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- PDB-1uvq: Crystal structure of HLA-DQ0602 in complex with a hypocretin peptide -

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Basic information

Entry
Database: PDB / ID: 1uvq
TitleCrystal structure of HLA-DQ0602 in complex with a hypocretin peptide
Components
  • (HLA CLASS II HISTOCOMPATIBILITY ...) x 2
  • OREXIN
KeywordsIMMUNE SYSTEM / IMMUNOLOGY / MHC CLASS II / DIABETES / NARCOLEPSY / AUTOIMMUNE DISEASE / STRUCTURAL PROTEOMICS IN EUROPE / SPINE / STRUCTURAL GENOMICS
Function / homology
Function and homology information


type 1 orexin receptor binding / type 2 orexin receptor binding / neuronal dense core vesicle lumen / negative regulation of transmission of nerve impulse / Orexin and neuropeptides FF and QRFP bind to their respective receptors / positive regulation of transmission of nerve impulse / regulation of neurotransmitter secretion / MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / neuropeptide hormone activity ...type 1 orexin receptor binding / type 2 orexin receptor binding / neuronal dense core vesicle lumen / negative regulation of transmission of nerve impulse / Orexin and neuropeptides FF and QRFP bind to their respective receptors / positive regulation of transmission of nerve impulse / regulation of neurotransmitter secretion / MHC class II receptor activity / antigen processing and presentation of peptide or polysaccharide antigen via MHC class II / neuropeptide hormone activity / positive regulation of calcium ion transport / sleep / response to alcohol / temperature homeostasis / transport vesicle membrane / eating behavior / response to starvation / negative regulation of DNA replication / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / negative regulation of potassium ion transport / humoral immune response / Generation of second messenger molecules / Co-inhibition by PD-1 / neuropeptide signaling pathway / rough endoplasmic reticulum / MHC class II antigen presentation / trans-Golgi network membrane / excitatory postsynaptic potential / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / 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 activation / Interferon gamma signaling / MHC class II protein complex binding / endocytic vesicle membrane / late endosome membrane / synaptic vesicle / Downstream TCR signaling / T cell receptor signaling pathway / positive regulation of cold-induced thermogenesis / positive regulation of cytosolic calcium ion concentration / phospholipase C-activating G protein-coupled receptor signaling pathway / chemical synaptic transmission / G alpha (q) signalling events / adaptive immune response / postsynapse / endosome membrane / immune response / Golgi membrane / lysosomal membrane / perinuclear region of cytoplasm / extracellular region / membrane / plasma membrane
Similarity search - Function
Prepro-orexin / Prepro-orexin / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / 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 ...Prepro-orexin / Prepro-orexin / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / GLYCINE / Major histocompatibility complex, class II, DQ alpha 1 / Hypocretin neuropeptide precursor / HLA class II histocompatibility antigen, DQ alpha 1 chain / HLA class II histocompatibility antigen, DQ beta 1 chain / HLA class II histocompatibility antigen, DQ beta 1 chain
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSiebold, C. / Hansen, B.E. / Wyer, J.R. / Harlos, K. / Esnouf, R.E. / Svejgaard, A. / Bell, J.I. / Strominger, J.L. / Jones, E.Y. / Fugger, L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Crystal Structure of Hla-Dq0602 that Protects Against Type 1 Diabetes and Confers Strong Susceptibility to Narcolepsy
Authors: Siebold, C. / Hansen, B.E. / Wyer, J.R. / Harlos, K. / Esnouf, R.E. / Svejgaard, A. / Bell, J.I. / Strominger, J.L. / Jones, E.Y. / Fugger, L.
History
DepositionJan 22, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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: OREXIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7869
Polymers48,4103
Non-polymers1,3766
Water6,684371
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9400 Å2
ΔGint-43.8 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.078, 129.304, 40.619
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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HLA CLASS II HISTOCOMPATIBILITY ... , 2 types, 2 molecules AB

#1: Protein HLA CLASS II HISTOCOMPATIBILITY ANTIGEN / QA1*0602 / DQ(5) ALPHA CHAIN / DC-1 ALPHA CHAIN


Mass: 22275.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): S2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: P01907, UniProt: E9PMV2*PLUS
#2: Protein HLA CLASS II HISTOCOMPATIBILITY ANTIGEN / DQB1*0602 / DQB1*0602 BETA CHAIN / DQ(5) / DC-1


Mass: 23029.709 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): S2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: P03992, UniProt: P01920*PLUS

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide OREXIN / HCRT / HYPOCRETIN-1 / HCRT1 / OREXIN-B / HYPOCRETIN-2 / HCRT2


Mass: 3104.396 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CHAIN C IS COVALENTLY CONNECTED AT THE N-TERMINUS OF CHAIN B VIA A GLYCINE-RICH LINKER. AS PER DEFINITION FOR THE MHC CLASS II MOLECULES, THE CHAINS OF THE PEPTIDE LIGAND (CHAIN C) AND THE ...Details: CHAIN C IS COVALENTLY CONNECTED AT THE N-TERMINUS OF CHAIN B VIA A GLYCINE-RICH LINKER. AS PER DEFINITION FOR THE MHC CLASS II MOLECULES, THE CHAINS OF THE PEPTIDE LIGAND (CHAIN C) AND THE BETA-CHAIN (CHAIN B) SHOULD BE DIFFERENT.
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: O43612

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Sugars , 2 types, 3 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 374 molecules

#5: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 371 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.71 Å3/Da / Density % sol: 54.27 %
Crystal growpH: 3.8 / Details: pH 3.80
Crystal grow
*PLUS
pH: 3.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMTris-HCl1drop
27 mg/mlprotein1drop
3100 mMglycine1reservoirpH3.5
416 %(w/v)PEG80001reservoir
5100 mMmagnesium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.956
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 49489 / % possible obs: 97.3 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.9
Reflection shellResolution: 1.8→1.85 Å / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.6 / % possible all: 78.7
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 78.7 % / Rmerge(I) obs: 0.296 / Mean I/σ(I) obs: 3.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→27.31 Å / Rfactor Rfree error: 0.004 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.205 2386 5 %
Rwork0.189 --
obs0.189 47894 94.3 %
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.39 Å20 Å20 Å2
2--0.65 Å20 Å2
3---1.73 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→27.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3075 0 86 371 3532
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.241.5
X-RAY DIFFRACTIONc_scbond_it0.112
X-RAY DIFFRACTIONc_scangle_it3.192.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.249 326 5.1 %
Rwork0.224 6060 -
obs--76.3 %
Refinement
*PLUS
Lowest resolution: 25 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.79
LS refinement shell
*PLUS
Lowest resolution: 1.85 Å / Rfactor Rfree: 0.25

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