[English] 日本語
Yorodumi
- PDB-1kjm: TAP-A-associated rat MHC class I molecule -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kjm
TitleTAP-A-associated rat MHC class I molecule
Components
  • B6 Peptide
  • RT1 class I histocompatibility antigen, AA alpha chain, heavy chain
  • beta-2-Microglobulin
KeywordsIMMUNE SYSTEM / peptide-MHC complex / heterodimer / extracellular domain
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Neutrophil degranulation / response to cadmium ion / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib ...Endosomal/Vacuolar pathway / DAP12 interactions / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Neutrophil degranulation / response to cadmium ion / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / cellular response to iron ion / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / response to xenobiotic stimulus / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / structural molecule activity / protein homodimerization activity / extracellular space / identical protein binding
Similarity search - Function
MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 ...MHC class I, alpha chain, C-terminal / MHC_I C-terminus / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Beta-2-microglobulin / RT1 class I histocompatibility antigen, AA alpha chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsRudolph, M.G. / Stevens, J. / Speir, J.A. / Trowsdale, J. / Butcher, G.W. / Joly, E. / Wilson, I.A.
Citation
Journal: J.Mol.Biol. / Year: 2002
Title: Crystal structures of two rat MHC class Ia (RT1-A) molecules that are associated differentially with peptide transporter alleles TAP-A and TAP-B.
Authors: Rudolph, M.G. / Stevens, J. / Speir, J.A. / Trowsdale, J. / Butcher, G.W. / Joly, E. / Wilson, I.A.
#1: Journal: Immunity / Year: 2001
Title: Two different, highly exposed, bulged structures for an unusually long peptide bound to rat MHC class I RT1-Aa
Authors: Speir, J.A. / Stevens, J.S. / Joly, E. / Butcher, G.W. / Wilson, I.A.
History
DepositionDec 4, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RT1 class I histocompatibility antigen, AA alpha chain, heavy chain
B: beta-2-Microglobulin
P: B6 Peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1314
Polymers46,0353
Non-polymers961
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-17 kcal/mol
Surface area19560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.049, 109.566, 45.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-361-

HOH

-
Components

#1: Protein RT1 class I histocompatibility antigen, AA alpha chain, heavy chain / MHC class I RT1-AA heavy chain


Mass: 33326.961 Da / Num. of mol.: 1
Fragment: extracellular domain, residues 25-300, numbered 1-276, plus C-terminal his tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P16391
#2: Protein beta-2-Microglobulin


Mass: 11783.478 Da / Num. of mol.: 1 / Fragment: residues 21-119, numbered 1-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P07151
#3: Protein/peptide B6 Peptide


Mass: 924.979 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide was derived from biochemical binding data.
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 2M (NH4)2SO4, 1% glycerol, 0.1 M Tris/HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
22 Mammonium sulfate1reservoir
31 %(v/v)glycerol1reservoir
40.1 MTris-HCl1reservoirp8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 4, 1999
RadiationMonochromator: Cyclindrically bent triangular Si(111) asymmetric cut, horizontal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.35→19.8 Å / Num. obs: 22313 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 2.76 % / Biso Wilson estimate: 32.7 Å2 / Rsym value: 0.08 / Net I/σ(I): 12.7
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 2.38 % / Mean I/σ(I) obs: 1.86 / Num. unique all: 2120 / Rsym value: 0.423 / % possible all: 92
Reflection
*PLUS
Redundancy: 2.8 % / Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 92 % / Redundancy: 2.4 % / Num. unique obs: 2120 / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 2.6

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ED3 MOLECULE 1

1ed3


Resolution: 2.35→19.8 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.894 / SU B: 12.91 / SU ML: 0.307 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.44 / ESU R Free: 0.271 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26803 2156 10 %RANDOM
Rwork0.2473 ---
obs0.24935 21660 97.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.686 Å2
Baniso -1Baniso -2Baniso -3
1--1.12 Å20 Å20 Å2
2--5.96 Å20 Å2
3----4.85 Å2
Refinement stepCycle: LAST / Resolution: 2.35→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3149 0 5 144 3298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213244
X-RAY DIFFRACTIONr_bond_other_d0.0010.022813
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.9414409
X-RAY DIFFRACTIONr_angle_other_deg0.78336547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0773382
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.48315583
X-RAY DIFFRACTIONr_chiral_restr0.0830.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023628
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02697
X-RAY DIFFRACTIONr_nbd_refined0.2490.3759
X-RAY DIFFRACTIONr_nbd_other0.2520.33091
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.5260
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2170.57
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.38
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2490.353
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.7510.56
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.3191.51925
X-RAY DIFFRACTIONr_mcangle_it0.61423108
X-RAY DIFFRACTIONr_scbond_it1.12631319
X-RAY DIFFRACTIONr_scangle_it1.9784.51301
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.412 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.348 135
Rwork0.36 1280
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0406-0.2830.6331.62670.23993.04590.1070.033-0.1069-0.0178-0.090.18520.0213-0.3833-0.01690.22930.049-0.00560.0435-0.01330.27739.6165.13914.553
24.3182.95770.11751.03910.81081.92410.27630.1025-0.06230.0142-0.17530.11630.2604-0.1397-0.1010.25860.0624-0.02280.0773-0.00720.218245.3831.69914.096
31.4569-1.553-0.83588.92642.9843.16670.18720.2815-0.1878-0.30050.0288-0.53350.19910.259-0.2160.39310.02270.00860.255-0.08060.530313.61230.80310.366
412.8844-2.8088-2.49912.5497-0.00075.3520.2084-0.30970.01180.2942-0.25570.8340.0537-0.72290.04740.49820.02190.0630.4537-0.17150.738217.34616.56927.766
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1801 - 180
2X-RAY DIFFRACTION2PC1 - 91 - 9
3X-RAY DIFFRACTION3AA181 - 277181 - 277
4X-RAY DIFFRACTION4BB1 - 992 - 100
Refinement
*PLUS
Lowest resolution: 19.8 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.268 / Rfactor Rwork: 0.246
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.52
LS refinement shell
*PLUS
Lowest resolution: 2.41 Å / Rfactor Rfree: 0.345 / Rfactor Rwork: 0.359

+
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