[English] 日本語
Yorodumi
- PDB-7n19: DR3 in complex with Aspergillus nidulans NAD-dependent histone de... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7n19
TitleDR3 in complex with Aspergillus nidulans NAD-dependent histone deacetylase hst4 peptide
Components
  • (HLA class II histocompatibility ...) x 2
  • HST4 peptide
KeywordsIMMUNE SYSTEM / MHCII / T cell
Function / homology
Function and homology information


myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / transport vesicle membrane ...myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / transport vesicle membrane / polysaccharide binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / Generation of second messenger molecules / immunological synapse / PD-1 signaling / T cell receptor binding / MHC class II antigen presentation / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / cognition / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / early endosome membrane / adaptive immune response / membrane => GO:0016020 / lysosome / endosome membrane / immune response / lysosomal membrane / Golgi membrane / cell surface / extracellular exosome / plasma membrane
Similarity search - Function
MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / 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
HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen DR beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsWang, Y. / Dai, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1R01ES025797-01 United States
CitationJournal: J.Exp.Med. / Year: 2021
Title: CD4+ T cells in the lungs of acute sarcoidosis patients recognize an Aspergillus nidulans epitope.
Authors: Greaves, S.A. / Ravindran, A. / Santos, R.G. / Chen, L. / Falta, M.T. / Wang, Y. / Mitchell, A.M. / Atif, S.M. / Mack, D.G. / Tinega, A.N. / Maier, L.A. / Dai, S. / Pinilla, C. / Grunewald, J. / Fontenot, A.P.
History
DepositionMay 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 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
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen DR beta chain
C: HST4 peptide
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen DR beta chain
F: HST4 peptide
G: HLA class II histocompatibility antigen, DR alpha chain
H: HLA class II histocompatibility antigen DR beta chain
I: HST4 peptide
J: HLA class II histocompatibility antigen, DR alpha chain
K: HLA class II histocompatibility antigen DR beta chain
L: HST4 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,48850
Polymers178,04312
Non-polymers4,44438
Water4,324240
1
A: HLA class II histocompatibility antigen, DR alpha chain
B: HLA class II histocompatibility antigen DR beta chain
C: HST4 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,71514
Polymers44,5113
Non-polymers1,20411
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9420 Å2
ΔGint-1 kcal/mol
Surface area18450 Å2
MethodPISA
2
D: HLA class II histocompatibility antigen, DR alpha chain
E: HLA class II histocompatibility antigen DR beta chain
F: HST4 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,52911
Polymers44,5113
Non-polymers1,0188
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint-11 kcal/mol
Surface area18500 Å2
MethodPISA
3
G: HLA class II histocompatibility antigen, DR alpha chain
H: HLA class II histocompatibility antigen DR beta chain
I: HST4 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,52911
Polymers44,5113
Non-polymers1,0188
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-7 kcal/mol
Surface area18680 Å2
MethodPISA
4
J: HLA class II histocompatibility antigen, DR alpha chain
K: HLA class II histocompatibility antigen DR beta chain
L: HST4 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,71514
Polymers44,5113
Non-polymers1,20411
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-4 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.461, 214.255, 74.554
Angle α, β, γ (deg.)90.000, 98.956, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

-
Components

-
HLA class II histocompatibility ... , 2 types, 8 molecules ADGJBEHK

#1: Protein
HLA class II histocompatibility antigen, DR alpha chain / MHC class II antigen DRA


Mass: 21084.826 Da / Num. of mol.: 4 / Fragment: UNP residues 26-206
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRA, HLA-DRA1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01903
#2: Protein
HLA class II histocompatibility antigen DR beta chain / HLA class II histocompatibility antigen / DRB1 beta chain / HLA-DRB1 protein / MHC class II antigen ...HLA class II histocompatibility antigen / DRB1 beta chain / HLA-DRB1 protein / MHC class II antigen / Major histocompatibility complex / class II / DR beta 1 (Clone P2-beta-3)


Mass: 22049.486 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-DRB1, RP1-93N13.1-001 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5Y7D1

-
Protein/peptide , 1 types, 4 molecules CFIL

#3: Protein/peptide
HST4 peptide


Mass: 1376.502 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Trichoplusia ni (cabbage looper)

-
Sugars , 2 types, 8 molecules

#4: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: 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.: 4 / Source method: isolated from a natural source / 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, 270 molecules

