[English] 日本語
Yorodumi
- PDB-3qiu: Crystal structure of the 226 TCR in complex with MCC/I-Ek -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qiu
TitleCrystal structure of the 226 TCR in complex with MCC/I-Ek
Components
  • H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K alpha chain
  • MCC peptide
  • MHC CLASS II H2-IA-BETA CHAIN
  • TCR 226 alpha chain
  • TCR 226 beta chain
KeywordsIMMUNE SYSTEM / immunoglobulin domain / T cell receptor / MHC molecule
Function / homology
Function and homology information


Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / Co-inhibition by PD-1 / Generation of second messenger molecules / Downstream TCR signaling / MHC class II antigen presentation / immunoglobulin mediated immune response / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II ...Phosphorylation of CD3 and TCR zeta chains / Translocation of ZAP-70 to Immunological synapse / Co-inhibition by PD-1 / Generation of second messenger molecules / Downstream TCR signaling / MHC class II antigen presentation / immunoglobulin mediated immune response / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / peptide antigen binding / mitochondrial intermembrane space / MHC class II protein complex binding / late endosome membrane / adaptive immune response / electron transfer activity / lysosome / lysosomal membrane / external side of plasma membrane / heme binding / metal ion binding / 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 / Cytochrome c, class IA/ IB / 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 ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Cytochrome c, class IA/ IB / 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 / Cytochrome c / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / 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
Cytochrome c / H-2 class II histocompatibility antigen, E-K alpha chain / H-2 class II histocompatibility antigen, E-B beta chain / MHC class II antigen IEk-beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
Manduca sexta (tobacco hornworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsKruse, A.C. / Ely, L.K. / Newell, E.W. / Davis, M.M. / Garcia, K.C.
CitationJournal: J.Immunol. / Year: 2011
Title: Structural basis of specificity and cross-reactivity in T cell receptors specific for cytochrome c-I-E(k).
Authors: Newell, E.W. / Ely, L.K. / Kruse, A.C. / Reay, P.A. / Rodriguez, S.N. / Lin, A.E. / Kuhns, M.S. / Garcia, K.C. / Davis, M.M.
History
DepositionJan 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K alpha chain
B: MHC CLASS II H2-IA-BETA CHAIN
C: TCR 226 alpha chain
D: TCR 226 beta chain
E: MCC peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0787
Polymers95,6365
Non-polymers4422
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14650 Å2
ΔGint-55 kcal/mol
Surface area34990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.790, 71.400, 106.070
Angle α, β, γ (deg.)90.000, 90.750, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 4 types, 4 molecules ABCD

#1: Protein H-2 CLASS II HISTOCOMPATIBILITY ANTIGEN, E-K alpha chain


Mass: 20833.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P04224
#2: Protein MHC CLASS II H2-IA-BETA CHAIN


Mass: 22972.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Eb1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q31163, UniProt: P04230*PLUS
#3: Protein TCR 226 alpha chain


Mass: 22822.301 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 226 beta chain


Mass: 27613.924 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)

-
Protein/peptide / Sugars / Non-polymers , 3 types, 102 molecules E

#5: Protein/peptide MCC peptide


Mass: 1393.628 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Manduca sexta (tobacco hornworm) / Production host: Escherichia coli (E. coli) / References: UniProt: P00039
#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.: 2
Source method: isolated from a genetically manipulated 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.88 Å3/Da / Density % sol: 57.32 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 6.5
Details: 15-20% PEG5000 MME, Bis tris, VAPOR DIFFUSION, temperature 295K, pH 6.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.7→106.061 Å / Num. all: 30151 / Num. obs: 30151 / % possible obs: 100 % / Redundancy: 5.1 % / Rsym value: 0.096 / Net I/σ(I): 11.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.7-2.855.20.4641.72256043730.464100
2.85-3.025.20.3052.62138041420.305100
3.02-3.235.20.2023.81998738670.202100
3.23-3.495.10.1375.21881836610.137100
3.49-3.825.20.0997.11717733250.099100
3.82-4.275.20.0828.41573130540.082100
4.27-4.935.20.06410.11380526750.064100
4.93-6.045.10.06111173322850.06100
6.04-8.545.10.06110.7901517740.061100
8.54-36.5814.90.0415.348309950.0498.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
PHASERphasing
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→36.581 Å / Occupancy max: 1 / Occupancy min: 0.29 / FOM work R set: 0.8076 / SU ML: 0.37 / σ(F): 1.34 / Phase error: 26.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2541 1528 5.07 %
Rwork0.2149 --
obs0.2169 30135 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20 Å2 / ksol: 0.303 e/Å3
Displacement parametersBiso max: 123.61 Å2 / Biso mean: 47.3117 Å2 / Biso min: 21.98 Å2
Baniso -1Baniso -2Baniso -3
1-6.7034 Å20 Å2-2.6586 Å2
2--5.806 Å20 Å2
3----12.1894 Å2
Refinement stepCycle: LAST / Resolution: 2.7→36.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6252 0 28 99 6379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036440
X-RAY DIFFRACTIONf_angle_d0.6978719
X-RAY DIFFRACTIONf_chiral_restr0.046945
X-RAY DIFFRACTIONf_plane_restr0.0041135
X-RAY DIFFRACTIONf_dihedral_angle_d15.5612323
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7-2.79650.31891380.266528482986
2.7965-2.90840.28191480.260228563004
2.9084-3.04070.33941600.259828152975
3.0407-3.20090.31371550.254228493004
3.2009-3.40130.29161320.240328652997
3.4013-3.66370.29321770.214428293006
3.6637-4.0320.24031390.202528643003
4.032-4.61450.19041470.16928803027
4.6145-5.810.20891670.169128583025
5.81-36.58410.22181650.215929433108

+
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