[English] 日本語
Yorodumi
- PDB-8vcl: Crystal structure of HLA-A*03:01 in complex with a mutant PIK3CA ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vcl
TitleCrystal structure of HLA-A*03:01 in complex with a mutant PIK3CA peptide
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A alpha chain
  • Mutant PIK3CA peptide
KeywordsIMMUNE SYSTEM / Peptide-class I Major Histocompatibility Complex / pMHC
Function / homology
Function and homology information


response to muscle inactivity / regulation of actin filament organization / negative regulation of actin filament depolymerization / response to butyrate / IRS-mediated signalling / PI3K events in ERBB4 signaling / response to L-leucine / cellular response to hydrostatic pressure / Activated NTRK2 signals through PI3K / Activated NTRK3 signals through PI3K ...response to muscle inactivity / regulation of actin filament organization / negative regulation of actin filament depolymerization / response to butyrate / IRS-mediated signalling / PI3K events in ERBB4 signaling / response to L-leucine / cellular response to hydrostatic pressure / Activated NTRK2 signals through PI3K / Activated NTRK3 signals through PI3K / phosphatidylinositol 3-kinase complex, class IB / phosphatidylinositol 3-kinase complex / TORC2 signaling / Co-stimulation by ICOS / positive regulation of protein localization to membrane / Signaling by cytosolic FGFR1 fusion mutants / vasculature development / Nephrin family interactions / anoikis / Signaling by LTK in cancer / 1-phosphatidylinositol-4-phosphate 3-kinase activity / Signaling by LTK / phosphatidylinositol 3-kinase complex, class IA / MET activates PI3K/AKT signaling / PI3K/AKT activation / phosphatidylinositol-4,5-bisphosphate 3-kinase / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / relaxation of cardiac muscle / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / T cell mediated cytotoxicity / phosphatidylinositol 3-kinase / phosphatidylinositol-3-phosphate biosynthetic process / Signaling by ALK / cardiac muscle cell contraction / vascular endothelial growth factor signaling pathway / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / 1-phosphatidylinositol-3-kinase activity / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / PI-3K cascade:FGFR3 / response to dexamethasone / negative regulation of macroautophagy / TAP complex binding / PI-3K cascade:FGFR2 / antigen processing and presentation of exogenous peptide antigen via MHC class I / PI-3K cascade:FGFR4 / Golgi medial cisterna / PI-3K cascade:FGFR1 / phosphatidylinositol phosphate biosynthetic process / CD8 receptor binding / Synthesis of PIPs at the plasma membrane / positive regulation of protein kinase activity / response to muscle stretch / protection from natural killer cell mediated cytotoxicity / phosphatidylinositol-mediated signaling / RET signaling / negative regulation of anoikis / Interleukin-3, Interleukin-5 and GM-CSF signaling / PI3K events in ERBB2 signaling / TAP binding / insulin receptor substrate binding / PI3K Cascade / endoplasmic reticulum exit site / Role of LAT2/NTAL/LAB on calcium mobilization / intercalated disc / RAC2 GTPase cycle / Interleukin receptor SHC signaling / CD28 dependent PI3K/Akt signaling / positive regulation of TOR signaling / Role of phospholipids in phagocytosis / detection of bacterium / GAB1 signalosome / endothelial cell migration / 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 / protein kinase activator activity / positive regulation of lamellipodium assembly / beta-2-microglobulin binding / phagocytosis / cardiac muscle contraction / GPVI-mediated activation cascade / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / T cell receptor binding / insulin-like growth factor receptor signaling pathway / Signaling by FGFR4 in disease / Signaling by FLT3 ITD and TKD mutants / RAC1 GTPase cycle / Signaling by FGFR3 in disease / Tie2 Signaling / Signaling by FGFR2 in disease / Signaling by FLT3 fusion proteins / FLT3 Signaling / positive regulation of smooth muscle cell proliferation / Signaling by FGFR1 in disease / Downstream signal transduction / regulation of natural killer cell mediated immunity
Similarity search - Function
PI3Kalpha, catalytic domain / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Phosphatidylinositol 3-kinase, adaptor-binding domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. / PI3-kinase family, Ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / PI3-kinase family, ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile. / C2 phosphatidylinositol 3-kinase-type domain ...PI3Kalpha, catalytic domain / PI3-kinase family, p85-binding domain / PI3-kinase family, p85-binding domain / Phosphatidylinositol 3-kinase, adaptor-binding domain / Phosphatidylinositol 3-kinase adaptor-binding (PI3K ABD) domain profile. / PI3-kinase family, Ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain / PI3-kinase family, ras-binding domain / Phosphatidylinositol 3-kinase Ras-binding (PI3K RBD) domain profile. / C2 phosphatidylinositol 3-kinase-type domain / Phosphoinositide 3-kinase C2 / C2 phosphatidylinositol 3-kinase (PI3K)-type domain profile. / Phosphoinositide 3-kinase, region postulated to contain C2 domain / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase family, accessory domain (PIK domain) / Phosphoinositide 3-kinase, accessory (PIK) domain superfamily / Phosphoinositide 3-kinase, accessory (PIK) domain / Phosphatidylinositol kinase / PIK helical domain profile. / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / C2 domain superfamily / 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 / Armadillo-type fold / Ubiquitin-like domain superfamily / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
FORMIC ACID / HLA class I histocompatibility antigen, A alpha chain / Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMa, J. / Baker, B.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118166 United States
CitationJournal: Nat Commun / Year: 2025
Title: Dynamic allostery in the peptide/MHC complex enables TCR neoantigen selectivity.
Authors: Ma, J. / Ayres, C.M. / Brambley, C.A. / Chandran, S.S. / Rosales, T.J. / Perera, W.W.J.G. / Eldaly, B. / Murray, W.T. / Corcelli, S.A. / Kovrigin, E.L. / Klebanoff, C.A. / Baker, B.M.
History
DepositionDec 14, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A alpha chain
B: Beta-2-microglobulin
C: Mutant PIK3CA peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7568
Polymers44,4803
Non-polymers2765
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-18 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.420, 156.420, 85.863
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z
#9: y,x,-z
#10: -y,-x,-z
#11: -x+y,y,-z
#12: x,x-y,-z
Components on special symmetry positions
IDModelComponents
11A-521-

