[English] 日本語
Yorodumi
- PDB-3ws3: Crystal Structure of H-2D in complex with an insulin derived peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ws3
TitleCrystal Structure of H-2D in complex with an insulin derived peptide
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-B alpha chain
  • Insulin derived 9-mer peptide
KeywordsIMMUNE SYSTEM / Class I MHC / Major histocompatibility complex / insulin / H-2D / Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC
Function / homology
Function and homology information


glucose transmembrane transport / 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 / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / positive regulation of nitric oxide mediated signal transduction ...glucose transmembrane transport / 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 / negative regulation of glycogen catabolic process / regulation of cellular amino acid metabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / negative regulation of feeding behavior / transmembrane receptor protein tyrosine kinase activator activity / regulation of protein secretion / positive regulation of respiratory burst / negative regulation of acute inflammatory response / alpha-beta T cell activation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / negative regulation of respiratory burst involved in inflammatory response / positive regulation of dendritic spine maintenance / positive regulation of glycogen biosynthetic process / negative regulation of protein secretion / regulation of protein localization to plasma membrane / fatty acid homeostasis / beta-2-microglobulin binding / negative regulation of lipid catabolic process / cellular defense response / negative regulation of reactive oxygen species biosynthetic process / positive regulation of insulin receptor signaling pathway / nitric oxide-cGMP-mediated signaling / response to cAMP / neuron projection maintenance / positive regulation of protein metabolic process / positive regulation of glycolytic process / Neutrophil degranulation / positive regulation of mitotic nuclear division / response to cytokine / positive regulation of cytokine production / acute-phase response / 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 / positive regulation of protein secretion / positive regulation of glucose import / negative regulation of proteolysis / lumenal side of endoplasmic reticulum membrane / cellular response to glucose stimulus / peptide binding / insulin-like growth factor receptor binding / cellular response to iron(III) ion / wound healing / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / insulin receptor binding / 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 / negative regulation of protein catabolic process / hormone activity / T cell mediated cytotoxicity / receptor internalization / 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 / positive regulation of protein localization to nucleus / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / vasodilation / phagocytic vesicle membrane / glucose metabolic process / 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 / regulation of protein localization / positive regulation of immune response / sensory perception of smell / positive regulation of T cell activation / insulin receptor signaling pathway / negative regulation of neuron projection development / MHC class II protein complex binding / glucose homeostasis / late endosome membrane / iron ion transport / T cell differentiation in thymus / protein refolding / protein homotetramerization / secretory granule lumen / collagen-containing extracellular matrix / intracellular iron ion homeostasis / protease binding / amyloid fibril formation / positive regulation of MAPK cascade
Similarity search - Function
Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily / MHC class I, alpha chain, C-terminal / MHC_I C-terminus ...Insulin / Insulin family / Insulin/IGF/Relaxin family / Insulin, conserved site / Insulin family signature. / Insulin-like / Insulin / insulin-like growth factor / relaxin family. / Insulin-like superfamily / 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
Insulin-1 / Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.335 Å
AuthorsKumar, P.R. / Mukherjee, G. / Samanta, D. / DiLorenzo, T.P. / Almo, S.C. / Immune Function Network / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: J. Immunol. / Year: 2014
Title: Compensatory mechanisms allow undersized anchor-deficient class I MHC ligands to mediate pathogenic autoreactive T cell responses
Authors: Lamont, D. / Mukherjee, G. / Kumar, P.R. / Samanta, D. / McPhee, C.G. / Kay, T.W.H. / Almo, S.C. / DiLorenzo, T.P. / Serreze, D.V.
History
DepositionFeb 28, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Structure summary / Category: audit_author
Revision 1.2Feb 7, 2018Group: Database references / Structure summary / Category: audit_author / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 8, 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 / 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: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
E: Insulin derived 9-mer peptide
F: Insulin derived 9-mer peptide


Theoretical massNumber of molelcules
Total (without water)89,4846
Polymers89,4846
Non-polymers00
Water1,892105
1
A: H-2 class I histocompatibility antigen, D-B alpha chain
B: Beta-2-microglobulin
E: Insulin derived 9-mer peptide