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


Mass: 62.068 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 3.3 Å3/Da / Density % sol: 62.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 18% w/v PEG20k, 0.1 M citrate pH 5.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.38→50.01 Å / Num. obs: 90818 / % possible obs: 98.53 % / Redundancy: 2 % / Biso Wilson estimate: 55.49 Å2 / CC1/2: 0.994 / Net I/σ(I): 10.86
Reflection shellResolution: 2.38→2.54 Å / Num. unique obs: 16544 / CC1/2: 0.467

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A6A

1a6a


Resolution: 2.38→48.41 Å / SU ML: 0.4214 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 30.3534
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 4432 4.88 %RANDOM
Rwork0.2001 86335 --
obs0.2025 90767 98.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.48 Å2
Refinement stepCycle: LAST / Resolution: 2.38→48.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12452 0 288 240 12980
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008713067
X-RAY DIFFRACTIONf_angle_d1.022217694
X-RAY DIFFRACTIONf_chiral_restr0.06821905
X-RAY DIFFRACTIONf_plane_restr0.00622299
X-RAY DIFFRACTIONf_dihedral_angle_d21.3471768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.410.45921160.39712651X-RAY DIFFRACTION88.26
2.41-2.440.41821250.37132750X-RAY DIFFRACTION95.17
2.44-2.470.39111720.35262836X-RAY DIFFRACTION97.69
2.47-2.50.34791130.32032876X-RAY DIFFRACTION97.87
2.5-2.530.34291450.31672858X-RAY DIFFRACTION99.21
2.53-2.560.40381760.31132888X-RAY DIFFRACTION98.62
2.56-2.60.34171660.28932836X-RAY DIFFRACTION99.14
2.6-2.640.32491540.27982903X-RAY DIFFRACTION98.9
2.64-2.680.34261340.26472890X-RAY DIFFRACTION99.31
2.68-2.720.31241340.26742866X-RAY DIFFRACTION99.17
2.72-2.770.38271550.27112931X-RAY DIFFRACTION98.94
2.77-2.820.33711270.26352871X-RAY DIFFRACTION99.6
2.82-2.880.36221470.25182925X-RAY DIFFRACTION99.06
2.88-2.930.34661400.24352874X-RAY DIFFRACTION99.01
2.93-30.28411330.2242930X-RAY DIFFRACTION99.29
3-3.070.32681570.23492843X-RAY DIFFRACTION98.46
3.07-3.140.27051620.22582817X-RAY DIFFRACTION97.38
3.14-3.230.29761780.21192920X-RAY DIFFRACTION99.42
3.23-3.320.30511340.21372867X-RAY DIFFRACTION99.67
3.33-3.430.24071530.21142908X-RAY DIFFRACTION99.58
3.43-3.550.28611620.19342933X-RAY DIFFRACTION99.61
3.55-3.70.25551510.19242844X-RAY DIFFRACTION99.34
3.7-3.870.24071540.18672907X-RAY DIFFRACTION99.71
3.87-4.070.221360.17282917X-RAY DIFFRACTION99.67
4.07-4.320.19721450.15642919X-RAY DIFFRACTION99.77
4.32-4.660.18881600.13572943X-RAY DIFFRACTION99.74
4.66-5.130.1461450.13342889X-RAY DIFFRACTION99.61
5.13-5.870.18691520.15862901X-RAY DIFFRACTION99.22
5.87-7.390.24781630.18572909X-RAY DIFFRACTION98.68
7.39-48.410.17861430.18982933X-RAY DIFFRACTION99.13
Refinement TLS params.Method: refined / Origin x: 19.1912610776 Å / Origin y: -0.59085179423 Å / Origin z: 22.6134231241 Å
111213212223313233
T0.335932830795 Å2-0.0250292915138 Å2-0.00552945185599 Å2-0.333194591196 Å20.0213374480332 Å2--0.334342803288 Å2
L0.0704778220208 °2-0.0436643285968 °2-0.0225705673703 °2-0.0534567941201 °20.0313474570418 °2--0.056986003448 °2
S0.0100583776351 Å °-0.0098183800807 Å °0.00398139198429 Å °0.0194606840477 Å °-0.0256115955948 Å °-0.0155191164161 Å °0.000875709088897 Å °0.00902494155626 Å °-1.42124018244E-12 Å °
Refinement TLS groupSelection details: all

+
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://pdbjlvh1.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