[English] 日本語
Yorodumi
- PDB-8tbv: Human Class I MHC HLA-A2 in complex with sorting nexin 24 (127-13... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tbv
TitleHuman Class I MHC HLA-A2 in complex with sorting nexin 24 (127-135) neoantigen KLSHQLVLL
Components
  • Beta-2-microglobulin
  • HLA-A*02:01 alpha chain
  • Sorting nexin 24 (127-135)(P132L) peptide
KeywordsIMMUNE SYSTEM / Complex / MHC-I / antigen presentation
Function / homology
Function and homology information


antigen processing and presentation / 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 / cellular response to iron ion / Endosomal/Vacuolar pathway ...antigen processing and presentation / 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 / 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 / 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 space / extracellular exosome / extracellular region / identical protein binding / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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, alpha chain, C-terminal / MHC_I C-terminus / 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
DI(HYDROXYETHYL)ETHER / Beta-2-microglobulin / HLA class I antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsArbuiso, A. / Weiss, L.I. / Brambley, C.A. / Ma, J. / Keller, G.L.J. / Ayres, C.M. / Baker, B.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
Citation
Journal: Structure / Year: 2024
Title: Accurate modeling of peptide-MHC structures with AlphaFold.
Authors: Mikhaylov, V. / Brambley, C.A. / Keller, G.L.J. / Arbuiso, A.G. / Weiss, L.I. / Baker, B.M. / Levine, A.J.
#1: Journal: bioRxiv / Year: 2023
Title: Accurate modeling of peptide-MHC structures with AlphaFold.
Authors: Mikhaylov, V. / Brambley, C.A. / Arbuiso, A. / Weiss, L. / Ma, J. / Keller, G.L.J. / Ayres, C.M. / Baker, B.M. / Levine, A.J.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
History
DepositionJun 29, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA-A*02:01 alpha chain
B: Beta-2-microglobulin
C: Sorting nexin 24 (127-135)(P132L) peptide
D: HLA-A*02:01 alpha chain
E: Beta-2-microglobulin
F: Sorting nexin 24 (127-135)(P132L) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8629
Polymers89,5726
Non-polymers2903
Water2,954164
1
A: HLA-A*02:01 alpha chain
B: Beta-2-microglobulin
C: Sorting nexin 24 (127-135)(P132L) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0766
Polymers44,7863
Non-polymers2903
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-15 kcal/mol
Surface area18740 Å2
MethodPISA
2
D: HLA-A*02:01 alpha chain
E: Beta-2-microglobulin
F: Sorting nexin 24 (127-135)(P132L) peptide


Theoretical massNumber of molelcules
Total (without water)44,7863
Polymers44,7863
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-20 kcal/mol
Surface area18820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.226, 86.726, 79.268
Angle α, β, γ (deg.)90.000, 90.070, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 1 through 275)
d_2ens_1chain "D"
d_1ens_2(chain "B" and resid 1 through 100)
d_2ens_2chain "E"
d_1ens_3chain "C"
d_2ens_3chain "F"

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1GLYGLYGLUGLUAA1 - 2751 - 275
d_2ens_1GLYGLYGLUGLUDD1 - 2751 - 275
d_1ens_2METMETMETMETBB1 - 1001 - 100
d_2ens_2METMETMETMETEE1 - 1001 - 100
d_1ens_3LYSLYSLEULEUCC1 - 91 - 9
d_2ens_3LYSLYSLEULEUFF1 - 91 - 9

NCS ensembles :
ID
ens_1
ens_2
ens_3

-
Components

-
Protein , 2 types, 4 molecules ADBE

#1: Protein HLA-A*02:01 alpha chain / HLA class I antigen / HLA class I histocompatibility antigen / HLA class I histocompatibility ...HLA class I antigen / HLA class I histocompatibility antigen / HLA class I histocompatibility antigen A alpha chain / A alpha chain / MHC class I antigen / MHC class I protein / MHC class I protein (HLA-A)


Mass: 31854.203 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLA / Production host: Escherichia coli (E. coli) / References: UniProt: Q53Z42
#2: 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

-
Protein/peptide , 1 types, 2 molecules CF

#3: Protein/peptide Sorting nexin 24 (127-135)(P132L) peptide


Mass: 1052.310 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 3 types, 167 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: Purified protein complexes were concentrated to 7.4 mg/mL before crystallization. The crystals were grown in 12.5% PEG 4000 and 0.1 M MES (pH 6.5) via hanging drop vapor diffusion. Crystals ...Details: Purified protein complexes were concentrated to 7.4 mg/mL before crystallization. The crystals were grown in 12.5% PEG 4000 and 0.1 M MES (pH 6.5) via hanging drop vapor diffusion. Crystals were harvested and cryoprotected in 8% glycerol/92% mother liquor and immediately stored in liquid nitrogen

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.64→62.23 Å / Num. obs: 23797 / % possible obs: 92.02 % / Redundancy: 6.6 % / Biso Wilson estimate: 27.18 Å2 / CC1/2: 0.944 / Net I/σ(I): 4.32
Reflection shellResolution: 2.64→2.734 Å / Num. unique obs: 2209 / CC1/2: 0.649 / % possible all: 88.75