Theoretical massNumber of molelcules
Total (without water)44,7423
Polymers44,7423
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-21 kcal/mol
Surface area19300 Å2
MethodPISA
2
C: H-2 class I histocompatibility antigen, D-B alpha chain
D: Beta-2-microglobulin
F: Insulin derived 9-mer peptide


Theoretical massNumber of molelcules
Total (without water)44,7423
Polymers44,7423
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-20 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.220, 101.130, 117.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein H-2 class I histocompatibility antigen, D-B alpha chain / H-2D(B)


Mass: 31804.420 Da / Num. of mol.: 2 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H-2Db, H2-D1 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01899
#2: Protein Beta-2-microglobulin


Mass: 11835.555 Da / Num. of mol.: 2
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) / Strain (production host): BL21(DE3) / References: UniProt: P01887
#3: Protein/peptide Insulin derived 9-mer peptide


Mass: 1102.218 Da / Num. of mol.: 2 / Source method: obtained synthetically
Details: Synthetic peptide corresponding to Insulin-1A, residues 101-107 followed by an artificial spacer
References: UniProt: P01325*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS SEQUENCE CORRESPONDS TO A NATURAL VARIANT, ALLELE A WHICH HAS A A->D MUTATION.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.9 Å3/Da / Density % sol: 57.53 %
Description: Initial data was integrated and processed by XDS. The anisotropic data was further subject to an ellipsoidal truncation and sharpening using the UCLA anisotropy server (http://services. ...Description: Initial data was integrated and processed by XDS. The anisotropic data was further subject to an ellipsoidal truncation and sharpening using the UCLA anisotropy server (http://services.mbi.ucla.edu/anisoscale/). The resulting isotropic data has ellipsoidal resolution boundaries of 3.4A along A*, 2.4A along B* and 2.6A along C*. This data set was used for final refinement.
Mosaicity: 0.27 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Ammonium Sulfate, 25% PEG 3350, 0.1M HEPES, 30% Ethylene Glycol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2013 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.335→50 Å / Num. obs: 33466 / % possible obs: 74.65 % / Redundancy: 5.7 % / Biso Wilson estimate: 39.72 Å2 / Rmerge(I) obs: 0.148 / Net I/σ(I): 8.4
Reflection shellResolution: 2.335→2.419 Å / Redundancy: 0.4 % / Rmerge(I) obs: 0.962 / Mean I/σ(I) obs: 2.1 / % possible all: 7.01

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
Aimless0.2.14data scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
CBASSdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YN6

