[English] 日本語
Yorodumi
- PDB-3utq: Human HLA-A*0201-ALWGPDPAAA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3utq
TitleHuman HLA-A*0201-ALWGPDPAAA
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • Insulin
KeywordsIMMUNE SYSTEM / Major Histocompatibility Complex / Human Leukocyte antigen / Type I Diabetes
Function / homology
Function and homology information


positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / negative regulation of feeding behavior ...positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / negative regulation of glycogen catabolic process / positive regulation of nitric oxide mediated signal transduction / negative regulation of fatty acid metabolic process / Signaling by Insulin receptor / negative regulation of feeding behavior / IRS activation / Insulin processing / regulation of protein secretion / positive regulation of peptide hormone secretion / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / positive regulation of respiratory burst / negative regulation of acute inflammatory response / Regulation of gene expression in beta cells / CD8 receptor binding / alpha-beta T cell activation / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / endoplasmic reticulum exit site / Synthesis, secretion, and deacylation of Ghrelin / TAP binding / positive regulation of dendritic spine maintenance / negative regulation of protein secretion / negative regulation of gluconeogenesis / positive regulation of glycogen biosynthetic process / fatty acid homeostasis / positive regulation of insulin receptor signaling pathway / Signal attenuation / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / detection of bacterium / negative regulation of respiratory burst involved in inflammatory response / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / negative regulation of lipid catabolic process / positive regulation of lipid biosynthetic process / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / regulation of protein localization to plasma membrane / nitric oxide-cGMP-mediated signaling / transport vesicle / positive regulation of nitric-oxide synthase activity / Insulin receptor recycling / COPI-mediated anterograde transport / negative regulation of reactive oxygen species biosynthetic process / T cell receptor binding / positive regulation of brown fat cell differentiation / insulin-like growth factor receptor binding / NPAS4 regulates expression of target genes / neuron projection maintenance / endoplasmic reticulum-Golgi intermediate compartment membrane / positive regulation of mitotic nuclear division / Insulin receptor signalling cascade / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / positive regulation of glycolytic process / endosome lumen / acute-phase response / positive regulation of cytokine production / positive regulation of long-term synaptic potentiation / positive regulation of D-glucose import across plasma membrane / positive regulation of protein secretion / Endosomal/Vacuolar pathway / T cell mediated cytotoxicity / insulin receptor binding / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / positive regulation of cell differentiation / cellular response to iron(III) ion / Regulation of insulin secretion / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / wound healing / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / response to molecule of bacterial origin / HFE-transferrin receptor complex / transferrin transport / MHC class I peptide loading complex / cellular response to iron ion / negative regulation of receptor-mediated endocytosis / hormone activity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of neuron projection development / MHC class I protein complex / negative regulation of protein catabolic process / peptide antigen assembly with MHC class II protein complex / regulation of synaptic plasticity / negative regulation of neurogenesis / cellular response to nicotine
Similarity search - Function
Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / Insulin-like superfamily / MHC class I, alpha chain, C-terminal / MHC_I C-terminus ...Insulin / Insulin family / Insulin-like / Insulin/IGF/Relaxin family / Insulin / insulin-like growth factor / relaxin family. / Insulin, conserved site / Insulin family signature. / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Insulin / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsRizkallah, P.J. / Cole, D.K. / Sewell, A.K. / Bulek, A.M.
CitationJournal: Nat.Immunol. / Year: 2012
Title: Structural basis for the killing of human beta cells by CD8(+) T cells in type 1 diabetes.
Authors: Bulek, A.M. / Cole, D.K. / Skowera, A. / Dolton, G. / Gras, S. / Madura, F. / Fuller, A. / Miles, J.J. / Gostick, E. / Price, D.A. / Drijfhout, J.W. / Knight, R.R. / Huang, G.C. / Lissin, N. ...Authors: Bulek, A.M. / Cole, D.K. / Skowera, A. / Dolton, G. / Gras, S. / Madura, F. / Fuller, A. / Miles, J.J. / Gostick, E. / Price, D.A. / Drijfhout, J.W. / Knight, R.R. / Huang, G.C. / Lissin, N. / Molloy, P.E. / Wooldridge, L. / Jakobsen, B.K. / Rossjohn, J. / Peakman, M. / Rizkallah, P.J. / Sewell, A.K.
History
DepositionNov 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
C: Insulin


