[English] 日本語
Yorodumi
- PDB-3rdt: Crystal Structure of 809.B5 TCR complexed with MHC Class II I-Ab/... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rdt
TitleCrystal Structure of 809.B5 TCR complexed with MHC Class II I-Ab/3k peptide
Components
  • 3K peptide, linker and MHC H-2 class II I-Ab beta chain
  • H-2 class II histocompatibility antigen, A-B alpha chain
  • TCR 809.B5 alpha chain
  • TCR 809.B5 beta chain
KeywordsIMMUNE SYSTEM / MHC / TCR / immune receptor / Ig-like domain
Function / homology
Function and homology information


positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / positive regulation of T-helper 1 type immune response / protein antigen binding / antigen processing and presentation of peptide antigen / B cell affinity maturation / positive regulation of T cell differentiation / response to type II interferon / antigen processing and presentation / toxic substance binding ...positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / positive regulation of T-helper 1 type immune response / protein antigen binding / antigen processing and presentation of peptide antigen / B cell affinity maturation / positive regulation of T cell differentiation / response to type II interferon / antigen processing and presentation / toxic substance binding / negative regulation of T cell proliferation / multivesicular body / cellular response to type II interferon / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / lysosome / early endosome / immune response / lysosomal membrane / external side of plasma membrane / ubiquitin protein ligase binding / protein-containing complex binding / Golgi apparatus / cell surface / membrane / plasma membrane
Similarity search - Function
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 / MHC classes I/II-like antigen recognition protein ...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 / 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 / Immunoglobulins / Roll / Immunoglobulin-like fold / 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
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsTrenh, P. / Huseby, E.S. / Stern, L.J.
CitationJournal: Immunity / Year: 2011
Title: A role for differential variable gene pairing in creating T cell receptors specific for unique major histocompatibility ligands.
Authors: Stadinski, B.D. / Trenh, P. / Smith, R.L. / Bautista, B. / Huseby, P.G. / Li, G. / Stern, L.J. / Huseby, E.S.
History
DepositionApr 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2012Group: Database references
Revision 1.2Aug 23, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 13, 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 / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: H-2 class II histocompatibility antigen, A-B alpha chain
D: 3K peptide, linker and MHC H-2 class II I-Ab beta chain
A: TCR 809.B5 alpha chain
B: TCR 809.B5 beta chain


Theoretical massNumber of molelcules
Total (without water)95,5974
Polymers95,5974
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)239.855, 73.016, 65.669
Angle α, β, γ (deg.)90.00, 90.71, 90.00
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 20597.957 Da / Num. of mol.: 1 / Fragment: UNP residues 27-208
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 3K peptide, linker and MHC H-2 class II I-Ab beta chain


Mass: 24966.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others), (gene. exp.) Mus musculus (house mouse)
Gene: H2-Ab1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14483
#3: Protein TCR 809.B5 alpha chain


Mass: 23029.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Protein TCR 809.B5 beta chain


Mass: 27002.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.01 Å3/Da / Density % sol: 59.1 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 12% PEG 4000, 100mM sodium citrate, 100mM sodium cacodylate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 20, 2010 / Details: Monochromator, mirror
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. all: 30664 / Num. obs: 30664 / % possible obs: 98.7 % / Redundancy: 4 % / Biso Wilson estimate: 45.74 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 18.6
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 4 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2.77 / Rsym value: 0.54 / % possible all: 97.6

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C60

3c60


Resolution: 2.7→30 Å / SU ML: 0.41 / Isotropic thermal model: isotropic / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.241 1530 5 %
Rwork0.206 --
obs0.208 30618 98.4 %
all-30618 -
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.85 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 52 Å2
Baniso -1Baniso -2Baniso -3
1--6.2305 Å20 Å24.0373 Å2
2--21.9925 Å20 Å2
3----15.762 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6399 0 0 0 6399
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086583
X-RAY DIFFRACTIONf_angle_d1.1028971
X-RAY DIFFRACTIONf_dihedral_angle_d15.0742309
X-RAY DIFFRACTIONf_chiral_restr0.078974
X-RAY DIFFRACTIONf_plane_restr0.0041175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.80540.35951500.30022812X-RAY DIFFRACTION96
2.8054-2.91760.31011310.25512878X-RAY DIFFRACTION98
2.9176-3.05030.26511490.24552897X-RAY DIFFRACTION98
3.0503-3.21090.28641460.23172890X-RAY DIFFRACTION98
3.2109-3.41180.27041430.20792913X-RAY DIFFRACTION99
3.4118-3.67480.22541460.19352918X-RAY DIFFRACTION99
3.6748-4.04380.24961390.19682945X-RAY DIFFRACTION99
4.0438-4.62720.22371620.16982921X-RAY DIFFRACTION99
4.6272-5.82270.20151860.18372920X-RAY DIFFRACTION99
5.8227-29.98140.22911780.2152994X-RAY DIFFRACTION99

+
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