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- PDB-7n2s: AS3.1-PRPF3-HLA*B27 -

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Basic information

Entry
Database: PDB / ID: 7n2s
TitleAS3.1-PRPF3-HLA*B27
Components
  • (T cell receptor ...) x 2
  • Beta-2-microglobulin
  • Human leukocyte antigen (HLA) B27
  • Pre-MRNA Processing Factor 3
KeywordsIMMUNE SYSTEM / TCR MHC HLA-B27
Function / homology
Function and homology information


: / : / 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 ...: / : / 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
Similarity search - Function
MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / : ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
MHC class I antigen / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsYang, X. / Jude, K.M. / Garcia, K.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5R01AI103867 United States
CitationJournal: Nature / Year: 2022
Title: Autoimmunity-associated T cell receptors recognize HLA-B*27-bound peptides.
Authors: Yang, X. / Garner, L.I. / Zvyagin, I.V. / Paley, M.A. / Komech, E.A. / Jude, K.M. / Zhao, X. / Fernandes, R.A. / Hassman, L.M. / Paley, G.L. / Savvides, C.S. / Brackenridge, S. / Quastel, M. ...Authors: Yang, X. / Garner, L.I. / Zvyagin, I.V. / Paley, M.A. / Komech, E.A. / Jude, K.M. / Zhao, X. / Fernandes, R.A. / Hassman, L.M. / Paley, G.L. / Savvides, C.S. / Brackenridge, S. / Quastel, M.N. / Chudakov, D.M. / Bowness, P. / Yokoyama, W.M. / McMichael, A.J. / Gillespie, G.M. / Garcia, K.C.
History
DepositionMay 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 2.0Dec 14, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / entity ...atom_site / entity / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym
Item: _entity.pdbx_number_of_molecules / _pdbx_struct_assembly_gen.asym_id_list
Revision 2.1Dec 21, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 2.2Jan 4, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Pre-MRNA Processing Factor 3
A: Human leukocyte antigen (HLA) B27
B: Beta-2-microglobulin
D: T cell receptor alpha chain
F: T cell receptor beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,2727
Polymers94,9595
Non-polymers3132
Water724
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)83.211, 52.789, 106.291
Angle α, β, γ (deg.)90.000, 98.278, 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 , 2 types, 2 molecules AB

#2: Protein Human leukocyte antigen (HLA) B27 / HLA-B27


Mass: 32086.250 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
#3: 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

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T cell receptor ... , 2 types, 2 molecules DF

#4: Protein T cell receptor alpha chain


Mass: 22682.059 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 T cell receptor beta chain


Mass: 27327.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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

#1: Protein/peptide Pre-MRNA Processing Factor 3


Mass: 984.236 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#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.: 1 / 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, 5 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25% PEG3350 with 0.2M Ammonium tartrate dibasic dihydrate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-1 / Wavelength: 0.97946 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.37→47.56 Å / Num. obs: 23506 / % possible obs: 97.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 33.76 Å2 / CC1/2: 0.974 / Net I/σ(I): 4.9
Reflection shellResolution: 2.75→2.88 Å / Num. unique obs: 2936 / CC1/2: 0.506

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122+SVNrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KSB, 1JGE

5ksb

1jge


Resolution: 2.37→47.18 Å / SU ML: 0.3344 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.7777
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3113 1623 8.54 %
Rwork0.2514 17374 -
obs0.2564 18997 50.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.26 Å2
Refinement stepCycle: LAST / Resolution: 2.37→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6439 0 20 5 6464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00156617
X-RAY DIFFRACTIONf_angle_d0.42458991
X-RAY DIFFRACTIONf_chiral_restr0.0384964
X-RAY DIFFRACTIONf_plane_restr0.00311178
X-RAY DIFFRACTIONf_dihedral_angle_d11.94792417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.440.298740.384349X-RAY DIFFRACTION1.72
2.44-2.520.403240.3575253X-RAY DIFFRACTION8.84
2.52-2.610.353470.3524510X-RAY DIFFRACTION18.23
2.61-2.710.3386770.3483825X-RAY DIFFRACTION29.26
2.71-2.840.39111120.33371073X-RAY DIFFRACTION38.09
2.84-2.990.46311130.35811307X-RAY DIFFRACTION45.4
2.99-3.170.37071410.32471454X-RAY DIFFRACTION51.7
3.17-3.420.35631670.31071747X-RAY DIFFRACTION61.01
3.42-3.760.31411840.27342031X-RAY DIFFRACTION70.47
3.76-4.30.32962210.22142436X-RAY DIFFRACTION84.94
4.31-5.420.25792610.20352793X-RAY DIFFRACTION96.13
5.42-47.180.26342720.21642896X-RAY DIFFRACTION97.42
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)
13.011535264880.1536655453480.22817756890.497358178393-0.254044365720.659481715474-0.1459739796630.2869483519810.20317042653-0.1455504026040.1600696216720.0927163441023-0.0484702836105-0.141479231412-0.004186267778280.00280338747339-0.00449780986591-0.07647652930860.0159191848390.01175103493660.1712707349484.50950120211-7.93733747638-14.4953973565
21.790093695610.3908669037311.032817914530.9321413216570.8958226161292.1185093280.191832709341-0.5370711901-0.3822621134460.6168225477990.0712687042659-0.07469688641060.1793531392210.000312059251024-0.2367217632330.42951014941-0.0169842251863-0.08786364272540.2366386220780.05138893081020.3219414208747.106029974-6.3191140517539.7307000652
31.871507817610.06120326745690.8670887948420.667327570610.4207417391041.67039535975-0.0306399603502-0.338352267405-0.00371063227920.2114348966690.0481648356328-0.040733159053-0.182404401895-0.145120283027-0.00867277267110.29181256358-0.00206446464607-0.02690964955330.04652123621030.02424057731460.22950542577247.72527306412.797653871937.5129343377
40.790403281135-0.2857822715540.03279242815752.011075962490.2223075182061.19063989963-0.177755128364-0.04521754101750.153025683321-0.126375409819-0.00708282149497-0.171080528458-0.04582349446360.100440959099-0.1508546611930.2038076542170.0371791808344-0.04883345323520.05784323153470.006678179988360.26174497599829.2146718522-5.874114713127.71611435313
51.10170072866-0.346959070370.05057534574650.831109645119-0.3880339114640.8018415138690.02927967720060.192094781322-0.159866397493-0.162762416329-0.10528918890.1548235544270.198831804183-0.1147734319520.007005670054-0.003258901357410.1074681126450.00197774169364-0.0578919253628-0.02228175391380.22559199502719.4185085714-15.9266269332-5.96611032441
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11(chain 'B' and resid 0 through 99)BD0 - 991 - 100
22(chain 'D' and resid 2 through 206)DE2 - 2061 - 181
33(chain 'F' and resid 3 through 241)FG3 - 2411 - 239
44(chain 'C' and resid 1 through 9)CA1 - 91 - 9
55(chain 'A' and resid 1 through 276)AB1 - 2761 - 276

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