[English] 日本語
Yorodumi
- PDB-4no0: Crystal structure of non-phosphorylated form of RQA_V phosphopept... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4no0
TitleCrystal structure of non-phosphorylated form of RQA_V phosphopeptide bound to HLA-A2 in complex with LILRB1
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Leukocyte immunoglobulin-like receptor subfamily B member 1
  • Lymphocyte-specific protein 1
KeywordsIMMUNE SYSTEM/ANTIGEN / Nonphosphorylated peptide / peptide-MHC complex / MHC / LILRB1 / post translational modification / peptide conformation / tumor immunology / tumor antigen / neoepitope / IMMUNE SYSTEM-ANTIGEN complex
Function / homology
Function and homology information


HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / negative regulation of serotonin secretion / MHC class Ib protein complex binding / HLA-B specific inhibitory MHC class I receptor activity / immune response-inhibiting cell surface receptor signaling pathway / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / Fc receptor mediated inhibitory signaling pathway / MHC class Ib receptor activity ...HLA-A specific inhibitory MHC class I receptor activity / positive regulation of gamma-delta T cell activation involved in immune response / negative regulation of serotonin secretion / MHC class Ib protein complex binding / HLA-B specific inhibitory MHC class I receptor activity / immune response-inhibiting cell surface receptor signaling pathway / inhibitory MHC class I receptor activity / negative regulation of dendritic cell differentiation / Fc receptor mediated inhibitory signaling pathway / MHC class Ib receptor activity / MHC class Ib protein binding / negative regulation of T cell mediated cytotoxicity / immune response-regulating signaling pathway / negative regulation of CD8-positive, alpha-beta T cell activation / MHC class I receptor activity / negative regulation of transforming growth factor beta production / negative regulation of alpha-beta T cell activation / negative regulation of cytokine production involved in immune response / dendritic cell differentiation / interleukin-10-mediated signaling pathway / negative regulation of osteoclast development / protein phosphatase 1 binding / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / negative regulation of interleukin-12 production / negative regulation of dendritic cell apoptotic process / negative regulation of endocytosis / negative regulation of interferon-beta production / negative regulation of mononuclear cell proliferation / negative regulation of natural killer cell mediated cytotoxicity / cellular response to interleukin-7 / T cell proliferation involved in immune response / positive regulation of macrophage cytokine production / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / 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 / negative regulation of interleukin-10 production / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / negative regulation of calcium ion transport / endoplasmic reticulum exit site / negative regulation of cell cycle / MHC class I protein binding / negative regulation of type II interferon production / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / protection from natural killer cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / negative regulation of tumor necrosis factor production / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / cellular defense response / detection of bacterium / T cell receptor binding / negative regulation of T cell proliferation / positive regulation of defense response to virus by host / SH2 domain binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / receptor internalization / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / response to virus / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane
Similarity search - Function
Lymphocyte-specific protein / Caldesmon/lymphocyte specific protein / Caldesmon / : / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / MHC class I-like antigen recognition-like ...Lymphocyte-specific protein / Caldesmon/lymphocyte specific protein / Caldesmon / : / Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 subtype / Immunoglobulin / 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
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Lymphocyte-specific protein 1 / Beta-2-microglobulin / Leukocyte immunoglobulin-like receptor subfamily B member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsMohammed, F. / Stones, D.H. / Willcox, B.E.
CitationJournal: Oncotarget / Year: 2017
Title: The antigenic identity of human class I MHC phosphopeptides is critically dependent upon phosphorylation status.
Authors: Mohammed, F. / Stones, D.H. / Zarling, A.L. / Willcox, C.R. / Shabanowitz, J. / Cummings, K.L. / Hunt, D.F. / Cobbold, M. / Engelhard, V.H. / Willcox, B.E.
History
DepositionNov 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 19, 2014Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2May 29, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.3Sep 20, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Lymphocyte-specific protein 1
D: Leukocyte immunoglobulin-like receptor subfamily B member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8115
Polymers66,7494
Non-polymers621
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-14 kcal/mol
Surface area28940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.300, 117.300, 96.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

-
Protein , 3 types, 3 molecules ABD

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2 / Class I histocompatibility antigen A*0201


Mass: 31951.316 Da / Num. of mol.: 1 / Fragment: extracellular domain (UNP residues 25-300)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11748.160 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 / Plasmid: pGMT7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P61769
#4: Protein Leukocyte immunoglobulin-like receptor subfamily B member 1 / LIR-1 / Leukocyte immunoglobulin-like receptor 1 / CD85 antigen-like family member J / ...LIR-1 / Leukocyte immunoglobulin-like receptor 1 / CD85 antigen-like family member J / Immunoglobulin-like transcript 2 / ILT-2 / Monocyte/macrophage immunoglobulin-like receptor 7 / MIR-7


Mass: 21747.340 Da / Num. of mol.: 1 / Fragment: UNP residues 27-221
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ILT2, LILRB1, LIR1, MIR7 / Plasmid: pET23a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8NHL6

-
Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Lymphocyte-specific protein 1 / 47 kDa actin-binding protein / 52 kDa phosphoprotein / pp52 / Lymphocyte-specific antigen WP34


Mass: 1302.520 Da / Num. of mol.: 1 / Fragment: peptide (UNP residues 249-260) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P33241

-
Non-polymers , 2 types, 49 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsIN LEUKOCYTE IMMUNOGLOBULIN-LIKE RECEPTOR 1, L68P, I142T, AND S155I ARE NATURAL VARIANTS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% PEG3350, 0.1 M HEPES, pH 7.4, 0.2 M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5417 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 2.7→29.325 Å / Num. obs: 21132 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 36 % / Biso Wilson estimate: 47.502 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 33.28
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.7-2.80.8166.22786012171199.5
2.8-2.90.628.02686281861199.4
2.9-30.5319.13609601652199.3
3-3.30.30215.161399613782198.9
3.3-3.50.18924.08688211857199.4
3.5-40.11537.731175653187198.6
4-50.07259.261161343173198.4
5-60.06265.18520651428199.3
6-100.05472.87565351575199.4
10-29.3250.04293.4914553446193.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1P7Q

1p7q


Resolution: 2.7→29.325 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.851 / WRfactor Rfree: 0.2545 / WRfactor Rwork: 0.2236 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7445 / SU B: 15.83 / SU ML: 0.315 / SU R Cruickshank DPI: 0.6386 / SU Rfree: 0.4092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.639 / ESU R Free: 0.409 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3094 1080 5.1 %RANDOM
Rwork0.2688 ---
obs0.2709 20054 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 132.38 Å2 / Biso mean: 54.8343 Å2 / Biso min: 2.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0.11 Å20 Å2
2---0.22 Å20 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 2.7→29.325 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4680 0 4 48 4732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214700
X-RAY DIFFRACTIONr_angle_refined_deg1.6311.9346410
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.355574
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68123.407226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.20915691
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2871532
X-RAY DIFFRACTIONr_chiral_restr0.1010.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213707
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 79 -
Rwork0.436 1463 -
all-1542 -
obs--99.68 %

+
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