[English] 日本語
Yorodumi
- PDB-5weu: Crystal Structure of H2-Dd with disulfide-linked 10mer peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5weu
TitleCrystal Structure of H2-Dd with disulfide-linked 10mer peptide
Components
  • Beta-2-microglobulin
  • Envelope glycoprotein gp160
  • H-2 class I histocompatibility antigen, D-D alpha chain
KeywordsIMMUNE SYSTEM / Antigen presentation / peptide editing / MAJOR HISTOMPATIBILITY COMPLEX CLASS I / MHC-I / TAPBPR / H2-Dd / H-2DD / TAPASIN / Peptide Loading Complex / PLC / IMMUNE RESPONSE
Function / homology
Function and homology information


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 ...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 / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / MHC class I protein complex / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / phagocytic vesicle membrane / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / clathrin-dependent endocytosis of virus by host cell / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / viral protein processing / fusion of virus membrane with host plasma membrane / external side of 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 / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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 / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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
Similarity search - Component
Biological speciesMus musculus (house mouse)
Human immunodeficiency virus type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.584 Å
AuthorsJiang, J.S. / Natarajan, K. / Boyd, L.F. / Margulies, D.H.
CitationJournal: Science / Year: 2017
Title: Crystal structure of a TAPBPR-MHC I complex reveals the mechanism of peptide editing in antigen presentation.
Authors: Jiang, J. / Natarajan, K. / Boyd, L.F. / Morozov, G.I. / Mage, M.G. / Margulies, D.H.
History
DepositionJul 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 4, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 9, 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 gp160
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3369
Polymers44,9643
Non-polymers3726
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-3 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.840, 90.841, 109.538
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

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


Mass: 32281.965 Da / Num. of mol.: 1 / Fragment: residues 26-301 / Mutation: S73C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: PET21-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01900
#2: Protein Beta-2-microglobulin


Mass: 11660.350 Da / Num. of mol.: 1 / Fragment: residues 21-119
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 Envelope glycoprotein gp160 / Env polyprotein


Mass: 1021.214 Da / Num. of mol.: 1 / Fragment: V3 domain residues 316-325 / Mutation: R5C / Source method: obtained synthetically
Source: (synth.) Human immunodeficiency virus type 1 group M subtype B
References: UniProt: P03377
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.81 Å3/Da / Density % sol: 56.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 10% PEG 10K, 0.1M Cacodylate

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 16, 2015
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.58→46.92 Å / Num. obs: 69110 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 23.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.026 / Net I/σ(I): 16.2
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6254 / CC1/2: 0.585 / Rpim(I) all: 0.503 / % possible all: 90.8

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ECB

3ecb


Resolution: 1.584→37.261 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2162 2000 2.89 %RANDOM
Rwork0.1863 ---
obs0.1872 69106 99.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.584→37.261 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3133 0 24 407 3564
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043278
X-RAY DIFFRACTIONf_angle_d0.7824442
X-RAY DIFFRACTIONf_dihedral_angle_d14.9881955
X-RAY DIFFRACTIONf_chiral_restr0.051449
X-RAY DIFFRACTIONf_plane_restr0.005580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5836-1.62320.36181250.30874221X-RAY DIFFRACTION88
1.6232-1.66710.29331410.2724672X-RAY DIFFRACTION99
1.6671-1.71620.27861420.25064801X-RAY DIFFRACTION100
1.7162-1.77160.21711430.22124791X-RAY DIFFRACTION100
1.7716-1.83490.23211420.21244759X-RAY DIFFRACTION100
1.8349-1.90840.22031420.20314800X-RAY DIFFRACTION100
1.9084-1.99520.23861440.2014814X-RAY DIFFRACTION100
1.9952-2.10040.23391430.18814816X-RAY DIFFRACTION100
2.1004-2.2320.20291440.18374815X-RAY DIFFRACTION100
2.232-2.40430.22891440.18594836X-RAY DIFFRACTION100
2.4043-2.64620.20041450.18824850X-RAY DIFFRACTION100
2.6462-3.02890.23631460.18954897X-RAY DIFFRACTION100
3.0289-3.81550.2141460.17294911X-RAY DIFFRACTION100
3.8155-37.27130.17471530.15355123X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 8.5776 Å / Origin y: 27.8231 Å / Origin z: 37.599 Å
111213212223313233
T0.0847 Å20.0021 Å20.0033 Å2-0.1253 Å2-0 Å2--0.1121 Å2
L0.2675 °20.3138 °2-0.0528 °2-1.2305 °2-0.2857 °2--0.5208 °2
S0.0126 Å °0.0238 Å °-0.0171 Å °0.0144 Å °-0.0765 Å °-0.097 Å °0.0169 Å °0.0209 Å °-0.0002 Å °
Refinement TLS groupSelection details: all

+
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