Theoretical massNumber of molelcules
Total (without water)44,7993
Polymers44,7993
Non-polymers00
Water9,458525
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-21 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.100, 81.150, 56.550
Angle α, β, γ (deg.)90.000, 112.870, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC Class I Heavy Chain / MHC class I antigen A*2


Mass: 31951.316 Da / Num. of mol.: 1 / Fragment: UNP residues 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta DE3 / References: UniProt: P61769
#3: Protein/peptide Insulin


Mass: 968.063 Da / Num. of mol.: 1
Fragment: Pre-pro-insulin Derived Peptide (UNP residues 15-24)
Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P01308
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.51 Å3/Da / Density % sol: 50.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 20% w/v PEG3350, 0.2 M potassium/sodium tartrate, 0.1 M Bis-tris propane, pH 6.5, VAPOR DIFFUSION, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2011 / Details: mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 1.67→45.587 Å / Num. all: 50250 / Num. obs: 50250 / % possible obs: 98.1 % / Redundancy: 4 % / Rsym value: 0.05 / Net I/σ(I): 16.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.67-1.7140.571.41452035940.5794.8
1.71-1.764.10.471.71493036180.4798.5
1.76-1.814.10.3712.11447135170.37199.1
1.81-1.874.10.3262.41419134440.32698.7
1.87-1.933.90.19641287832660.19697.4
1.93-24.10.2113.71308632200.21198.9
2-2.074.10.136.11288931390.1399
2.07-2.164.10.1087.31236030110.10899.2
2.16-2.253.90.0987.91073627370.09894.1
2.25-2.3640.0977.91037026130.09794.3
2.36-2.4940.06611.91051926280.06699.4
2.49-2.6440.05414.6984324670.05498.7
2.64-2.8240.04318941523570.04399.3
2.82-3.0540.03620.4865821820.03699.3
3.05-3.343.90.02626.4788020120.02699.2
3.34-3.733.90.02328.9708618010.02398.8
3.73-4.314.20.01739.2671016130.01799.4
4.31-5.284.20.01442.4568413640.01499.9
5.28-7.474.10.01641.4444510780.016100
7.47-45.5873.90.01441.723135890.01497.6

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
GDAdata collection
xia2data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→45.587 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.868 / SU ML: 0.084 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 2545 5.1 %RANDOM
Rwork0.195 ---
obs0.1975 50142 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 71.95 Å2 / Biso mean: 23.8571 Å2 / Biso min: 7.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å2-1.28 Å2
2---0.82 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.67→45.587 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 0 525 3685
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0213255
X-RAY DIFFRACTIONr_bond_other_d0.0010.022229
X-RAY DIFFRACTIONr_angle_refined_deg2.1611.9234422
X-RAY DIFFRACTIONr_angle_other_deg1.07935359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3695383
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.37723.161174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.48215521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.651528
X-RAY DIFFRACTIONr_chiral_restr0.1420.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213667
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02721
X-RAY DIFFRACTIONr_mcbond_it1.1211.51925
X-RAY DIFFRACTIONr_mcbond_other0.41.5774
X-RAY DIFFRACTIONr_mcangle_it1.80823100
X-RAY DIFFRACTIONr_scbond_it2.9831330
X-RAY DIFFRACTIONr_scangle_it4.5984.51322
LS refinement shellResolution: 1.67→1.714 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 188 -
Rwork0.246 3397 -
all-3585 -
obs--100 %
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)
10.7689-0.02780.28572.5562-0.61571.2822-0.01630.0532-0.03630.0882-0.0337-0.25620.00080.06820.050.0042-0.0024-0.00720.0213-0.0080.036123.96979.078613.364
26.82242.53273.45822.08841.63231.9340.15990.1481-0.40740.00420.008-0.02440.09590.0024-0.16790.05370.0026-0.00590.064-0.00820.04110.2924-18.183112.8473
33.3751.0182-1.8123.8105-1.84333.5402-0.0632-0.14880.06940.1010.18190.3703-0.0105-0.1243-0.11860.00770.02030.010.07230.01320.03770.86151.03225.3949
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 180
2X-RAY DIFFRACTION1C1 - 10
3X-RAY DIFFRACTION2A181 - 276
4X-RAY DIFFRACTION3B0 - 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://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