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- PDB-9dl1: Crystal Structure of HLA-A*02:01/NY-ESO-1 (SLLMWITQV) and a targe... -

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Basic information

Entry
Database: PDB / ID: 9dl1
TitleCrystal Structure of HLA-A*02:01/NY-ESO-1 (SLLMWITQV) and a target specific TRACeR-I
Components
  • Beta-2-microglobulin
  • Cancer/testis antigen 1
  • MHC class I antigen, A-2 alpha chain
  • TRACeR-I
KeywordsIMMUNE SYSTEM / Major Histocompatibility Complex I(MHC)
Function / homology
Function and homology information


tRNA threonylcarbamoyladenosine metabolic process / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway ...tRNA threonylcarbamoyladenosine metabolic process / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / Amyloid fiber formation / endoplasmic reticulum lumen / 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 space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CTAG/Pcc1 family / Transcription factor Pcc1 / 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 / : ...CTAG/Pcc1 family / Transcription factor Pcc1 / 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 / Beta-2-microglobulin / Cancer/testis antigen 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMallik, L. / Du, H. / Huang, P. / Sgourakis, N.G.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI143997 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM125034 United States
CitationJournal: Nat.Biotechnol. / Year: 2024
Title: Targeting peptide antigens using a multiallelic MHC I-binding system.
Authors: Du, H. / Mallik, L. / Hwang, D. / Sun, Y. / Kaku, C. / Hoces, D. / Sun, S.M. / Ghinnagow, R. / Carro, S.D. / Phan, H.A.T. / Gupta, S. / Blackson, W. / Lee, H. / Choe, C.A. / Dersh, D. / Liu, ...Authors: Du, H. / Mallik, L. / Hwang, D. / Sun, Y. / Kaku, C. / Hoces, D. / Sun, S.M. / Ghinnagow, R. / Carro, S.D. / Phan, H.A.T. / Gupta, S. / Blackson, W. / Lee, H. / Choe, C.A. / Dersh, D. / Liu, J. / Bell, B. / Yang, H. / Papadaki, G.F. / Young, M.C. / Zhou, E. / El Nesr, G. / Goli, K.D. / Eisenlohr, L.C. / Minn, A.J. / Hernandez-Lopez, R.A. / Jardine, J.G. / Sgourakis, N.G. / Huang, P.S.
History
DepositionSep 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRACeR-I
B: MHC class I antigen, A-2 alpha chain
C: Beta-2-microglobulin
D: TRACeR-I
E: Cancer/testis antigen 1
F: MHC class I antigen, A-2 alpha chain
G: Beta-2-microglobulin
H: Cancer/testis antigen 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,48911
Polymers122,2018
Non-polymers2883
Water9,404522
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.421, 95.614, 259.703
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 6 molecules ADBFCG

#1: Protein TRACeR-I


Mass: 16145.409 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Protein MHC class I antigen, A-2 alpha chain


Mass: 31985.398 Da / Num. of mol.: 2
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
#3: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / 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

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Protein/peptide , 1 types, 2 molecules EH

#4: Protein/peptide Cancer/testis antigen 1 / Autoimmunogenic cancer/testis antigen NY-ESO-1 / Cancer/testis antigen 6.1 / CT6.1 / L antigen ...Autoimmunogenic cancer/testis antigen NY-ESO-1 / Cancer/testis antigen 6.1 / CT6.1 / L antigen family member 2 / LAGE-2


Mass: 1090.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P78358

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Non-polymers , 2 types, 525 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.58 Å3/Da / Density % sol: 52.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Sodium Sulfate and 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.92 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.3→95.61 Å / Num. obs: 55335 / % possible obs: 99.1 % / Redundancy: 6.2 % / CC1/2: 0.985 / Rmerge(I) obs: 0.282 / Rpim(I) all: 0.122 / Rrim(I) all: 0.308 / Net I/σ(I): 5.7
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 6.2 % / Rmerge(I) obs: 1.717 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4538 / CC1/2: 0.444 / Rpim(I) all: 0.747 / Rrim(I) all: 1.877 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→89.73 Å / SU ML: 0.32 / Cross valid method: NONE / σ(F): 1.33 / Phase error: 26.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2654 1999 3.62 %
Rwork0.1962 --
obs0.1986 55274 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→89.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8362 0 15 522 8899
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078595
X-RAY DIFFRACTIONf_angle_d0.88111635
X-RAY DIFFRACTIONf_dihedral_angle_d6.2691115
X-RAY DIFFRACTIONf_chiral_restr0.0491195
X-RAY DIFFRACTIONf_plane_restr0.0131505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.360.34031430.28063802X-RAY DIFFRACTION100
2.36-2.420.36051400.26493740X-RAY DIFFRACTION100
2.42-2.490.3511440.26053821X-RAY DIFFRACTION100
2.49-2.570.28981410.24383780X-RAY DIFFRACTION100
2.57-2.660.32321410.2373750X-RAY DIFFRACTION99
2.67-2.770.31461430.22323819X-RAY DIFFRACTION100
2.77-2.90.30991450.22283843X-RAY DIFFRACTION100
2.9-3.050.30851430.20853806X-RAY DIFFRACTION100
3.05-3.240.25691420.20023804X-RAY DIFFRACTION100
3.24-3.490.25511440.18713844X-RAY DIFFRACTION100
3.49-3.840.26711300.17413466X-RAY DIFFRACTION89
3.84-4.40.24391450.15353852X-RAY DIFFRACTION99
4.4-5.540.1791480.14953926X-RAY DIFFRACTION100
5.54-89.730.22881500.19554022X-RAY DIFFRACTION97

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