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- PDB-8ral: CL3E peptide bound to the I-Ab murine MHC class II receptor -

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Entry
Database: PDB / ID: 8ral
TitleCL3E peptide bound to the I-Ab murine MHC class II receptor
Components
  • (H-2 class II histocompatibility antigen, ...) x 2
  • CL3E peptide
KeywordsIMMUNE SYSTEM / MHC class II / receptor / diabetes
Function / homology
Function and homology information


positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / positive regulation of T-helper 1 type immune response / antigen processing and presentation of peptide antigen / B cell affinity maturation / protein antigen binding / positive regulation of T cell differentiation / antigen processing and presentation / response to type II interferon / toxic substance binding ...positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / positive regulation of T-helper 1 type immune response / antigen processing and presentation of peptide antigen / B cell affinity maturation / protein antigen binding / positive regulation of T cell differentiation / antigen processing and presentation / response to type II interferon / toxic substance binding / multivesicular body / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / cellular response to type II interferon / adaptive immune response / early endosome / lysosome / immune response / external side of plasma membrane / ubiquitin protein ligase binding / Golgi apparatus / membrane / plasma membrane
Similarity search - Function
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 / MHC classes I/II-like antigen recognition protein / : / Immunoglobulin/major histocompatibility complex, conserved site ...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 / 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
Similarity search - Domain/homology
H-2 class II histocompatibility antigen, A-B alpha chain / H-2 class II histocompatibility antigen, A beta chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsErausquin, E. / Urdiciain, A. / Serra, P. / Santamaria, P. / Lopez-Sagaseta, J.
Funding support Spain, European Union, 3items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesRYC201721683 Spain
Spanish Ministry of Science, Innovation, and UniversitiesPID2021-125493OB-I00 Spain
European Foundation for the Study of Diabetes (EFSD)European Union
CitationJournal: To be published
Title: CL3E peptide bound to the I-Ab murine MHC class II receptor
Authors: Lopez-Sagaseta, J. / Erausquin, E. / Urdiciain, A. / Serra, P. / Santamaria, P.
History
DepositionDec 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2024Provider: repository / Type: Initial release
Revision 2.0Nov 27, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / cell / chem_comp / chem_comp_atom / chem_comp_bond / entity / pdbx_audit_support / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_contact_author / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conf / struct_conn / struct_conn_type / struct_mon_prot_cis / struct_sheet_range / symmetry
Item: _cell.volume / _chem_comp.formula ..._cell.volume / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_audit_support.funding_organization / _pdbx_branch_scheme.asym_id / _pdbx_branch_scheme.auth_asym_id / _pdbx_branch_scheme.auth_mon_id / _pdbx_branch_scheme.auth_seq_num / _pdbx_branch_scheme.entity_id / _pdbx_branch_scheme.mon_id / _pdbx_branch_scheme.num / _pdbx_branch_scheme.pdb_asym_id / _pdbx_branch_scheme.pdb_mon_id / _pdbx_branch_scheme.pdb_seq_num / _pdbx_entity_branch_list.comp_id / _pdbx_entity_branch_list.entity_id / _pdbx_entity_branch_list.num / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][2] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[2][3] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_overall_phase_error / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_solvent_vdw_probe_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _software.name / _software.version / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_class / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.pdbx_omega_angle / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_comp_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_comp_id / _struct_sheet_range.end_label_seq_id / _symmetry.space_group_name_Hall
Description: Polymer backbone linkage
Details: Sugar identity and linkages have been corrected. Na+ ions have been replaced by water molecules.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class II histocompatibility antigen, A-B alpha chain
B: H-2 class II histocompatibility antigen, A beta chain
C: CL3E peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1106
Polymers49,0753
Non-polymers1,0353
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8040 Å2
ΔGint-26 kcal/mol
Surface area17230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.057, 76.032, 133.037
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

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H-2 class II histocompatibility antigen, ... , 2 types, 2 molecules AB

#1: Protein H-2 class II histocompatibility antigen, A-B alpha chain


Mass: 22030.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: V76C mutation to create cys trap with peptide / Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P14434
#2: Protein H-2 class II histocompatibility antigen, A beta chain


Mass: 25683.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal CL3E peptide (chain C identifier) fused through G-S linker
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Ab1, H2-iabeta / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P14483

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Protein/peptide / Sugars , 2 types, 2 molecules C