1yn6


Resolution: 2.335→46.449 Å / FOM work R set: 0.7209 / SU ML: 0.37 / σ(F): 1.36 / Phase error: 36.04 / Stereochemistry target values: ML
Details: The original processed data was further subject to ellipsoidal truncation along the three axes (a*, b* & c*) to provide the final data used for refinement. The structure factor data contains ...Details: The original processed data was further subject to ellipsoidal truncation along the three axes (a*, b* & c*) to provide the final data used for refinement. The structure factor data contains all reflections before anisotropic correction.
RfactorNum. reflection% reflection
Rfree0.2938 1692 5.06 %
Rwork0.2171 --
obs0.221 33449 74.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 178.83 Å2 / Biso mean: 60.75 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 2.335→46.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6241 0 0 105 6346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016436
X-RAY DIFFRACTIONf_angle_d1.4148723
X-RAY DIFFRACTIONf_chiral_restr0.055876
X-RAY DIFFRACTIONf_plane_restr0.0071136
X-RAY DIFFRACTIONf_dihedral_angle_d17.0612389
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3351-2.40380.4626160.31562102266
2.4038-2.48140.3086300.307562765718
2.4814-2.57010.3694720.31791370144239
2.5701-2.6730.33211020.31192136223861
2.673-2.79460.37051430.28782686282977
2.7946-2.94190.3191730.27533303347694
2.9419-3.12620.34451870.264635353722100
3.1262-3.36750.33472230.24635053728100
3.3675-3.70630.28361780.208135453723100
3.7063-4.24220.26811820.18593540372299
4.2422-5.34350.24071820.16783565374799
5.3435-46.45840.2822040.194437353939100
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)
12.9560.24490.85124.5275-0.42542.0441-0.0185-0.45430.0059-0.10370.08510.07170.5929-0.0757-0.00550.78270.08250.04260.0215-0.08410.138519.626.00710.936
25.18011.4242-1.51873.393-0.36622.1773-0.1261-0.8701-0.25770.68730.0869-0.3731-0.07350.48620.00110.59480.0847-0.15510.2586-0.0290.187625.80927.67119.848
33.26620.8903-0.94822.9102-1.4243.1798-0.05890.4030.1241-0.18680.27570.1975-0.0686-0.4026-0.18080.70860.0047-0.0560.1160.08140.03478.31928.53512.933
44.0432-1.0799-0.57081.2716-1.12151.71460.28410.5645-0.7416-0.5545-0.23290.09640.9112-0.4841-0.10420.9648-0.0446-0.00130.2547-0.07770.280826.10510.707-1.691
56.7231-4.88580.20845.9060.41572.0244-0.1274-0.0991-0.24530.3140.05960.0963-0.11530.07750.01180.596-0.0953-0.03270.14750.02930.275528.4492.1811.534
62.4432-2.56950.96354.5942-0.61020.6847-0.2094-0.1172-0.28990.2699-0.0585-0.24390.18970.11370.20150.7674-0.0258-0.06790.26530.08260.380526.5935.38217.535
75.23560.35530.06614.43030.60622.69050.16680.29290.00940.3505-0.1062-0.3210.11270.10140.02280.72830.0188-0.02370.14640.00880.320417.9426.088-35.116
82.76651.5098-0.73983.39221.63241.815-0.05050.28280.38930.5961-0.14140.69470.0912-0.1430.12390.66560.06110.12420.17460.00150.457621.86819.362-40.54
93.13620.79281.10043.9242-0.9182.9803-0.0055-0.24290.29351.0453-0.02450.83220.6068-0.4439-0.01890.8903-0.07470.27060.3363-0.05480.61854.53722.934-29.234
105.1058-3.1172-1.27313.36752.93133.610.6682-0.26540.4503-1.2579-0.72140.264-0.2963-0.00220.0391.0274-0.1562-0.03520.41110.06280.353818.97712.288-25.401
112.50911.11941.27072.59940.02412.25810.2125-0.44310.34580.5853-0.32830.1702-0.9836-0.50090.18741.0730.08930.07840.3505-0.07290.185326.80447.518-15.77
122.22723.5806-0.6756.9660.53434.257-0.02730.12880.03660.2932-0.16650.55530.3835-0.11380.25760.43360.16290.1350.12830.06970.380126.73648.303-31.411
134.75173.26570.3357.5902-0.02481.32460.01850.31820.18760.1358-0.12560.36850.44990.11720.15290.4310.05590.11080.22650.0490.180524.44945.125-37.128
143.36881.1771-1.80952.14950.47934.7115-0.692-0.21970.35280.23130.56370.1617-0.3170.28110.11280.84080.119-0.14270.33670.01350.188712.24835.592915.2635
153.3882-2.8933.93725.9926-2.83946.2307-0.63760.2495-0.62590.62620.9730.5424-0.1333-0.139-0.33840.66450.07120.12260.3985-0.04850.336410.171114.8093-34.7344
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 26:37 )
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 38:84 )
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 85:175 )
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 180:274 )
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 20:45 )
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 46:99 )
7X-RAY DIFFRACTION7CHAIN C AND (RESSEQ 26:56 )
8X-RAY DIFFRACTION8CHAIN C AND (RESSEQ 57:103 )
9X-RAY DIFFRACTION9CHAIN C AND (RESSEQ 104:177 )
10X-RAY DIFFRACTION10CHAIN C AND (RESSEQ 178:197 )
11X-RAY DIFFRACTION11CHAIN C AND (RESSEQ 198:274 )
12X-RAY DIFFRACTION12CHAIN D AND (RESSEQ 20:45 )
13X-RAY DIFFRACTION13CHAIN D AND (RESSEQ 46:99 )
14X-RAY DIFFRACTION14CHAIN E AND (RESSEQ 1:9 )
15X-RAY DIFFRACTION15CHAIN F AND (RESSEQ 1:9 )

+
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