[English] 日本語
Yorodumi
- PDB-1nan: MCH CLASS I H-2KB MOLECULE COMPLEXED WITH PBM1 PEPTIDE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1nan
TitleMCH CLASS I H-2KB MOLECULE COMPLEXED WITH PBM1 PEPTIDE
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, K-B alpha chain
  • pBM1 peptide
KeywordsIMMUNE SYSTEM / class I MHC / H-2Kb / alloreactivity / crossreactivity
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of phosphorylation ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antigen processing and presentation of exogenous peptide antigen via MHC class I / inner ear development / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of phosphorylation / cellular defense response / Neutrophil degranulation / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to bacterium / external side of plasma membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / cytoplasm / cytosol
Similarity search - Function
BTBD10/KCTD20, BTB/POZ domain / BTBD10/KCTD20 / BTB/POZ domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / SKP1/BTB/POZ domain superfamily / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 ...BTBD10/KCTD20, BTB/POZ domain / BTBD10/KCTD20 / BTB/POZ domain / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / SKP1/BTB/POZ domain superfamily / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / Beta-2-Microglobulin / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain / BTB/POZ domain-containing protein KCTD20
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsReiser, J.-B. / Darnault, C. / Gregoire, C. / Mosser, T. / Mazza, G. / Kearnay, A. / van der Merwe, P.A. / Fontecilla-Camps, J.C. / Housset, D. / Malissen, B.
Citation
Journal: Nat.Immunol. / Year: 2003
Title: CDR3 loop flexibility contributes to the degeneracy of TCR recognition
Authors: Reiser, J.-B. / Darnault, C. / Gregoire, C. / Mosser, T. / Mazza, G. / Kearnay, A. / van der Merwe, P.A. / Fontecilla-Camps, J.C. / Housset, D. / Malissen, B.
#1: Journal: Immunity / Year: 2002
Title: A T-Cell Receptor Cdr3Beta Loop Undergoes Conformational Changes of Unprecedented Magnitude Upon Binding to a Peptide/Mhc Class I Complex
Authors: Reiser, J.-B. / Gregoire, C. / Darnault, C. / Mosser, T. / Guimezanes, A. / Schmitt-Verhulst, A.-M. / Fontecilla-Camps, J.C. / Mazza, G. / Malissen, B. / Housset, D.
History
DepositionNov 28, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: H-2 class I histocompatibility antigen, K-B alpha chain
L: H-2 class I histocompatibility antigen, K-B alpha chain
P: Beta-2-microglobulin
I: Beta-2-microglobulin
M: pBM1 peptide
Q: pBM1 peptide


Theoretical massNumber of molelcules
Total (without water)89,5126
Polymers89,5126
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.981, 88.614, 89.174
Angle α, β, γ (deg.)90.00, 111.60, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein H-2 class I histocompatibility antigen, K-B alpha chain / H-2KB


Mass: 32068.777 Da / Num. of mol.: 2 / Fragment: Extracellular Domains (alpha1, alpha2, alpha3)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-K / Production host: Escherichia coli (E. coli) / References: UniProt: P01901
#2: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein/peptide pBM1 peptide / RIKEN cDNA 2410004N11


Mass: 983.076 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence is naturally found in mus muculus (mouse).
References: GenBank: 13385376, UniProt: Q8CDD8*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG6000 16-17%, NaAc 0.2M, NaCl 0.3M, Mes 0.1M, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlprotein1drop
216-17 %PEG60001reservoir
30.1 MMES1reservoirpH6.8
40.2 M1reservoirNaAc
50.3 M1reservoirNaCl

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.94 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 2.3→61.26 Å / Num. all: 41983 / Num. obs: 41983 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 44.8 Å2 / Rsym value: 0.067 / Net I/σ(I): 7.1
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 5761 / Rsym value: 0.272 / % possible all: 97.3
Reflection
*PLUS
Lowest resolution: 61.3 Å / % possible obs: 98.6 % / Redundancy: 6 % / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 97 % / Rmerge(I) obs: 0.27

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KJ3

1kj3


Resolution: 2.3→12 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.279 2792 RANDOM
Rwork0.224 --
all0.229 37223 -
obs0.229 37223 -
Displacement parametersBiso mean: 42.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.61 Å20 Å2-1.2 Å2
2--3.93 Å20 Å2
3----3.2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6306 0 0 156 6462
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.021
X-RAY DIFFRACTIONp_angle_d1.2931.937
LS refinement shellResolution: 2.3→2.36 Å
RfactorNum. reflection
Rfree0.388 280
Rwork0.313 -
obs-2792
Refinement
*PLUS
Rfactor Rfree: 0.278
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.291.937

+
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