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- PDB-9sol: Structure of TCR-581 in complex with Peptide-HLA -

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Basic information

Entry
Database: PDB / ID: 9sol
TitleStructure of TCR-581 in complex with Peptide-HLA
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • Piwi-like protein 1
  • TCR alpha
  • TCR beta
KeywordsIMMUNE SYSTEM / HLA / MHC / TCR / T cell receptor
Function / homology
Function and homology information


primary piRNA processing / mRNA cap binding complex binding / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / transposable element silencing by piRNA-mediated heterochromatin formation / piRNA processing / sperm DNA condensation / chromatoid body / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / dense body ...primary piRNA processing / mRNA cap binding complex binding / piRNA binding / piRNA-mediated gene silencing by mRNA destabilization / transposable element silencing by piRNA-mediated heterochromatin formation / piRNA processing / sperm DNA condensation / chromatoid body / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / dense body / regulatory ncRNA-mediated gene silencing / P granule / spermatid development / PIWI-interacting RNA (piRNA) biogenesis / RNA endonuclease activity / regulation of natural killer cell mediated immunity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / 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 / 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 / peptide antigen assembly with MHC class II protein complex / MHC class I protein complex / negative regulation of epithelial cell proliferation / cellular response to nicotine / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / negative regulation of neurogenesis / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / specific granule lumen / peptide antigen binding / phagocytic vesicle membrane / positive regulation of T cell activation / Interferon gamma signaling / recycling endosome membrane / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / sensory perception of smell / tertiary granule lumen / Modulation by Mtb of host immune system / positive regulation of cellular senescence / MHC class II protein complex binding / DAP12 signaling / late endosome membrane / ER-Phagosome pathway / early endosome membrane / spermatogenesis / amyloid fibril formation / protein homotetramerization / intracellular iron ion homeostasis / learning or memory / single-stranded RNA binding / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / external side of plasma membrane / Golgi membrane / focal adhesion / lysosomal membrane / mRNA binding / Neutrophil degranulation / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / : / protein homodimerization activity / extracellular exosome / extracellular region / membrane / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
GAGE / GAGE protein / GAGE / Piwi, N-terminal domain / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi ...GAGE / GAGE protein / GAGE / Piwi, N-terminal domain / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain profile. / Piwi domain / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain profile. / PAZ domain / 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 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 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 / Piwi-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.93 Å
AuthorsKaruppiah, V. / Rangel, V.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other private United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: Isolation of Human TCRs specific to any peptide-HLA complex
Authors: Karuppiah, V. / Rangel, V.L.
History
DepositionSep 14, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: Piwi-like protein 1
D: TCR alpha
E: TCR beta
F: MHC class I antigen
G: Beta-2-microglobulin
H: Piwi-like protein 1
I: TCR alpha
J: TCR beta
K: MHC class I antigen
L: Beta-2-microglobulin
M: Piwi-like protein 1
N: TCR alpha
O: TCR beta
P: MHC class I antigen
Q: Beta-2-microglobulin
R: Piwi-like protein 1
S: TCR alpha
T: TCR beta


Theoretical massNumber of molelcules
Total (without water)382,22020
Polymers382,22020
Non-polymers00
Water00
1
A: MHC class I antigen
B: Beta-2-microglobulin
C: Piwi-like protein 1
D: TCR alpha
E: TCR beta


Theoretical massNumber of molelcules
Total (without water)95,5555
Polymers95,5555
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: MHC class I antigen
G: Beta-2-microglobulin
H: Piwi-like protein 1
I: TCR alpha
J: TCR beta


Theoretical massNumber of molelcules
Total (without water)95,5555
Polymers95,5555
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
K: MHC class I antigen
L: Beta-2-microglobulin
M: Piwi-like protein 1
N: TCR alpha
O: TCR beta


Theoretical massNumber of molelcules
Total (without water)95,5555
Polymers95,5555
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
P: MHC class I antigen
Q: Beta-2-microglobulin
R: Piwi-like protein 1
S: TCR alpha
T: TCR beta


Theoretical massNumber of molelcules
Total (without water)95,5555
Polymers95,5555
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)237.232, 238.081, 175.587
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
MHC class I antigen


Mass: 31951.316 Da / Num. of mol.: 4
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: A0A5B8RNS7
#2: Protein
Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 4
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
#3: Protein/peptide
Piwi-like protein 1


Mass: 1129.288 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q96J94, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#4: Protein
TCR alpha


Mass: 22996.207 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein
TCR beta


Mass: 27598.951 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
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: 3.24 Å3/Da / Density % sol: 62.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium citrate tribasic dihydrate, 0.1 M Bis-Tris propane pH 7.5 and 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Aug 11, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.93→168.05 Å / Num. obs: 106930 / % possible obs: 100 % / Redundancy: 14.1 % / CC1/2: 1 / Rrim(I) all: 0.223 / Net I/σ(I): 8
Reflection shellResolution: 2.93→2.98 Å / Redundancy: 14.5 % / Mean I/σ(I) obs: 0.7 / Num. unique obs: 5274 / CC1/2: 0.4 / Rrim(I) all: 4.334 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.93→168.05 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.916 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26999 5318 -RANDOM
Rwork0.23183 ---
obs0.23378 101378 99.76 %-
Displacement parametersBiso mean: 94.912 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å2-0 Å20 Å2
2--0.88 Å2-0 Å2
3----1.59 Å2
Refinement stepCycle: LAST / Resolution: 2.93→168.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26430 0 0 0 26430
LS refinement shellResolution: 2.93→2.98 Å /
Rfactor% reflection
Rfree0.396 -
Rwork0.396 -
obs-97 %
Refinement TLS params.

