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- PDB-1lek: Crystal Structure of H-2Kbm3 bound to dEV8 -

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Basic information

Entry
Database: PDB / ID: 1lek
TitleCrystal Structure of H-2Kbm3 bound to dEV8
Components
  • Beta-2-microglobulin
  • H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN
  • dEV8
KeywordsIMMUNE SYSTEM / MHC class I allogeneic complex with peptide
Function / homology
Function and homology information


Complex IV assembly / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / Respiratory electron transport / natural killer cell lectin-like receptor binding / TAP2 binding / TAP1 binding / cis-Golgi network membrane / respiratory chain complex IV / Endosomal/Vacuolar pathway ...Complex IV assembly / TP53 Regulates Metabolic Genes / Cytoprotection by HMOX1 / Respiratory electron transport / natural killer cell lectin-like receptor binding / TAP2 binding / TAP1 binding / cis-Golgi network membrane / respiratory chain complex IV / Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / DAP12 signaling / cellular response to iron(III) ion / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / MHC class Ib protein complex / response to molecule of bacterial origin / regulation of erythrocyte differentiation / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / inner ear development / TAP complex binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / Golgi medial cisterna / multicellular organismal-level iron ion homeostasis / regulation of membrane depolarization / CD8 receptor binding / TAP binding / endoplasmic reticulum exit site / T cell differentiation in thymus / respiratory chain complex I / MHC class I protein binding / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / beta-2-microglobulin binding / cellular defense response / T cell receptor binding / Neutrophil degranulation / 14-3-3 protein binding / positive regulation of T cell mediated cytotoxicity / respiratory electron transport chain / negative regulation of neuron projection development / lumenal side of endoplasmic reticulum membrane / regulation of iron ion transport / negative regulation of iron ion transport / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / peptide antigen assembly with MHC class I protein complex / iron ion transport / HFE-transferrin receptor complex / MHC class I peptide loading complex / transferrin transport / negative regulation of receptor-mediated endocytosis / cellular response to iron ion / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / peptide antigen assembly with MHC class II protein complex / protein refolding / MHC class I protein complex / negative regulation of epithelial cell proliferation / cellular response to nicotine / negative regulation of neurogenesis / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / positive regulation of immune response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / phagocytic vesicle membrane / positive regulation of T cell activation / sensory perception of smell / positive regulation of cellular senescence / MHC class II protein complex binding / late endosome membrane / cellular response to lipopolysaccharide / protein-folding chaperone binding / antimicrobial humoral immune response mediated by antimicrobial peptide / early endosome membrane / antibacterial humoral response / defense response to Gram-negative bacterium / amyloid fibril formation / protein homotetramerization / early endosome / intracellular iron ion homeostasis / learning or memory / defense response to bacterium / defense response to Gram-positive bacterium / mitochondrial inner membrane / immune response / receptor ligand activity / external side of plasma membrane / signaling receptor binding / Golgi membrane / innate immune response / lysosomal membrane / protein-containing complex binding / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum
Similarity search - Function
NADH-ubiquinone reductase complex 1 MLRQ subunit / NADH-ubiquinone reductase complex 1 MLRQ subunit / 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 / : ...NADH-ubiquinone reductase complex 1 MLRQ subunit / NADH-ubiquinone reductase complex 1 MLRQ subunit / 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
PHOSPHATE ION / Beta-2-microglobulin / H-2 class I histocompatibility antigen, K-B alpha chain / Cytochrome c oxidase subunit FA4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLuz, J.G. / Huang, M. / Garcia, K.C. / Rudolph, M.G. / Apostolopoulos, V. / Teyton, L. / Wilson, I.A.
CitationJournal: J.Exp.Med. / Year: 2002
Title: Structural comparison of allogeneic and syngeneic T cell receptor-peptide-major histocompatibility complex complexes: a buried alloreactive mutation subtly alters peptide presentation ...Title: Structural comparison of allogeneic and syngeneic T cell receptor-peptide-major histocompatibility complex complexes: a buried alloreactive mutation subtly alters peptide presentation substantially increasing V(beta) Interactions.
Authors: Luz, J.G. / Huang, M. / Garcia, K.C. / Rudolph, M.G. / Apostolopoulos, V. / Teyton, L. / Wilson, I.A.
History
DepositionApr 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 13, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE THE CONFLICTS BETWEEN THE SEQUENCE AND THE SEQUENCE DATABASE REFERENCE ARE POLYMORPHISMS ...SEQUENCE THE CONFLICTS BETWEEN THE SEQUENCE AND THE SEQUENCE DATABASE REFERENCE ARE POLYMORPHISMS IN THE BM3 ALLOGENEIC VARIANT OF H2KB.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN
B: Beta-2-microglobulin
P: dEV8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2336
Polymers44,3473
Non-polymers8873
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-21 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.894, 87.123, 45.231
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN / MHC CLASS I H-2KB HEAVY CHAIN


Mass: 31578.209 Da / Num. of mol.: 1
Fragment: EXTRACELLULAR DOMAIN, SEQUENCE DATABASE RESIDUES 22-295, NUMBERED 1-274
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET22B(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01901
#2: Protein Beta-2-microglobulin


Mass: 11704.359 Da / Num. of mol.: 1 / Fragment: SEQUENCE DATABASE RESIDUES 21-119, NUMBERED 1-99
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET22B(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01887

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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide dEV8


Mass: 1064.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide is chemically synthesized. / References: UniProt: Q62425*PLUS

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Sugars , 2 types, 2 molecules

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


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: 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 , 2 types, 207 molecules

#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 3.02 Å3/Da / Density % sol: 59.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.8
Details: sodium potassium phosphate, pH 6.8, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Dec 13, 1997
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.15→10 Å / Num. all: 29655 / Num. obs: 29655 / % possible obs: 98.6 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 4
Reflection shellResolution: 2.15→2.23 Å / % possible all: 99.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.258 1738 RANDOM
Rwork0.206 --
all-27550 -
obs-27550 -
Refinement stepCycle: LAST / Resolution: 2.15→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3124 0 57 206 3387
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d1.72
X-RAY DIFFRACTIONc_bond_d0.012

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