[English] 日本語
Yorodumi
- PDB-3czf: Crystal structure of HLA-B*2709 complexed with the glucagon recep... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3czf
TitleCrystal structure of HLA-B*2709 complexed with the glucagon receptor (GR) peptide (residues 412-420)
Components
  • BETA-2-MICROGLOBULIN
  • GLUCAGON RECEPTOR PEPTIDE
  • HLA CLASS I HISTOCOMPATIBILITY ANTIGEN
KeywordsIMMUNE SYSTEM / MHC (MAJOR HISTOCOMPATIBILITY COMPLEX / HLA- B*2709
Function / homology
Function and homology information


regulation of glycogen metabolic process / glucagon receptor activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / response to starvation / exocytosis / peptide hormone binding / TAP binding ...regulation of glycogen metabolic process / glucagon receptor activity / regulation of interleukin-12 production / regulation of dendritic cell differentiation / regulation of T cell anergy / regulation of interleukin-6 production / response to starvation / exocytosis / peptide hormone binding / TAP binding / protection from natural killer cell mediated cytotoxicity / 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 / hormone-mediated signaling pathway / response to nutrient / cellular response to glucagon stimulus / : / : / secretory granule membrane / positive regulation of receptor binding / guanyl-nucleotide exchange factor activity / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to starvation / cellular response to iron ion / generation of precursor metabolites and energy / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / 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 / defense response / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / regulation of blood pressure / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / specific granule lumen / adenylate cyclase-activating G protein-coupled receptor signaling pathway / recycling endosome membrane / phagocytic vesicle membrane / Glucagon signaling in metabolic regulation / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / Glucagon-type ligand receptors / Interferon alpha/beta signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / glucose homeostasis / protein-folding chaperone binding / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / G alpha (s) signalling events / protein homotetramerization / G alpha (q) signalling events / adaptive immune response / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / cell surface receptor signaling pathway / endosome / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane
Similarity search - Function
GPCR, family 2, glucagon receptor / GPCR, family 2, glucagon-like peptide-1/glucagon receptor / G-protein coupled receptors family 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. ...GPCR, family 2, glucagon receptor / GPCR, family 2, glucagon-like peptide-1/glucagon receptor / G-protein coupled receptors family 2 signature 1. / : / GPCR, family 2, extracellular hormone receptor domain / G-protein coupled receptors family 2 profile 1. / Domain present in hormone receptors / Hormone receptor domain / GPCR family 2, extracellular hormone receptor domain superfamily / G-protein coupled receptors family 2 signature 2. / GPCR, family 2, secretin-like, conserved site / GPCR, family 2, secretin-like / 7 transmembrane receptor (Secretin family) / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / 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
HLA class I histocompatibility antigen, B alpha chain / HLA class I histocompatibility antigen, B alpha chain / Glucagon receptor / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsLoll, B. / Fiorillo, M.T. / Rueckert, C. / Saenger, W. / Sorrentino, R. / Ziegler, A. / Uchanska-Ziegler, B.
CitationJournal: Front Immunol / Year: 2020
Title: Conformational Plasticity of HLA-B27 Molecules Correlates Inversely With Efficiency of Negative T Cell Selection.
Authors: Loll, B. / Ruckert, C. / Uchanska-Ziegler, B. / Ziegler, A.
History
DepositionApr 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Apr 15, 2020Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HLA CLASS I HISTOCOMPATIBILITY ANTIGEN
B: BETA-2-MICROGLOBULIN
C: GLUCAGON RECEPTOR PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5356
Polymers45,2583
Non-polymers2763
Water12,809711
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5420 Å2
ΔGint-13.1 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.946, 81.933, 65.397
Angle α, β, γ (deg.)90.00, 108.91, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein HLA CLASS I HISTOCOMPATIBILITY ANTIGEN / MHC class I antigen B*27


Mass: 31951.219 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 25-300
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P03989, UniProt: P01889*PLUS
#2: Protein BETA-2-MICROGLOBULIN


Mass: 11879.356 Da / Num. of mol.: 1 / Fragment: RESIDUES 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P61769
#3: Protein/peptide GLUCAGON RECEPTOR PEPTIDE / pGR


Mass: 1427.708 Da / Num. of mol.: 1 / Fragment: RESIDUES 412-420 / Source method: obtained synthetically
Details: THIS SEQUENCE OCCURS NATURALLY IN HOMO SAPIENS (HUMAN)
References: UniProt: P47871
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 711 / 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: 2.85 Å3/Da / Density % sol: 56.89 %
Crystal growTemperature: 291 K / pH: 7.5
Details: 14% (w/v) PEG 4000, 20mM Tris/HCl pH 7.5, 150mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 7.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 5, 2003
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.1→30 Å / Num. obs: 196702 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 14.7 Å2 / Rsym value: 0.043 / Net I/σ(I): 20.8
Reflection shellResolution: 1.1→1.12 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.288 / % possible all: 90.4

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1K5N

1k5n


Resolution: 1.2→15 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 0.765 / SU ML: 0.016 / Cross valid method: THROUGHOUT / ESU R: 0.031 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.149 3852 2.5 %RANDOM
Rwork0.129 ---
obs0.13 149186 96.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å2-0.22 Å2
2---0.15 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3192 0 18 711 3921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213670
X-RAY DIFFRACTIONr_bond_other_d0.0020.022630
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.9365045
X-RAY DIFFRACTIONr_angle_other_deg0.9053.0026358
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0985470
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.89222.972212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3115638
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7241543
X-RAY DIFFRACTIONr_chiral_restr0.0940.2509
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024186
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02829
X-RAY DIFFRACTIONr_nbd_refined0.2140.2600
X-RAY DIFFRACTIONr_nbd_other0.2090.22864
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21669
X-RAY DIFFRACTIONr_nbtor_other0.0850.22022
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2518
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0960.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3110.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1430.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6961.52760
X-RAY DIFFRACTIONr_mcbond_other0.6311.5820
X-RAY DIFFRACTIONr_mcangle_it1.98323426
X-RAY DIFFRACTIONr_scbond_it2.64531890
X-RAY DIFFRACTIONr_scangle_it3.3984.51572
X-RAY DIFFRACTIONr_rigid_bond_restr1.45338100
X-RAY DIFFRACTIONr_sphericity_free6.4333712
X-RAY DIFFRACTIONr_sphericity_bonded3.84936157
LS refinement shellResolution: 1.2→1.23 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.159 264 -
Rwork0.138 10620 -
obs--94.1 %

+
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