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- PDB-6iwg: Crystal structure of rhesus macaque MHC class I molecule Mamu-B*0... -

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Basic information

Entry
Database: PDB / ID: 6iwg
TitleCrystal structure of rhesus macaque MHC class I molecule Mamu-B*05104 complexed with N-myristoylated 4-mer lipopeptide derived from SIV nef protein
Components
  • Beta-2-microglobulin
  • MHC class I antigen
  • N-myristoylated 4-mer lipopeptide
KeywordsIMMUNE SYSTEM / Antigen presentation / Major histocompatibility complex / N-myristoylation / AIDS / nef
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation ...antigen processing and presentation of peptide antigen via MHC class I / lumenal side of endoplasmic reticulum membrane / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / MHC class II protein complex / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of erythrocyte differentiation / regulation of iron ion transport / MHC class I peptide loading complex / response to molecule of bacterial origin / HFE-transferrin receptor complex / T cell mediated cytotoxicity / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / antigen processing and presentation of exogenous peptide antigen via MHC class II / MHC class I protein complex / positive regulation of immune response / peptide antigen binding / negative regulation of neurogenesis / positive regulation of T cell mediated cytotoxicity / positive regulation of receptor-mediated endocytosis / multicellular organismal-level iron ion homeostasis / positive regulation of T cell activation / cellular response to nicotine / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / late endosome membrane / sensory perception of smell / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / external side of plasma membrane / lysosomal membrane / structural molecule activity / cell surface / Golgi apparatus / protein homodimerization activity / extracellular region / cytosol
Similarity search - Function
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 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
BORIC ACID / B protein / Beta-2-microglobulin
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Simian immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYamamoto, Y. / Morita, D. / Sugita, M.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16K19151 Japan
Japan Society for the Promotion of Science15J04072 Japan
Japan Agency for Medical Research and Development (AMED)16K15517 Japan
Japan Society for the Promotion of Science17H05791 Japan
CitationJournal: J Immunol. / Year: 2019
Title: Identification and Structure of an MHC Class I-Encoded Protein with the Potential to PresentN-Myristoylated 4-mer Peptides to T Cells.
Authors: Yamamoto, Y. / Morita, D. / Shima, Y. / Midorikawa, A. / Mizutani, T. / Suzuki, J. / Mori, N. / Shiina, T. / Inoko, H. / Tanaka, Y. / Mikami, B. / Sugita, M.
History
DepositionDec 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MHC class I antigen
B: Beta-2-microglobulin
C: N-myristoylated 4-mer lipopeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,57228
Polymers44,1773
Non-polymers1,39525
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-41 kcal/mol
Surface area19450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.823, 81.756, 106.635
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein MHC class I antigen / Major histocompatibility complex class I / MHC-class I protein


Mass: 31919.098 Da / Num. of mol.: 1 / Mutation: R128E,K177E,D223E,K264E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: Mamu-B*05104 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: B2ZHY7
#2: Protein Beta-2-microglobulin


Mass: 11731.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: B2M / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q6V7J5

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide N-myristoylated 4-mer lipopeptide


Mass: 526.710 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Simian immunodeficiency virus

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Non-polymers , 4 types, 329 molecules

#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-BO3 / BORIC ACID


Mass: 61.833 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: BH3O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O

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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: 2.66 Å3/Da / Density % sol: 53.68 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 100mM MIB, 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 44246 / % possible obs: 99.9 % / Redundancy: 7.1 % / Net I/σ(I): 43.9
Reflection shellResolution: 1.8→1.84 Å

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Processing

Software
NameClassification
HKL-2000data scaling
HKL-2000data collection
HKL-2000data reduction
PHENIXrefinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZFZ

4zfz


Resolution: 1.8→44.7 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.215 2256 -
Rwork0.179 --
obs-44052 99.9 %
Refinement stepCycle: LAST / Resolution: 1.8→44.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3120 0 88 304 3512

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