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- PDB-1d5x: X-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH DIPEPTIDE MIMET... -

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Basic information

Entry
Database: PDB / ID: 1d5x
TitleX-RAY CRYSTAL STRUCTURE OF HLA-DR4 COMPLEXED WITH DIPEPTIDE MIMETIC AND SEB
Components
  • (HLA CLASS II HISTOCOMPATIBILITY ANTIGEN) x 2
  • DIPEPTIDE MIMETIC INHIBITOR
  • ENTEROTOXIN TYPE B
KeywordsIMMUNE SYSTEM/PEPTIDE INHIBITOR / MHC CLASS II-SUPERANTIGEN COMPLEX / IMMUNE SYSTEM-PEPTIDE INHIBITOR COMPLEX / PEPTIDEOMIMETIC INHIBITOR
Function / homology
Function and homology information


regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation ...regulation of interleukin-4 production / regulation of interleukin-10 production / positive regulation of T cell mediated immune response to tumor cell / myeloid dendritic cell antigen processing and presentation / antigen processing and presentation of endogenous peptide antigen via MHC class II / autolysosome membrane / regulation of T-helper cell differentiation / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / MHC class II receptor activity / positive regulation of CD4-positive, alpha-beta T cell activation / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / positive regulation of memory T cell differentiation / positive regulation of monocyte differentiation / CD4 receptor binding / positive regulation of kinase activity / inflammatory response to antigenic stimulus / intermediate filament / transport vesicle membrane / T-helper 1 type immune response / polysaccharide binding / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / positive regulation of insulin secretion involved in cellular response to glucose stimulus / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / Generation of second messenger molecules / immunological synapse / PD-1 signaling / epidermis development / negative regulation of inflammatory response to antigenic stimulus / negative regulation of T cell proliferation / MHC class II antigen presentation / detection of bacterium / T cell receptor binding / trans-Golgi network membrane / lumenal side of endoplasmic reticulum membrane / protein tetramerization / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / structural constituent of cytoskeleton / cognition / positive regulation of T cell mediated cytotoxicity / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / endocytic vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / Interferon gamma signaling / positive regulation of immune response / positive regulation of T cell activation / Downstream TCR signaling / MHC class II protein complex binding / late endosome membrane / toxin activity / T cell receptor signaling pathway / early endosome membrane / positive regulation of canonical NF-kappaB signal transduction / positive regulation of MAPK cascade / adaptive immune response / positive regulation of viral entry into host cell / lysosome / positive regulation of ERK1 and ERK2 cascade / immune response / positive regulation of protein phosphorylation / lysosomal membrane / external side of plasma membrane / Golgi membrane / positive regulation of DNA-templated transcription / cell surface / signal transduction / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / plasma membrane
Similarity search - Function
Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Ubiquitin-like (UB roll) - #120 ...Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Ubiquitin-like (UB roll) - #120 / Superantigen toxin, C-terminal / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / Enterotoxin / MHC classes I/II-like antigen recognition protein / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / 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 / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACE-HAC-ARG-MAA-HAQ-SEL / Enterotoxin type B / HLA class II histocompatibility antigen, DR alpha chain / HLA class II histocompatibility antigen, DRB1 beta chain / HLA class II histocompatibility antigen, DRB1 beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.45 Å
AuthorsSwain, A. / Crowther, R. / Kammlott, U.
CitationJournal: J.Med.Chem. / Year: 2000
Title: Peptide and peptide mimetic inhibitors of antigen presentation by HLA-DR class II MHC molecules. Design, structure-activity relationships, and X-ray crystal structures.
Authors: Bolin, D.R. / Swain, A.L. / Sarabu, R. / Berthel, S.J. / Gillespie, P. / Huby, N.J. / Makofske, R. / Orzechowski, L. / Perrotta, A. / Toth, K. / Cooper, J.P. / Jiang, N. / Falcioni, F. / ...Authors: Bolin, D.R. / Swain, A.L. / Sarabu, R. / Berthel, S.J. / Gillespie, P. / Huby, N.J. / Makofske, R. / Orzechowski, L. / Perrotta, A. / Toth, K. / Cooper, J.P. / Jiang, N. / Falcioni, F. / Campbell, R. / Cox, D. / Gaizband, D. / Belunis, C.J. / Vidovic, D. / Ito, K. / Crowther, R. / Kammlott, U. / Zhang, X. / Palermo, R. / Weber, D. / Guenot, J. / Nagy, Z. / Olson, G.L.
History
DepositionOct 12, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4May 31, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_validate_polymer_linkage / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.ptnr1_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN
B: HLA CLASS II HISTOCOMPATIBILITY ANTIGEN
C: ENTEROTOXIN TYPE B
D: DIPEPTIDE MIMETIC INHIBITOR


Theoretical massNumber of molelcules
Total (without water)72,7574
Polymers72,7574
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.838, 104.252, 107.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HLA CLASS II HISTOCOMPATIBILITY ANTIGEN / HLA-DR4


Mass: 21084.826 Da / Num. of mol.: 1 / Fragment: DR ALPHA CHAIN, EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P01903
#2: Protein HLA CLASS II HISTOCOMPATIBILITY ANTIGEN / HLA-DR4


Mass: 22520.021 Da / Num. of mol.: 1 / Fragment: DR-4 BETA CHAIN, EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P13760, UniProt: P01911*PLUS
#3: Protein ENTEROTOXIN TYPE B / / SEB / SUPERANTIGEN


Mass: 28411.064 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / References: UniProt: P01552
#4: Protein/peptide DIPEPTIDE MIMETIC INHIBITOR


Type: Peptide-like / Class: Inhibitor / Mass: 740.914 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. / References: ACE-HAC-ARG-MAA-HAQ-SEL
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Compound detailsINHIBITOR WAS BOUND TO MHC; SUBSEQUENTLY COMPLEX WITH SEB WAS FORMED

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 64.93 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
25 %PEG40001reservoir
310 mMsodium acetate1reservoir
42.4 %ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1994
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.45→20 Å / Num. obs: 38325 / % possible obs: 99.4 % / Biso Wilson estimate: 45.3 Å2 / Rmerge(I) obs: 0.095
Reflection shellHighest resolution: 2 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.5refinement
RefinementResolution: 2.45→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 328232.69 / Data cutoff high rms absF: 328232.69 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.268 3561 10 %RANDOM
Rwork0.237 ---
obs0.237 35655 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.15 Å2 / ksol: 0.263 e/Å3
Displacement parametersBiso mean: 45 Å2
Baniso -1Baniso -2Baniso -3
1-3.91 Å20 Å20 Å2
2---2.4 Å20 Å2
3----1.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.37 Å
Luzzati d res low-20 Å
Luzzati sigma a0.5 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4900 0 0 10 4910
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.24
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.151.5
X-RAY DIFFRACTIONc_mcangle_it3.572
X-RAY DIFFRACTIONc_scbond_it3.222
X-RAY DIFFRACTIONc_scangle_it4.792.5
LS refinement shellResolution: 2.45→2.6 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.381 563 10.4 %
Rwork0.367 4846 -
obs--86.1 %
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.242 / Rfactor Rfree: 0.272 / Rfactor Rwork: 0.242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.24

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