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALS2.2.10data reduction
DIALS2.2.10data scaling
PHENIX1.20rc3_4406phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→62.23 Å / SU ML: 0.3745 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 29.0484
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2744 2268 9.9 %
Rwork0.2292 20652 -
obs0.2337 22920 92.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.6 Å2
Refinement stepCycle: LAST / Resolution: 2.64→62.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6316 0 19 164 6499
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00156508
X-RAY DIFFRACTIONf_angle_d0.42128819
X-RAY DIFFRACTIONf_chiral_restr0.0385900
X-RAY DIFFRACTIONf_plane_restr0.00271148
X-RAY DIFFRACTIONf_dihedral_angle_d12.33892383
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.822506075325
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS0.805420578925
ens_3d_2CCX-RAY DIFFRACTIONTorsion NCS0.553056676168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.70.34361380.29451230X-RAY DIFFRACTION88.83
2.7-2.760.41591320.31141242X-RAY DIFFRACTION89.69
2.76-2.830.41431460.29941279X-RAY DIFFRACTION89.85
2.83-2.910.32511350.28281278X-RAY DIFFRACTION92.96
2.91-2.990.31861410.2691305X-RAY DIFFRACTION92.22
2.99-3.090.29721410.25651291X-RAY DIFFRACTION93.05
3.09-3.20.29521390.24541307X-RAY DIFFRACTION93.71
3.2-3.330.28971470.24361319X-RAY DIFFRACTION94.28
3.33-3.480.30171500.24681321X-RAY DIFFRACTION94.05
3.48-3.660.25431360.22361221X-RAY DIFFRACTION87.72
3.66-3.890.25261340.20651221X-RAY DIFFRACTION86.86
3.89-4.190.24481470.20911330X-RAY DIFFRACTION95.05
4.19-4.610.22191480.18481348X-RAY DIFFRACTION95.9
4.61-5.280.22641480.17691335X-RAY DIFFRACTION95.25
5.28-6.650.26881420.22431308X-RAY DIFFRACTION91.77
6.65-62.230.22581440.20971317X-RAY DIFFRACTION91.43
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)
12.244201110560.191409750603-0.2126307395551.422249392250.2252412792140.9780763129950.01333378163920.314450538059-0.01904195581340.0905303256415-0.033337904538-0.2911338147590.07568718895580.2471864338110.01151208683960.1495498202980.0119939448386-0.1043326828260.3455511361650.05782555574010.22587275271525.8338846432-3.4514600482919.8337705883
22.094619738650.3452061851171.480158514891.116528296150.5377149326712.311068052160.01046981795210.2657752717310.0604731277702-0.103094676430.06759540461690.0966169353950.1333811675970.0313177484315-0.1076961667460.15147050867-0.0147899441368-0.08450528638610.475098644048-0.08100220248650.308805740067-5.48288221528-7.787595026133.98570145843
33.80455784798-0.235990374732-0.009228720792490.787085426893-0.4703126575290.700329228861-0.02994280688080.1655952756020.593428894909-0.1048348323470.01336025992770.203213161926-0.0179483563146-0.1071105875340.04268158829350.1815793514230.0308199615211-0.09407648320390.483965123807-0.07807265177870.2973703834354.6857804265810.684817384411.5518639179
46.829412490842.38078780578-5.501036394940.939397404642-2.375444044718.48762435041-0.0699442979183-0.507769801387-0.103261996729-0.00610747895106-0.513220568415-0.69016934972-0.102929698241.248231592430.5567397379110.204786477543-0.0279851105349-0.04770627393420.3052974342710.1091222296560.46668932646733.0281981639-4.5225269998223.5223345446
51.8088969930.07057226971351.087493355531.026482432950.1936842945670.97020738172-0.0315312493421-0.04465807714840.0742291566481-0.08545856434450.04774895863460.2432490007140.0113080550954-0.006318552787630.006894865807350.162394171826-0.0280260862392-0.05297040067270.5990059671010.05598879600670.2332591620375.2323986003-39.794662210134.791031207
61.849877043070.593746218855-1.225301097620.7148599970250.04433675843411.708135940410.131027260390.495027930923-0.0964053886547-0.1445890703450.17085687874-0.180600578996-0.02124134272460.0990958902278-0.2301290468970.1550285079650.0213376193558-0.01990105510510.596557141292-0.02938461884270.25890141962536.7452067529-35.295867469918.6933947389
71.26893424433-0.09601264979010.7469038426680.445530857608-0.06534484297340.4609101433440.1191762744490.155872937504-0.217645536593-0.039864262755-0.0182631263579-0.01280182577570.07230096547080.0649495508259-0.1192437915630.193057324555-0.00948969849321-0.1028175591190.5719133361160.01938462644710.25820374393326.4161960943-53.809732207826.1642063485
87.505169404736.737964042337.613454062336.053761003876.839610591387.72760602404-0.305290765804-0.7668544881440.878272875632-0.172691528731-0.4276132503181.10454997617-0.564930603981-1.005391247050.7229390165390.3761664648360.0327200791865-0.0006117780943080.4072997781310.09141034146820.511509407568-1.9301936521-39.00490398638.3925935804
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 180 )AA1 - 1801 - 180
22chain 'A' and (resid 181 through 275 )AA181 - 275181 - 275
33chain 'B' and (resid 1 through 100 )BD1 - 1001 - 100
44chain 'C' and (resid 1 through 9 )CF1 - 91 - 9
55chain 'D' and (resid 1 through 180)DG1 - 1801 - 180
66chain 'D' and (resid 181 through 275 )DG181 - 275181 - 275
77chain 'E' and (resid 1 through 100 )EH1 - 1001 - 100
88chain 'F' and (resid 1 through 9 )FI1 - 91 - 9

+
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