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- PDB-1qlf: MHC CLASS I H-2DB COMPLEXED WITH GLYCOPEPTIDE K3G -

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Basic information

Entry
Database: PDB / ID: 1qlf
TitleMHC CLASS I H-2DB COMPLEXED WITH GLYCOPEPTIDE K3G
Components
  • HUMAN BETA-2-MICROGLOBULIN
  • MHC CLASS I H-2DB HEAVY CHAIN
  • SYNTHETIC GLYCOPEPTIDE
KeywordsIMMUNE SYSTEM/PEPTIDE / MURINE CLASS I MHC-PEPTIDE COMPLEX / MHC / GLYCOPEPTIDE / ANTIGEN / HISTOCOMPATIBILITY / IMMUNOLOGY / IMMUNE SYSTEM-PEPTIDE complex
Function / homology
Function and homology information


: / : / : / : / : / regulation of membrane depolarization / retina homeostasis / helical viral capsid / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of protein binding ...: / : / : / : / : / regulation of membrane depolarization / retina homeostasis / helical viral capsid / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / positive regulation of protein binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / 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 / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / antimicrobial humoral immune response mediated by antimicrobial peptide / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / antibacterial humoral response / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / cellular response to lipopolysaccharide / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / defense response to Gram-negative bacterium / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / host cell cytoplasm / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / ribonucleoprotein complex / Amyloid fiber formation / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / RNA binding / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein / 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 / : ...Paramyxovirus nucleocapsid protein / Paramyxovirus nucleocapsid protein / 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
Beta-2-microglobulin / H-2 class I histocompatibility antigen, D-B alpha chain / Nucleoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
SENDAI VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsTormo, J. / Jones, E.Y.
CitationJournal: Immunity / Year: 1999
Title: Crystal Structures of Two H-2Db/Glycopeptide Complexes Suggest a Molecular Basis for Ctl Cross-Reactivity
Authors: Glithero, A. / Tormo, J. / Haurum, J.S. / Arsequell, G. / Valencia, G. / Edwards, J. / Springer, S. / Townsend, A. / Pao, Y.-L. / Wormald, M. / Dwek, R.A. / Jones, E.Y. / Elliot, T.
History
DepositionAug 30, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Derived calculations / Category: struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id ..._struct_conn.pdbx_leaving_atom_flag / _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_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
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MHC CLASS I H-2DB HEAVY CHAIN
B: HUMAN BETA-2-MICROGLOBULIN
C: SYNTHETIC GLYCOPEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3167
Polymers44,8153
Non-polymers5014
Water2,882160
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-31.2 kcal/mol
Surface area23140 Å2
MethodPQS
Unit cell
Length a, b, c (Å)61.073, 58.272, 77.146
Angle α, β, γ (deg.)90.00, 108.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC CLASS I H-2DB HEAVY CHAIN / DB / H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN / D-B ALPHA CHAIN / (H-2D(B))


Mass: 32087.703 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAINS
Source method: isolated from a genetically manipulated source
Details: FORMS HETEROTRIMER WITH CHAIN B (BETA-2-MICROGLOBULIN) AND CHAIN C (PEPTIDE ANTIGEN)
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Cell: MOST NUCLEATED CELLS / Cellular location: CELL SURFACE / Cell (production host): CHO K1 CELLS / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P01899
#2: Protein HUMAN BETA-2-MICROGLOBULIN / B2M


Mass: 11748.160 Da / Num. of mol.: 1 / Fragment: MHC ASSOCIATED LIGHT CHAIN
Source method: isolated from a genetically manipulated source
Details: FORMS HETEROTRIMER WITH CHAIN A AND CHAIN C / Source: (gene. exp.) HOMO SAPIENS (human) / Cell: MOST NUCLEATED CELLS / Cellular location: CELL SURFACE / Cell (production host): CHO K1 CELLS / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P01884, UniProt: P61769*PLUS

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

#3: Protein/peptide SYNTHETIC GLYCOPEPTIDE


Mass: 979.086 Da / Num. of mol.: 1
Fragment: H-2DB-BOUND GLYCOPEPTIDE FROM NUCLEOCAPSID PROTEIN
Source method: obtained synthetically
Details: PEPTIDE DERIVED FROM SENDAI VIRUS NUCLEOPROTEIN RESIDUES 324-332, GLY327 HAS BEEN REPLACED BY AN O-GLCNAC SUBSTITUTED SERINE
Source: (synth.) SENDAI VIRUS / References: UniProt: P04857
#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.: 1
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 , 3 types, 163 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.8 Å3/Da / Density % sol: 55 %
Crystal growpH: 5 / Details: pH 5.00
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlpeptide complex1drop
315-23 %PEG60001reservoir
4100 mMammonium sulfate1reservoir
5100 mMMES1reservoir
2Tris buffered saline1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→10 Å / Num. obs: 14363 / % possible obs: 97 % / Biso Wilson estimate: 39.3 Å2 / Rsym value: 0.06
Reflection shellResolution: 2.65→2.73 Å / Rsym value: 0.17 / % possible all: 95.1
Reflection
*PLUS
% possible obs: 97 % / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 95.1 % / Rmerge(I) obs: 0.176

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Processing

Software
NameVersionClassification
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CE6

1ce6


Resolution: 2.65→20 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE CARBOHYDRATE ATTACHED TO THE GLYCOPEPTIDE IS DISORDERED. ONLY ONE OF THE TWO MAJOR CONFORMATIONS HAS BEEN MODELLED WITH HALF OCCUPANCY.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1480 10.1 %RANDOM
Rwork0.204 ---
obs0.204 14614 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.7963 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 33.7 Å2
Baniso -1Baniso -2Baniso -3
1--9.32 Å20 Å25.25 Å2
2---8.58 Å20 Å2
3---17.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3164 0 31 160 3355
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_d24.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.282
X-RAY DIFFRACTIONc_scbond_it1.732
X-RAY DIFFRACTIONc_scangle_it2.72.5
LS refinement shellResolution: 2.65→2.74 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.322 133 9.4 %
Rwork0.269 1276 -
obs--95.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION4GOL.PARGOL.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.75

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