#3: Protein/peptide CL3E peptide


Mass: 1361.606 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal Cys for cys trap linkage with I-Ab alpha chain
Source: (gene. exp.) synthetic construct (others) / Production host: Cricetulus griseus (Chinese hamster)
#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_d2-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 130 molecules

#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 54.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M magnesium chloride hexahydrate, 0.1 M sodium acetate pH 5.0, 20% w/v PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979181 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2022
RadiationMonochromator: Si(111) channel-cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979181 Å / Relative weight: 1
ReflectionResolution: 2.1→46.85 Å / Num. obs: 30076 / % possible obs: 99.2 % / Redundancy: 4.3 % / Biso Wilson estimate: 40.37 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.07 / Rrim(I) all: 0.112 / Net I/σ(I): 7.5
Reflection shellResolution: 2.1→2.16 Å / Rmerge(I) obs: 0.936 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2449 / CC1/2: 0.783 / Rpim(I) all: 0.739 / Rrim(I) all: 1.199

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→46.85 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.318 / SU ML: 0.195 / Cross valid method: FREE R-VALUE / ESU R: 0.198 / ESU R Free: 0.183
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.263 1495 4.974 %
Rwork0.2165 28561 -
all0.219 --
obs-30056 98.732 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 45.744 Å2
Baniso -1Baniso -2Baniso -3
1-6.844 Å2-0 Å2-0 Å2
2---6.063 Å2-0 Å2
3----0.781 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2816 0 69 128 3013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122969
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162545
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.8184051
X-RAY DIFFRACTIONr_angle_other_deg0.5881.7345833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.975359
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.054513
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10710379
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.76110133
X-RAY DIFFRACTIONr_chiral_restr0.080.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023475
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02695
X-RAY DIFFRACTIONr_nbd_refined0.2090.2581
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.22418
X-RAY DIFFRACTIONr_nbtor_refined0.1870.21435
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1170.21546
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2179
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1110.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1720.217
X-RAY DIFFRACTIONr_nbd_other0.1750.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.110.27
X-RAY DIFFRACTIONr_mcbond_it4.3075.0771459
X-RAY DIFFRACTIONr_mcbond_other4.3045.0771459
X-RAY DIFFRACTIONr_mcangle_it5.8979.0891809
X-RAY DIFFRACTIONr_mcangle_other5.8969.0891810
X-RAY DIFFRACTIONr_scbond_it5.1955.3441510
X-RAY DIFFRACTIONr_scbond_other5.1935.3451511
X-RAY DIFFRACTIONr_scangle_it7.0839.6782242
X-RAY DIFFRACTIONr_scangle_other7.0829.6782243
X-RAY DIFFRACTIONr_lrange_it8.47550.9393271
X-RAY DIFFRACTIONr_lrange_other8.47550.9393272
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1540.3421070.3712100X-RAY DIFFRACTION99.774
2.154-2.2130.3781030.3462031X-RAY DIFFRACTION99.4872
2.213-2.2770.341060.3162005X-RAY DIFFRACTION99.6695
2.277-2.3470.312880.2931918X-RAY DIFFRACTION99.6523
2.347-2.4240.3011060.2761862X-RAY DIFFRACTION99.5951
2.424-2.5090.301990.2531828X-RAY DIFFRACTION99.5351
2.509-2.6030.299920.2221751X-RAY DIFFRACTION99.7834
2.603-2.7090.316770.2211691X-RAY DIFFRACTION99.2701
2.709-2.8290.323870.2081617X-RAY DIFFRACTION99.0698
2.829-2.9670.268770.1891554X-RAY DIFFRACTION98.9084
2.967-3.1270.261830.1851461X-RAY DIFFRACTION98.6581
3.127-3.3150.258710.1891394X-RAY DIFFRACTION98.5868
3.315-3.5430.211690.1781299X-RAY DIFFRACTION97.7841
3.543-3.8250.258780.2051219X-RAY DIFFRACTION97.5922
3.825-4.1870.206560.1831127X-RAY DIFFRACTION97.4465
4.187-4.6770.207520.1681014X-RAY DIFFRACTION97.0856
4.677-5.3920.228450.185915X-RAY DIFFRACTION96.8718
5.392-6.5820.325450.243766X-RAY DIFFRACTION95.7497
6.582-9.2180.23340.22619X-RAY DIFFRACTION95.7478
9.218-46.50.289200.267390X-RAY DIFFRACTION95.3488

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