[English] 日本語
Yorodumi
- PDB-2h6p: Crystal structure of HLA-B*3501 presenting the human cytochrome P... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2h6p
TitleCrystal structure of HLA-B*3501 presenting the human cytochrome P450 derived peptide, KPIVVLHGY
Components
  • 9 mer peptide from Cytochrome P450
  • Beta-2-microglobulin
  • HLA-B35
KeywordsIMMUNE SYSTEM / gene regulation
Function / homology
Function and homology information


linoleic acid epoxygenase activity / arachidonate epoxygenase activity / epoxygenase P450 pathway / retinoic acid 4-hydroxylase activity / linoleic acid metabolic process / Xenobiotics / regulation of interleukin-12 production / regulation of dendritic cell differentiation / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / regulation of T cell anergy ...linoleic acid epoxygenase activity / arachidonate epoxygenase activity / epoxygenase P450 pathway / retinoic acid 4-hydroxylase activity / linoleic acid metabolic process / Xenobiotics / regulation of interleukin-12 production / regulation of dendritic cell differentiation / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / regulation of T cell anergy / retinoic acid metabolic process / regulation of interleukin-6 production / retinol metabolic process / unspecific monooxygenase / aromatase activity / TAP binding / protection from natural killer cell mediated cytotoxicity / detection of bacterium / xenobiotic metabolic process / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / 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 / monooxygenase activity / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / ER to Golgi transport vesicle membrane / 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 / oxygen binding / MHC class I protein complex / defense response / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / multicellular organismal-level iron ion homeostasis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / positive regulation of immune response / Interferon gamma signaling / positive regulation of T cell activation / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / MHC class II protein complex binding / late endosome membrane / protein-folding chaperone binding / iron ion transport / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / immune response / iron ion binding / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / intracellular membrane-bounded organelle / innate immune response / signaling receptor binding / focal adhesion / heme binding
Similarity search - Function
: / Cytochrome P450, E-class, group I / 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 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily ...: / Cytochrome P450, E-class, group I / 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 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / 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-B35 / HLA class I histocompatibility antigen, B alpha chain / Cytochrome P450 2C18 / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsArchbold, J.K. / Macdonald, W.A. / Rossjohn, J.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Alloreactivity between disparate cognate and allogeneic pMHC-I complexes is the result of highly focused, peptide-dependent structural mimicry
Authors: Archbold, J.K. / Macdonald, W.A. / Miles, J.J. / Brennan, R.M. / Kjer-Nielsen, L. / McCluskey, J. / Burrows, S.R. / Rossjohn, J.
History
DepositionMay 31, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA-B35
B: Beta-2-microglobulin
C: 9 mer peptide from Cytochrome P450


Theoretical massNumber of molelcules
Total (without water)44,7163
Polymers44,7163
Non-polymers00
Water7,224401
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-21 kcal/mol
Surface area19160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.279, 82.070, 109.881
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein HLA-B35 / HLA class I histocompatibility antigen / B-35 alpha chain


Mass: 31940.246 Da / Num. of mol.: 1 / Fragment: Extracellular domains alpha 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (de3) / References: UniProt: O19626, UniProt: P01889*PLUS
#2: Protein Beta-2-microglobulin / Beta-2-microglobin


Mass: 11748.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 (de3) / References: UniProt: P61769
#3: Protein/peptide 9 mer peptide from Cytochrome P450 / CYPIIC18 / P450-6B/29C


Mass: 1027.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic construct / References: UniProt: P33260
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.58 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 18% PEG 3350, 0.1M ammonium acetate, 0.1M cacodylate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jun 17, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→65.8 Å / Num. obs: 36699
Reflection shellResolution: 1.9→1.97 Å / % possible all: 83.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalClear(MSC/RIGAKU)data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→65.8 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.191 / SU ML: 0.11 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 1.9 / ESU R: 0.17 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23914 1831 5 %RANDOM
Rwork0.20985 ---
obs0.21133 34808 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.982 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 1.9→65.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3156 0 0 401 3557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0213247
X-RAY DIFFRACTIONr_angle_refined_deg0.8751.9354414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0295381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39323.182176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.56115525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9091531
X-RAY DIFFRACTIONr_chiral_restr0.060.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022573
X-RAY DIFFRACTIONr_nbd_refined0.1560.21417
X-RAY DIFFRACTIONr_nbtor_refined0.2930.22128
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0720.2343
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0990.224
X-RAY DIFFRACTIONr_mcbond_it0.70232003
X-RAY DIFFRACTIONr_mcangle_it1.08253103
X-RAY DIFFRACTIONr_scbond_it1.68771481
X-RAY DIFFRACTIONr_scangle_it2.461101311
LS refinement shellResolution: 1.897→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 114 -
Rwork0.321 2002 -
obs--79.34 %
Refinement TLS params.Method: refined / Origin x: 12.957 Å / Origin y: 9.604 Å / Origin z: 36.048 Å
111213212223313233
T-0.1266 Å20.0021 Å2-0.0079 Å2--0.0929 Å2-0.0131 Å2---0.1839 Å2
L1.1321 °2-0.2786 °2-0.3177 °2-0.7796 °2-0.2119 °2--0.6014 °2
S-0.0557 Å °-0.0383 Å °-0.0919 Å °0.0392 Å °0.0343 Å °0.0029 Å °-0.0015 Å °-0.0423 Å °0.0214 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2761 - 276
2X-RAY DIFFRACTION1BB1 - 991 - 99
3X-RAY DIFFRACTION1CC1 - 91 - 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://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