[English] 日本語
Yorodumi
- PDB-3fol: Crystal structure of the Class I MHC Molecule H-2Kwm7 with a Sing... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fol
TitleCrystal structure of the Class I MHC Molecule H-2Kwm7 with a Single Self Peptide VNDIFERI
Components
  • 8 residue synthetic peptide
  • Beta-2-microglobulin
  • MHC
KeywordsIMMUNE SYSTEM / Class I MHC / peptide complex / Diabetes-protective Effect / Immune response / Immunoglobulin domain / MHC I / Secreted / Chromosomal protein / DNA-binding / Methylation / Nucleosome core / Nucleus / Phosphoprotein
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 / cellular defense response / Neutrophil degranulation / 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 / 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 / cellular defense response / Neutrophil degranulation / 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(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 / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / 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 / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / cytosol
Similarity search - Function
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. ...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
MHC / Beta-2-microglobulin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsBrims, D.R. / Qian, J. / Jarchum, I. / Yamada, T. / Mikesh, L. / Palmieri, E. / Lund, T. / Hattori, M. / Shabanowitz, J. / Hunt, D.F. ...Brims, D.R. / Qian, J. / Jarchum, I. / Yamada, T. / Mikesh, L. / Palmieri, E. / Lund, T. / Hattori, M. / Shabanowitz, J. / Hunt, D.F. / Ramagopal, U.A. / Malashkevich, V.N. / Almo, S.C. / Nathenson, S.G. / DiLorenzo, T.P.
CitationJournal: Int.Immunol. / Year: 2010
Title: Predominant occupation of the class I MHC molecule H-2Kwm7 with a single self-peptide suggests a mechanism for its diabetes-protective effect
Authors: Brims, D.R. / Qian, J. / Jarchum, I. / Mikesh, L. / Palmieri, E. / Ramagopal, U.A. / Malashkevich, V.N. / Chaparro, R.J. / Lund, T. / Hattori, M. / Shabanowitz, J. / Hunt, D.F. / Nathenson, ...Authors: Brims, D.R. / Qian, J. / Jarchum, I. / Mikesh, L. / Palmieri, E. / Ramagopal, U.A. / Malashkevich, V.N. / Chaparro, R.J. / Lund, T. / Hattori, M. / Shabanowitz, J. / Hunt, D.F. / Nathenson, S.G. / Almo, S.C. / Dilorenzo, T.P.
History
DepositionDec 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MHC
B: Beta-2-microglobulin
P: 8 residue synthetic peptide


Theoretical massNumber of molelcules
Total (without water)44,3293
Polymers44,3293
Non-polymers00
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4500 Å2
ΔGint-17 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.393, 66.630, 56.211
Angle α, β, γ (deg.)90.000, 93.660, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein MHC


Mass: 31487.088 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: Pet3a / Production host: Escherichia coli (E. coli) / References: UniProt: D2YW38*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11835.555 Da / Num. of mol.: 1 / Fragment: IgC
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: Pet3a / Production host: Escherichia coli (E. coli) / References: UniProt: P01887
#3: Protein/peptide 8 residue synthetic peptide


Mass: 1006.134 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. It is found naturally in mouse.
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% PEG 3350, 200 mM ammonium sulfate, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 27, 2007
RadiationMonochromator: Osmic / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 18990 / % possible obs: 97.4 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.068 / Χ2: 1.072 / Net I/σ(I): 19.169
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.384.20.81914770.856176.4
2.38-2.485.80.76718861.08197.8
2.48-2.597.30.63119531.226199.9
2.59-2.737.50.49219461.1511100
2.73-2.97.40.33519301.14199.9
2.9-3.127.50.19419471.083199.9
3.12-3.447.60.09719361.0481100
3.44-3.937.60.05419520.9421100
3.93-4.957.60.03319581.0781100
4.95-507.40.03520050.987199.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
StructureStudiodata collection
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.5→19.84 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.238 / WRfactor Rwork: 0.175 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.79 / SU B: 25.664 / SU ML: 0.27 / SU R Cruickshank DPI: 0.71 / SU Rfree: 0.311 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.709 / ESU R Free: 0.313 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.261 757 5 %RANDOM
Rwork0.192 ---
obs0.196 15063 99.91 %-
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 max: 92.58 Å2 / Biso mean: 39.517 Å2 / Biso min: 2.11 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.02 Å2
2---0.02 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3117 0 0 65 3182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213222
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.9394377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9335383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55223.353167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.47315539
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1061528
X-RAY DIFFRACTIONr_chiral_restr0.0990.2452
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212516
X-RAY DIFFRACTIONr_mcbond_it0.9853.51912
X-RAY DIFFRACTIONr_mcangle_it2.418203095
X-RAY DIFFRACTIONr_scbond_it3.463201310
X-RAY DIFFRACTIONr_scangle_it0.8394.51280
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 51 -
Rwork0.315 1050 -
all-1101 -
obs--99.46 %
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)
13.62132.22242.44611.4921.36732.62640.01910.32690.1367-0.02520.11310.0285-0.10510.3815-0.13220.06240.00070.07050.10520.0240.126421.1576-0.560513.7448
23.32810.45021.6225.52434.40058.62150.3522-0.36840.12680.0571-0.16160.1234-0.4521-0.0669-0.19060.1985-0.09620.1380.2051-0.00290.138318.95892.511232.6636
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 274
2X-RAY DIFFRACTION1A275 - 379
3X-RAY DIFFRACTION2B0 - 99

+
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