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- PDB-1hqr: CRYSTAL STRUCTURE OF A SUPERANTIGEN BOUND TO THE HIGH-AFFINITY, Z... -

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Entry
Database: PDB / ID: 1hqr
TitleCRYSTAL STRUCTURE OF A SUPERANTIGEN BOUND TO THE HIGH-AFFINITY, ZINC-DEPENDENT SITE ON MHC CLASS II
Components
  • HLA-DR ALPHA CHAIN
  • HLA-DR BETA CHAIN
  • MYELIN BASIC PROTEIN
  • STREPTOCOCCAL PYROGENIC EXOTOXIN C
KeywordsIMMUNE SYSTEM / Superantigen-MHC class II complex
Function / homology
Function and homology information


compact myelin / structural constituent of myelin sheath / positive regulation of metalloendopeptidase activity / internode region of axon / axon ensheathment / negative regulation of heterotypic cell-cell adhesion / 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 ...compact myelin / structural constituent of myelin sheath / positive regulation of metalloendopeptidase activity / internode region of axon / axon ensheathment / negative regulation of heterotypic cell-cell adhesion / 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 / EGR2 and SOX10-mediated initiation of Schwann cell myelination / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / membrane organization / positive regulation of memory T cell differentiation / positive regulation of chemokine (C-X-C motif) ligand 2 production / transport vesicle membrane / maintenance of blood-brain barrier / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / polysaccharide binding / Generation of second messenger molecules / immunological synapse / Co-inhibition by PD-1 / T cell receptor binding / substantia nigra development / myelination / MHC class II antigen presentation / central nervous system development / trans-Golgi network membrane / cell periphery / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / sensory perception of sound / MHC class II protein complex / clathrin-coated endocytic vesicle membrane / ER to Golgi transport vesicle membrane / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / peptide antigen binding / positive regulation of T cell mediated cytotoxicity / positive regulation of interleukin-6 production / positive regulation of T cell activation / cognition / response to toxic substance / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / MAPK cascade / Downstream TCR signaling / myelin sheath / toxin activity / protease binding / early endosome membrane / chemical synaptic transmission / adaptive immune response / lysosome / calmodulin binding / immune response / Golgi membrane / lysosomal membrane / neuronal cell body / synapse / lipid binding / cell surface / protein-containing complex / extracellular exosome / extracellular region / nucleus / plasma membrane / cytosol
Similarity search - Function
Myelin basic protein / Myelin basic protein / Myelin basic protein signature. / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Ubiquitin-like (UB roll) - #120 ...Myelin basic protein / Myelin basic protein / Myelin basic protein signature. / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1. / Staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, OB-fold / Staphylococcal/Streptococcal toxin, OB-fold domain / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Ubiquitin-like (UB roll) - #120 / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
HLA class II histocompatibility antigen, DR alpha chain / Myelin basic protein / Exotoxin type C / HLA class II histocompatibility antigen, DR beta 5 chain / HLA class II histocompatibility antigen, DR beta 5 chain / Exotoxin type C
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLi, Y. / Li, H. / Dimasi, N. / Schlievert, P. / Mariuzza, R.
CitationJournal: Immunity / Year: 2001
Title: Crystal structure of a superantigen bound to the high-affinity, zinc-dependent site on MHC class II.
Authors: Li, Y. / Li, H. / Dimasi, N. / McCormick, J.K. / Martin, R. / Schuck, P. / Schlievert, P.M. / Mariuzza, R.A.
History
DepositionDec 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA-DR ALPHA CHAIN
B: HLA-DR BETA CHAIN
C: MYELIN BASIC PROTEIN
D: STREPTOCOCCAL PYROGENIC EXOTOXIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3255
Polymers69,2604
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.827, 111.950, 216.617
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein HLA-DR ALPHA CHAIN / DRA*0101


Mass: 21084.826 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P01903
#2: Protein HLA-DR BETA CHAIN / DRB5*0101


Mass: 22231.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q29703, UniProt: Q30154*PLUS
#3: Protein/peptide MYELIN BASIC PROTEIN / MBP


Mass: 1558.843 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P02686
#4: Protein STREPTOCOCCAL PYROGENIC EXOTOXIN C / SPE-C


Mass: 24384.285 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P13380, UniProt: Q8NKX2*PLUS
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 54.53 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Ammonium sulfate, PEG 400, sodium cacodylate, ZnCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K
Crystal grow
*PLUS
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
21.8 Mammonium sulfate1reservoir
35 %PEG4001reservoir
40.1 Msodium cacodylate1reservoir
55 mM1reservoirZnCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.2→100 Å / Num. all: 141485 / Num. obs: 11585 / % possible obs: 90.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 54.9 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.4
Reflection shellResolution: 3.2→3.3 Å / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 5.1 / Rsym value: 0.36 / % possible all: 92.7
Reflection
*PLUS
Num. measured all: 141485
Reflection shell
*PLUS
% possible obs: 92.7 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS0.4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→100 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1943820.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.288 1187 10.2 %RANDOM
Rwork0.224 ---
obs0.224 11585 90.2 %-
all-141485 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.48 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso mean: 41.8 Å2
Baniso -1Baniso -2Baniso -3
1-12.45 Å20 Å20 Å2
2---14.05 Å20 Å2
3---1.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 3.2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4538 0 1 0 4539
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it10.111.5
X-RAY DIFFRACTIONc_mcangle_it15.292
X-RAY DIFFRACTIONc_scbond_it10.92
X-RAY DIFFRACTIONc_scangle_it15.392.5
LS refinement shellResolution: 3.2→3.4 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 234 12 %
Rwork0.273 1715 -
obs--92.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87

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