HOH

21A-540-

HOH

-
Components

-
Protein , 2 types, 2 molecules AB

#1: Protein HLA class I histocompatibility antigen, A alpha chain / Human leukocyte antigen A / HLA-A


Mass: 31628.838 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P04439
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
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, 1 molecules C

#3: Protein/peptide Mutant PIK3CA peptide / Phosphatidylinositol 4 / 5-bisphosphate 3-kinase catalytic subunit alpha isoform / PtdIns-3-kinase ...Phosphatidylinositol 4 / 5-bisphosphate 3-kinase catalytic subunit alpha isoform / PtdIns-3-kinase subunit alpha / Phosphatidylinositol 4 / 5-bisphosphate 3-kinase 110 kDa catalytic subunit alpha / p110alpha / Phosphoinositide-3-kinase catalytic alpha polypeptide / Serine/threonine protein kinase PIK3CA


Mass: 972.098 Da / Num. of mol.: 1 / Mutation: H2L / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P42336

-
Non-polymers , 3 types, 187 molecules

#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.91 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12% w/v Polyethylene glycol 3,350, 4% v/v TacsimateTM, pH 6.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→43.98 Å / Num. obs: 24683 / % possible obs: 97.93 % / Redundancy: 30.5 % / Biso Wilson estimate: 31.1 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.1953 / Rpim(I) all: 0.03545 / Rrim(I) all: 0.1987 / Net I/σ(I): 16.18
Reflection shellResolution: 2.4→2.486 Å / Redundancy: 16.9 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 4.53 / Num. unique obs: 1965 / CC1/2: 0.616 / CC star: 0.873 / Rpim(I) all: 0.1536 / Rrim(I) all: 0.6167 / % possible all: 81.2

