-0.0291995143281-0.0634353492719-0.1523634846720.296926162175-0.06188472936060.1265254468870.08263050951920.001733859299020.09217879463050.286820894829-0.01012932564210.05922873547280.2970065745980.05674708806220.2536242851157.9513.7842.943
73.63559911362-3.52615129322-0.5520646148466.6933282388-0.6038155407423.25664877973-0.004991944605830.191163710729-0.753123945352-0.0484600859730.1017710420370.4040332307670.254073942777-0.0369984784343-0.1105830751570.26115583357-0.009957394437340.01005691754830.312932179563-0.03346095057470.29318567455512.8522.167-9.556
82.60006386417-0.7131777084461.314737155362.36414951159-0.1961634251366.664797578320.053688042287-0.3407609597-0.3367733229470.6269669825370.169788031192-0.1759254466420.7931615231530.0868205883432-0.2195538626780.4814697523260.0760611939795-0.04685290053660.3764946792310.09123238406210.55020370149435.066-8.37319.563
90.6247807645620.72191883111-1.029351748634.080445378531.7355624344.239815083980.206275052801-0.266698603415-1.08008867954-0.459272452579-0.4115431347881.1250948974-0.217486461139-0.6327805445910.07245455346670.280908556601-0.0301280623782-0.03684681933360.522633535784-0.08586153582080.41843015297429.19212.66317.584
106.642082038073.085241012590.0760284704252.100283834381.090064545561.8347946347-0.06011906628910.594205267546-0.375694602625-0.1068586305510.622087919098-0.9369153007540.292839307270.607379136561-0.4889056538520.3204792496140.102611922929-0.02659271061280.545156592505-0.2062481820420.79504975520949.3521.58911.64
117.0135050913-2.70129696747-0.799533609432.903028778270.8735853914952.749581247790.1707015446280.340510112143-0.955604153426-0.210024312579-0.2325929149280.141291447204-0.1901664925970.03138393252850.03992513975930.2727083437020.02468348194790.02296353902790.416505206482-0.02563047669150.33381642254436.9219.91411.86
124.13594060192-3.020425343132.184171088153.74021205503-0.6121147248563.30722920049-0.123637217646-0.1402317109211.31132395396-0.266127384398-0.100523381422-0.444043015937-0.8891390021280.1400473127240.144728386160.340394968001-0.0631683228768-0.02822137410930.434201854226-0.03881668494440.44631486768434.09620.08413.388
137.77245761605-1.002003803943.186796434442.473341125910.8886454985348.784897278730.00347316872373-0.0509472917730.7049567563120.00634582733050.478873447240.0584179933641-1.066804279580.868579605576-0.3437908079660.310838682938-0.140804614951-0.0007865497604690.6024950636980.05771907369420.75445698230547.87320.90715.268
145.189933176096.32334526618-2.08533122628.73518913471-1.624543313664.58623021070.0864183428642.022670498890.85836245586-0.3867222430.464592998152-0.583784706148-1.044177145391.24548338515-0.4287385683740.402456314303-0.1792295057140.02860626302250.6039797755840.08419987423710.56855816405341.97617.7874.914
152.67403407573-0.4673114952512.387512108132.07323140820.1285068126932.19797038252-0.05093133509330.064427518441-0.805605103623-0.1163897250740.0470996303056-0.289321319573-0.1165191858770.2086927406750.03056221533450.233571563054-0.004218614037170.02929842371820.3385532778830.04618361304530.3259603719830.3411.8768.221
161.37937697997-1.38923484354-0.369523997986.47882907053-2.687923389512.96169539703-0.168313580480.258245114391-0.2078448913941.5506881145-0.275955706426-1.20931660237-0.01439748477371.240946606750.3669509540730.380842195007-0.02617166234240.01043445164050.62880337555-0.1071209109620.92851699018153.84810.09719.406
178.65243332289-5.62009585966-1.541564011964.60832492880.07748664532521.14780857383-0.322332456130.499585409142-0.803613016728-0.07181430111340.1010258865920.380536273018-0.575885259180.02322771937390.08124064854490.3003715646040.0116504644473-0.04259086921290.581417383486-0.1653873804420.5431632193840.03917.92517.726
189.58708696312-3.39184384578-4.750416218983.52503105876-1.973852652698.30500614347-0.592769009665-1.504590662180.7614907826250.7335873006480.273386703294-1.00175379093-0.07882660290330.2612828861060.3805473174220.4009002926780.0833870148322-0.07011866080810.488447544182-0.1185869705520.48552517745929.52223.52521.813
195.82118988517-2.471089775660.7889537819482.01542197901-1.660775623984.91957254681-0.167195197398-0.448596749502-0.576732688430.9389064888520.258837060175-0.1306650720830.07111150971460.4375666758780.03684815776530.477838324350.047869604144-0.117562056670.45558001139-0.009485541481960.44792680957742.1798.65521.888
202.84783004756-1.243547323-0.4535334030720.7374681749650.6091505433681.725301476460.0870168844592-0.2698778426270.09800443434490.252567641197-0.07802385264310.1955559660710.002910592137490.1057480533590.121604087720.326426172831-0.038172891590.09266025688570.291146475279-0.008592854994230.37623316735911.86515.542-7.674
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN D AND ( RESID 2:124 OR RESID 301:301 ) )D2 - 124
2X-RAY DIFFRACTION1( CHAIN D AND ( RESID 2:124 OR RESID 301:301 ) )D301
3X-RAY DIFFRACTION2( CHAIN D AND RESID 125:206 )D125 - 206
4X-RAY DIFFRACTION3( CHAIN E AND ( RESID 1:108 OR RESID 301:301 ) )E1 - 108
5X-RAY DIFFRACTION3( CHAIN E AND ( RESID 1:108 OR RESID 301:301 ) )E301
6X-RAY DIFFRACTION4( CHAIN E AND RESID 109:243 )E109 - 243
7X-RAY DIFFRACTION5( CHAIN A AND RESID 1:84 )A1 - 84
8X-RAY DIFFRACTION6( CHAIN A AND RESID 85:150 )A85 - 150
9X-RAY DIFFRACTION7( CHAIN A AND RESID 151:174 )A151 - 174
10X-RAY DIFFRACTION8( CHAIN A AND RESID 175:276 )A175 - 276
11X-RAY DIFFRACTION9( CHAIN B AND RESID 1:11 )B1 - 11
12X-RAY DIFFRACTION10( CHAIN B AND RESID 12:19 )B12 - 19
13X-RAY DIFFRACTION11( CHAIN B AND RESID 20:30 )B20 - 30
14X-RAY DIFFRACTION12( CHAIN B AND RESID 31:41 )B31 - 41
15X-RAY DIFFRACTION13( CHAIN B AND RESID 42:46 )B42 - 46
16X-RAY DIFFRACTION14( CHAIN B AND RESID 47:51 )B47 - 51
17X-RAY DIFFRACTION15( CHAIN B AND RESID 52:71 )B52 - 71
18X-RAY DIFFRACTION16( CHAIN B AND RESID 72:77 )B72 - 77
19X-RAY DIFFRACTION17( CHAIN B AND RESID 78:83 )B78 - 83
20X-RAY DIFFRACTION18( CHAIN B AND RESID 84:90 )B84 - 90
21X-RAY DIFFRACTION19( CHAIN B AND RESID 91:99 )B91 - 99
22X-RAY DIFFRACTION20( CHAIN C AND RESID 1:9 )C1 - 9

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