[English] 日本語
Yorodumi
- PDB-7n2s: AS3.1-PRPF3-HLA*B27 -

+
Open data


ID or keywords:

Loading...

-
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 ferrous iron binding / positive regulation of transferrin receptor binding / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion ...positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / 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 / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / specific granule lumen / positive regulation of cellular senescence / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / Modulation by Mtb of host immune system / positive regulation of T cell activation / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / iron ion transport / ER-Phagosome pathway / T cell differentiation in thymus / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / lysosomal membrane / Golgi membrane / external side of plasma membrane / signaling receptor binding / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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. ...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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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)

-
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

-
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

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more