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)
11.1473-0.22980.19412.1371-1.81643.04930.0581-0.32090.3852-0.3209-0.1040.35960.38520.35960.04590.05960.01930.00350.23520.17960.3827-83.8017-21.50212.4763
22.4429-0.58131.26453.2133-1.51427.2709-0.2807-0.52020.23-0.52020.0162-0.68340.23-0.68340.26450.152-0.1035-0.09890.33170.19150.4389-101.4321-19.6745-5.502
36.5593-4.2152-1.62372.71481.19899.5135-0.10930.0580.77810.0580.1270.85130.77810.8513-0.01770.2239-0.04560.02620.29720.10960.3538-80.5935-33.616218.6479
41.84270.26120.76712.9154-2.52784.53760.23110.59460.30760.5946-0.39880.63350.30760.63350.16770.43760.09960.02510.49890.11830.5803-67.9072-45.321153.5721
52.0054-0.25280.21931.7217-2.59974.4444-0.12320.3941-0.19670.39410.2036-0.2639-0.1967-0.2639-0.08040.43430.07660.26340.27280.05510.5996-86.9906-49.153954.7997
61.52380.33320.3411.8981.82213.08990.12530.37870.36280.3787-0.1955-0.34460.3628-0.34460.07020.0988-0.0205-0.06990.0769-0.11660.5162-28.9375-21.657285.8172
73.41920.10681.32392.92470.84496.9313-0.13120.50120.23410.50120.06630.55730.23410.55730.06490.12430.0704-0.13040.1689-0.11310.5071-11.3142-19.547393.7412
80.89562.0925-0.74594.9479-2.14846.10170.08490.13490.47270.13490.0541-0.63990.4727-0.6399-0.13910.14490.027-0.04650.2435-0.0960.4757-32.0378-33.973269.7775
91.1492-0.84260.16293.14961.7063.94620.1978-0.64120.5308-0.6412-0.3458-0.46010.5308-0.46010.1480.4135-0.14430.02710.8751-0.26860.6808-44.6556-46.18135.001
102.0179-0.1768-0.16391.34742.22024.5862-0.1071-0.3095-0.1108-0.30950.03810.1276-0.11080.12760.0690.3255-0.02220.26720.3334-0.02030.7891-25.5319-49.809533.7751
112.1532-0.15131.88511.2751-0.55273.2787-0.02630.1414-0.2350.14140.1284-0.3806-0.235-0.3806-0.10210.0587-0.0052-0.02790.11970.10720.2772-83.7041-27.1981129.6058
122.3569-0.02480.35383.2994-0.69496.26990.05950.28850.58990.2885-0.0274-0.3820.5899-0.382-0.03210.143-0.0919-0.11530.18520.18950.3996-81.9592-44.7509137.7714
135.0423-5.2101-1.64615.9203-0.40768.85590.17-0.0009-0.7166-0.00090.1853-0.5334-0.7166-0.5334-0.35530.2094-0.1125-0.03940.21780.02330.3071-95.8231-24.0999113.4163
143.1760.42181.53812.2685-0.44233.0732-0.2685-0.6078-0.448-0.6078-0.0198-0.2576-0.448-0.25760.28840.52180.1202-0.06880.42170.03040.4607-107.5082-11.728878.3727
151.137-0.22051.92421.6075-0.09294.67470.1481-0.58210.2584-0.5821-0.21340.14290.25840.14290.06530.30210.05740.00920.4366-0.17740.4924-111.4443-30.803777.3563
161.83370.4631-1.76831.3191-0.29163.2243-0.0951-0.17940.2647-0.17940.1648-0.37410.2647-0.3741-0.06970.0739-0.01150.05770.10240.0540.3293-77.9645-91.430346.0912
172.01750.4162-0.94293.4998-0.54456.94630.0417-0.38-0.6846-0.38-0.0767-0.3005-0.6846-0.30050.0350.15050.06960.0730.15240.16430.3746-76.009-73.740538.2765
185.13073.78625.945912.0487-0.22889.19490.40120.10920.58310.10920.16930.50140.58310.5014-0.57050.11930.08420.09960.2285-0.01840.2881-90.1119-94.702762.225
193.6214-0.6527-2.73121.9925-0.2774.4556-0.2550.63580.43770.63580.2001-0.11160.4377-0.11160.05480.5143-0.08660.14960.4842-0.00160.5266000
201.8135-0.152-2.69071.4511-0.13374.65110.15940.6507-0.40210.6507-0.16930.5089-0.40210.50890.010.4082-0.10520.08050.579-0.27310.6531-105.63-88.530398.4243
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 276
2X-RAY DIFFRACTION2B0 - 99
3X-RAY DIFFRACTION3C1 - 9
4X-RAY DIFFRACTION4D3 - 197
5X-RAY DIFFRACTION5E2 - 241
6X-RAY DIFFRACTION6F1 - 276
7X-RAY DIFFRACTION7G0 - 99
8X-RAY DIFFRACTION8H1 - 9
9X-RAY DIFFRACTION9I3 - 197
10X-RAY DIFFRACTION10J2 - 241
11X-RAY DIFFRACTION11K1 - 276
12X-RAY DIFFRACTION12L0 - 99
13X-RAY DIFFRACTION13M1 - 9
14X-RAY DIFFRACTION14N3 - 197
15X-RAY DIFFRACTION15O2 - 241
16X-RAY DIFFRACTION16P1 - 276
17X-RAY DIFFRACTION17Q0 - 99
18X-RAY DIFFRACTION18R1 - 9
19X-RAY DIFFRACTION19S3 - 197
20X-RAY DIFFRACTION20T2 - 241

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