[English] 日本語
Yorodumi
- PDB-3c5z: Crystal structure of mouse MHC class II I-Ab/3K peptide complexed... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3c5z
TitleCrystal structure of mouse MHC class II I-Ab/3K peptide complexed with mouse TCR B3K506
Components
  • 3K peptide, Linker, and H-2 class II histocompatibility antigen (A beta chain)
  • H-2 class II histocompatibility antigen, A-B alpha chain
  • TCR B3K506 Alpha Chain
  • TCR B3K506 Beta Chain
KeywordsSUGAR BINDING PROTEIN/IMMUNE SYSTEM / TCR-pMHC complex / Glycoprotein / Immune response / Membrane / MHC II / Transmembrane / SUGAR BINDING PROTEIN-IMMUNE SYSTEM COMPLEX
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsDai, S. / Kappler, J.
CitationJournal: Immunity / Year: 2008
Title: Crossreactive T Cells spotlight the germline rules for alphabeta T cell-receptor interactions with MHC molecules.
Authors: Dai, S. / Huseby, E.S. / Rubtsova, K. / Scott-Browne, J. / Crawford, F. / Macdonald, W.A. / Marrack, P. / Kappler, J.W.
History
DepositionFeb 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 16, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TCR B3K506 Alpha Chain
B: TCR B3K506 Beta Chain
C: H-2 class II histocompatibility antigen, A-B alpha chain
D: 3K peptide, Linker, and H-2 class II histocompatibility antigen (A beta chain)
E: TCR B3K506 Alpha Chain
F: TCR B3K506 Beta Chain
G: H-2 class II histocompatibility antigen, A-B alpha chain
H: 3K peptide, Linker, and H-2 class II histocompatibility antigen (A beta chain)


Theoretical massNumber of molelcules
Total (without water)189,9198
Polymers189,9198
Non-polymers00
Water1,18966
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.300, 117.800, 136.200
Angle α, β, γ (deg.)90.000, 99.560, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein TCR B3K506 Alpha Chain


Mass: 22465.676 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Description: The mouse Va and Vb of B3K506 TCRs fused to human Ca and Cb
Plasmid: PET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
#2: Protein TCR B3K506 Beta Chain


Mass: 26956.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Description: The mouse Va and Vb of B3K506 TCRs fused to human Ca and Cb
Plasmid: PET30 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
#3: Protein H-2 class II histocompatibility antigen, A-B alpha chain / IAalpha


Mass: 20597.957 Da / Num. of mol.: 2 / 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) / Strain (production host): Sf9 / References: UniProt: P14434
#4: Protein 3K peptide, Linker, and H-2 class II histocompatibility antigen (A beta chain)


Mass: 24938.830 Da / Num. of mol.: 2
Fragment: Fusion protein of ealpha 3K peptide residues 1-13, linker 14-28 and MHC class II Ab UNP residues 30-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Ab1, H2-iabeta / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P14483
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsBASED ON RELATED ENTRY 1LNU,TWO SEPARATE SEQUENCES, AN EALPHA3KPEPTIDE(1-13) AND LINKER(14-28), ...BASED ON RELATED ENTRY 1LNU,TWO SEPARATE SEQUENCES, AN EALPHA3KPEPTIDE(1-13) AND LINKER(14-28), WHICH START FROM RESIDUE 1 TO RESIDUE 28 WERE ADDED TO THE N-TERMINUS OF THE BETACHAIN OF THE CLASS II MHC IAB OF CHAINS D AND H

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 12% PEG 4000 , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97243 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 18, 2006 / Details: Mirrors
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97243 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 57142 / % possible obs: 86.1 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 45.9 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 14
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 1.8 / Num. unique all: 3558 / % possible all: 54

-
Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→40 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2155857.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 2882 4.3 %RANDOM
Rwork0.246 ---
obs-56990 86 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 27.549 Å2 / ksol: 0.291 e/Å3
Displacement parametersBiso mean: 66.7 Å2
Baniso -1Baniso -2Baniso -3
1-25.667 Å20 Å2-8.698 Å2
2---31.622 Å20 Å2
3---5.955 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.43 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.66 Å
Refinement stepCycle: LAST / Resolution: 2.55→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13222 0 0 66 13288
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011.5
X-RAY DIFFRACTIONc_angle_deg1.92
X-RAY DIFFRACTIONc_dihedral_angle_d27.32
X-RAY DIFFRACTIONc_improper_angle_d1.072.5
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.55→2.71 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.434 325 5.2 %
Rwork0.425 5867 -
all-6192 -
obs-5867 56.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.param&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2water_rep.param&_1_TOPOLOGY_INFILE_2
X-RAY DIFFRACTION3ion.param&_1_TOPOLOGY_INFILE_3
X-RAY DIFFRACTION4fs2.par&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5fs4.par&_1_TOPOLOGY_INFILE_5
X-RAY DIFFRACTION6CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION7CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION8CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION9CNS_TOPPAR:ion.param

+
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