[English] 日本語
Yorodumi
- PDB-5iek: Structure of HLA-B*40:02 in complex with the endogenous peptide R... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5iek
TitleStructure of HLA-B*40:02 in complex with the endogenous peptide REFSKEPEL
Components
  • ARG-GLU-PHE-SER-LYS-GLU-PRO-GLU-LEU
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, B-40 alpha chain
KeywordsIMMUNE SYSTEM / Human Leukocyte Antigen system
Function / homology
Function and homology information


meiotic spindle midzone / meiotic spindle midzone assembly / central element / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / chromocenter ...meiotic spindle midzone / meiotic spindle midzone assembly / central element / positive regulation of mitotic sister chromatid separation / positive regulation of mitotic cytokinesis / metaphase chromosome alignment / positive regulation of mitotic cell cycle spindle assembly checkpoint / mitotic spindle midzone assembly / positive regulation of attachment of mitotic spindle microtubules to kinetochore / chromocenter / lateral element / chromosome passenger complex / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / SUMOylation of DNA replication proteins / mitotic cytokinesis / chromosome, centromeric region / mitotic spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / pericentric heterochromatin / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / TAP binding / protection from natural killer cell mediated cytotoxicity / Resolution of Sister Chromatid Cohesion / 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 / detection of bacterium / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / early endosome lumen / positive regulation of receptor binding / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / molecular function activator activity / chromosome segregation / RHO GTPases Activate Formins / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / defense response / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / spindle / kinetochore / 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 / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / negative regulation of neurogenesis / MHC class II protein complex / positive regulation of receptor-mediated endocytosis / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / specific granule lumen / peptide antigen binding / Separation of Sister Chromatids / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / microtubule cytoskeleton / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / negative regulation of epithelial cell proliferation / Modulation by Mtb of host immune system / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / tertiary granule lumen / DAP12 signaling / mitotic cell cycle / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / positive regulation of protein binding / midbody / ER-Phagosome pathway / iron ion transport / protein-folding chaperone binding / protein refolding / early endosome membrane / protein homotetramerization
Similarity search - Function
Inner centromere protein, ARK-binding domain / Chromosome passenger complex (CPC) protein INCENP N-terminal / Inner centromere protein, ARK binding region / Chromosome passenger complex (CPC) protein INCENP N terminal / 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 ...Inner centromere protein, ARK-binding domain / Chromosome passenger complex (CPC) protein INCENP N-terminal / Inner centromere protein, ARK binding region / Chromosome passenger complex (CPC) protein INCENP N terminal / 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
HLA class I histocompatibility antigen, B alpha chain / Beta-2-microglobulin / HLA class I histocompatibility antigen, B alpha chain / Inner centromere protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.8 Å
AuthorsAlpizar, A. / Marcilla, M. / Santiago, C.
CitationJournal: To Be Published
Title: Structure of HLA-B*40:02 in complex with the endogenous peptide REFSKEPEL
Authors: Alpizar, A. / Marcilla, M. / Santiago, C.
History
DepositionFeb 25, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_variant
Revision 1.2Oct 16, 2019Group: Data collection / Category: reflns_shell

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA class I histocompatibility antigen, B-40 alpha chain
B: Beta-2-microglobulin
C: ARG-GLU-PHE-SER-LYS-GLU-PRO-GLU-LEU


Theoretical massNumber of molelcules
Total (without water)45,1533
Polymers45,1533
Non-polymers00
Water9,476526
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-16 kcal/mol
Surface area19040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.260, 82.201, 111.145
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein HLA class I histocompatibility antigen, B-40 alpha chain / Bw-60 / MHC class I antigen B*40


Mass: 32137.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-B, HLAB / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta-gami pLys / References: UniProt: Q04826, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLys / References: UniProt: P61769
#3: Protein/peptide ARG-GLU-PHE-SER-LYS-GLU-PRO-GLU-LEU


Mass: 1136.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NQS7*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 526 / 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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 150 mM Tris 8.5, 23% PEG8K, 70 mM potassium thiocyanate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.00556 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00556 Å / Relative weight: 1
ReflectionNum. obs: 46622 / % possible obs: 99.9 % / Redundancy: 6.1 % / Net I/σ(I): 10.8

-
Processing

Software
NameVersionClassification
PHENIX1.10_2148refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MIR / Resolution: 1.8→24.975 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.21
RfactorNum. reflection% reflection
Rfree0.1881 2211 5 %
Rwork0.1616 --
obs0.163 44245 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.34 Å2 / Biso mean: 26.2613 Å2 / Biso min: 6.52 Å2
Refinement stepCycle: final / Resolution: 1.8→24.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3176 0 0 526 3702
Biso mean---34.72 -
Num. residues----385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093283
X-RAY DIFFRACTIONf_angle_d1.0364463
X-RAY DIFFRACTIONf_chiral_restr0.062455
X-RAY DIFFRACTIONf_plane_restr0.006590
X-RAY DIFFRACTIONf_dihedral_angle_d17.0521973
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.83910.30931420.265425572699
1.8391-1.88190.24051430.229225702713
1.8819-1.9290.25751270.202126072734
1.929-1.98110.22811190.178126292748
1.9811-2.03940.21131290.173925692698
2.0394-2.10510.21631340.172926152749
2.1051-2.18030.21281340.165526052739
2.1803-2.26760.2131300.155926172747
2.2676-2.37070.2141540.155825812735
2.3707-2.49560.19581390.163526242763
2.4956-2.65180.21111130.159926472760
2.6518-2.85630.16541530.166326332786
2.8563-3.14320.21261310.162526402771
3.1432-3.59690.17811660.153826352801
3.5969-4.52730.14351450.131126822827
4.5273-24.9770.15131520.155728232975

+
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