[English] 日本語
Yorodumi
- PDB-3e6f: MHC CLASS I H-2Dd Heavy chain complexed with Beta-2 Microglobulin... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3e6f
TitleMHC CLASS I H-2Dd Heavy chain complexed with Beta-2 Microglobulin and a variant peptide, PA9, from the Human immunodeficiency virus (BaL) envelope glycoprotein 120
Components
  • BETA-2 MICROGLOBULIN
  • Envelope glycoprotein 9-residue peptide
  • H-2 class I histocompatibility antigen, D-D alpha chain
KeywordsIMMUNE SYSTEM / COMPLEX (HISTOCOMPATIBILITY-ANTIGEN) / Glycoprotein / Immune response / Membrane / MHC I / Phosphoprotein / Transmembrane / Immunoglobulin domain / Secreted / Envelope protein
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / 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 / Dectin-2 family / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response ...membrane fusion involved in viral entry into host cell / 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 / Dectin-2 family / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / Neutrophil degranulation / host cell endosome membrane / 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 / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / cellular response to nicotine / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / sensory perception of smell / iron ion transport / negative regulation of neuron projection development / T cell differentiation in thymus / protein refolding / clathrin-dependent endocytosis of virus by host cell / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / viral protein processing / symbiont entry into host cell / external side of plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / : / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / membrane / plasma membrane / cytosol
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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 ...Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-D alpha chain / Envelope glycoprotein gp160 / Beta-2-microglobulin / Envelope glycoprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.41 Å
AuthorsWang, R. / Natarajan, K. / Robinson, H. / Margulies, D.H.
CitationJournal: J.Immunol. / Year: 2009
Title: Different vaccine vectors delivering the same antigen elicit CD8+ T cell responses with distinct clonotype and epitope specificity
Authors: Honda, M. / Wang, R. / Kong, W.P. / Kanekiyo, M. / Akahata, W. / Xu, L. / Matsuo, K. / Natarajan, K. / Robinson, H. / Asher, T.E. / Price, D.A. / Douek, D.C. / Margulies, D.H. / Nabel, G.J.
History
DepositionAug 15, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 26, 2016Group: Structure summary
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-D alpha chain
B: BETA-2 MICROGLOBULIN
P: Envelope glycoprotein 9-residue peptide


Theoretical massNumber of molelcules
Total (without water)44,5813
Polymers44,5813
Non-polymers00
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-19 kcal/mol
Surface area19210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.810, 109.515, 53.762
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

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


Mass: 31950.557 Da / Num. of mol.: 1 / Fragment: UNP residues 26 to 298
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P01900
#2: Protein BETA-2 MICROGLOBULIN


Mass: 11678.388 Da / Num. of mol.: 1 / Fragment: UNP residues 21 to 119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m, RP23-34E24.5-001 / Plasmid: PET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q91XJ8, UniProt: P01887*PLUS
#3: Protein/peptide Envelope glycoprotein 9-residue peptide


Mass: 952.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: Q9YZ87, UniProt: P05878*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.25 Å3/Da / Density % sol: 45.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 12% PEG 20000, 0.1M MES, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 24, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. all: 16068 / Num. obs: 15011 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 18.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 11.5 / Num. unique all: 975 / % possible all: 61.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QO3

1qo3


Resolution: 2.41→28.83 Å / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 590 3.7 %RANDOM
Rwork0.223 ---
all0.25 16028 --
obs-14569 90.7 %-
Solvent computationBsol: 47.945 Å2
Displacement parametersBiso max: 97.65 Å2 / Biso mean: 28.165 Å2 / Biso min: 1.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å20 Å20 Å2
2--3.049 Å20 Å2
3----1.799 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati sigma a0.3 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.41→28.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3131 0 0 125 3256
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_d1.37
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

+
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