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→43.98 Å / SU ML: 0.2775 / Cross valid method: FREE R-VALUE / σ(F): 0.51 / Phase error: 20.1329
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2299 2428 10.01 %
Rwork0.1935 21830 -
obs0.1971 24258 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.53 Å2
Refinement stepCycle: LAST / Resolution: 2.4→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3127 0 18 182 3327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00243225
X-RAY DIFFRACTIONf_angle_d0.49214367
X-RAY DIFFRACTIONf_chiral_restr0.04443
X-RAY DIFFRACTIONf_plane_restr0.0045575
X-RAY DIFFRACTIONf_dihedral_angle_d13.36141184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.2844970.2404868X-RAY DIFFRACTION66.97
2.44-2.50.29361330.24091193X-RAY DIFFRACTION93.98
2.5-2.560.2781420.25261276X-RAY DIFFRACTION98.95
2.56-2.620.29611430.23391293X-RAY DIFFRACTION100
2.62-2.690.25661440.22071289X-RAY DIFFRACTION99.93
2.69-2.770.29471440.22561297X-RAY DIFFRACTION99.86
2.77-2.860.25981430.21481286X-RAY DIFFRACTION100
2.86-2.960.26141440.20961302X-RAY DIFFRACTION99.93
2.96-3.080.2191450.2121298X-RAY DIFFRACTION99.86
3.08-3.220.2421450.20831295X-RAY DIFFRACTION99.93
3.22-3.390.22731450.20091313X-RAY DIFFRACTION99.93
3.39-3.60.23081460.19371305X-RAY DIFFRACTION99.79
3.6-3.880.20311460.17651325X-RAY DIFFRACTION99.73
3.88-4.270.20941480.1561325X-RAY DIFFRACTION99.86
4.27-4.890.1781480.14551341X-RAY DIFFRACTION100
4.89-6.150.18671520.17861366X-RAY DIFFRACTION99.8
6.16-43.980.2461630.19831458X-RAY DIFFRACTION99.69
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)
11.185774804040.32715112465-0.6421854585521.72950428136-0.4412178025261.68304195834-0.06180956182420.06136684233340.08170778419360.1795947761020.2586412341180.1573647974580.0711650909953-0.0497963043574-0.1560005048450.3321264822230.01702924192410.03360408530050.1107317510490.002253906591010.19487066586-66.469152972-7.232813823626.5394115101
21.0964263038-1.11902140116-0.5134698895691.906858361550.83324547880.365956037578-0.142467385013-0.2530071729450.3491327857820.2068723688990.210212421593-0.430812611233-0.200661194922-0.0311215428016-0.4157153220320.961126539110.3851388173370.007895786335320.316142364498-0.05722283182870.404286117269-38.9196694813-29.665220349224.9222517267
30.8483484652750.1072545184670.1383275315171.10324216682-0.01125704554710.0286997314524-0.3477641078970.0213518143556-0.431017889590.05294806018930.1676246426840.1306281848130.5232750913520.0982112500354-0.01355999527430.7817153397430.01366893119430.1232468221010.199809639701-0.03871408426190.368309637639-59.0998523409-30.702188283915.147087443
40.082737558742-0.4991665194310.741975746053.31533504181-4.987276472017.514669169650.0257958934977-0.165433259158-0.04153593516410.4279752825510.6345733370071.05725933059-0.451620986737-0.967287813487-0.6402198653510.3267778091350.009268049274640.08343731072270.304937743590.05616749475740.432840801781-71.220671019-0.80287392433726.4228583206
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 274 )AA181 - 274181 - 274
33chain 'B' and (resid 1 through 99 )BB1 - 991 - 99
44chain 'C' and (resid 1 through 9 )CC1 - 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