[English] 日本語
Yorodumi
- PDB-6mnm: 6256 TCR bound to I-Ab Padi4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6mnm
Title6256 TCR bound to I-Ab Padi4
Components
  • 6256 TCR alpha chain
  • 6256 TCR beta chain
  • H-2 class II histocompatibility antigen, A-B alpha chain
  • Padi4 (92-105) peptide and MHC Class II I-Ab beta chain
KeywordsIMMUNE SYSTEM / T cell receptor / Major Histocompatibility Complex
Function / homology
Function and homology information


positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / Chromatin modifying enzymes / histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / positive regulation of T-helper 1 type immune response ...positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / Chromatin modifying enzymes / histone H3R2 arginine deiminase activity / histone H3R8 arginine deiminase activity / histone H3R17 arginine deiminase activity / histone H3R26 arginine deiminase activity / protein-arginine deiminase / protein-arginine deiminase activity / positive regulation of T-helper 1 type immune response / antigen processing and presentation of peptide antigen / B cell affinity maturation / protein antigen binding / positive regulation of T cell differentiation / stem cell population maintenance / antigen processing and presentation / response to type II interferon / toxic substance binding / multivesicular body / post-translational protein modification / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / cellular response to type II interferon / nucleosome assembly / chromatin organization / adaptive immune response / early endosome / lysosome / immune response / chromatin remodeling / innate immune response / external side of plasma membrane / calcium ion binding / ubiquitin protein ligase binding / Golgi apparatus / protein-containing complex / identical protein binding / nucleus / membrane / plasma membrane / cytoplasm
Similarity search - Function
Protein-arginine deiminase / Protein-arginine deiminase, C-terminal / Protein-arginine deiminase (PAD), N-terminal / Protein-arginine deiminase (PAD), central domain / Protein-arginine deiminase, central domain superfamily / PAD, N-terminal domain superfamily / Protein-arginine deiminase (PAD) / Protein-arginine deiminase (PAD) N-terminal domain / Protein-arginine deiminase (PAD) middle domain / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 ...Protein-arginine deiminase / Protein-arginine deiminase, C-terminal / Protein-arginine deiminase (PAD), N-terminal / Protein-arginine deiminase (PAD), central domain / Protein-arginine deiminase, central domain superfamily / PAD, N-terminal domain superfamily / Protein-arginine deiminase (PAD) / Protein-arginine deiminase (PAD) N-terminal domain / Protein-arginine deiminase (PAD) middle domain / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / 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 / Cupredoxin / 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
H-2 class II histocompatibility antigen, A-B alpha chain / H-2 class II histocompatibility antigen, A beta chain / Protein-arginine deiminase type-4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsBlevins, S.J. / Stadinski, B.D. / Huseby, E.S.
CitationJournal: Nat.Immunol. / Year: 2019
Title: A temporal thymic selection switch and ligand binding kinetics constrain neonatal Foxp3+Tregcell development.
Authors: Stadinski, B.D. / Blevins, S.J. / Spidale, N.A. / Duke, B.R. / Huseby, P.G. / Stern, L.J. / Huseby, E.S.
History
DepositionOct 2, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: H-2 class II histocompatibility antigen, A-B alpha chain
D: Padi4 (92-105) peptide and MHC Class II I-Ab beta chain
A: 6256 TCR alpha chain
B: 6256 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)95,2854
Polymers95,2854
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10960 Å2
ΔGint-63 kcal/mol
Surface area34980 Å2
Unit cell
Length a, b, c (Å)254.351, 73.771, 63.142
Angle α, β, γ (deg.)90.000, 90.520, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein H-2 class II histocompatibility antigen, A-B alpha chain / IAalpha


Mass: 20313.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14434
#2: Protein Padi4 (92-105) peptide and MHC Class II I-Ab beta chain / Peptidylarginine deiminase IV / Protein-arginine deiminase type IV


Mass: 25027.908 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Padi4, Pad4, Pdi4, H2-Ab1, H2-iabeta / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9Z183, UniProt: P14483, protein-arginine deiminase
#3: Protein 6256 TCR alpha chain


Mass: 23186.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#4: Protein 6256 TCR beta chain


Mass: 26756.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.11 Å3/Da / Density % sol: 60.47 % / Mosaicity: 0.13 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 14% PEG 4000, 100mM NaCacodylate, 100 mM NaCitrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.1→29.06 Å / Num. obs: 21458 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 55.49 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.045 / Rrim(I) all: 0.117 / Net I/σ(I): 11.5
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.313 / Num. unique obs: 3884 / CC1/2: 0.983 / Rpim(I) all: 0.129 / Rrim(I) all: 0.339 / % possible all: 100

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.2data scaling
PHASERphasing
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6MKD

6mkd


Resolution: 3.1→28.868 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.2
RfactorNum. reflection% reflection
Rfree0.2645 1437 6.71 %
Rwork0.2197 --
obs0.2226 21402 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.34 Å2 / Biso mean: 62.3718 Å2 / Biso min: 30 Å2
Refinement stepCycle: final / Resolution: 3.1→28.868 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6069 0 0 0 6069
Num. residues----808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046250
X-RAY DIFFRACTIONf_angle_d0.6988573
X-RAY DIFFRACTIONf_chiral_restr0.045955
X-RAY DIFFRACTIONf_plane_restr0.0041115
X-RAY DIFFRACTIONf_dihedral_angle_d10.2813616
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1001-3.21080.33681460.264319872133100
3.2108-3.33910.33931400.257219962136100
3.3391-3.49090.29811440.243819712115100
3.4909-3.67460.32231400.23831980212099
3.6746-3.90430.29121450.228819822127100
3.9043-4.20490.26431420.219219942136100
4.2049-4.62650.22881440.19241981212599
4.6265-5.29240.21131430.18120032146100
5.2924-6.65430.26611440.22720122156100
6.6543-28.86960.23611490.216820592208100

+
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