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- PDB-3rwd: rhesus macaque MHC class I molecule Mamu-B*17-IW11 -

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Basic information

Entry
Database: PDB / ID: 3rwd
Titlerhesus macaque MHC class I molecule Mamu-B*17-IW11
Components
  • Beta-2-microglobulin
  • Major histocompatibility complex class I
  • Nef IW11 peptide from Protein Nef
KeywordsIMMUNE SYSTEM / antigenic peptides / T lymphocytes / immune response
Function / homology
Function and homology information


antigen processing and presentation of peptide antigen via MHC class I / receptor-mediated endocytosis of virus by host cell / 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 ...antigen processing and presentation of peptide antigen via MHC class I / receptor-mediated endocytosis of virus by host cell / 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 / phagocytic vesicle membrane / recycling endosome 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 / iron ion transport / negative regulation of neuron projection development / 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 / GTP binding / host cell plasma membrane / structural molecule activity / cell surface / Golgi apparatus / protein homodimerization activity / extracellular region / cytosol
Similarity search - Function
HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / 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 ...HIV negative factor Nef / HIV-1 Nef protein, core domain superfamily / Negative factor, (F-Protein) or Nef / 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
Protein Nef / Beta-2-microglobulin / Major histocompatibility complex class I
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Simian immunodeficiency virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.602 Å
AuthorsWu, Y. / Gao, F. / Liu, J. / Qi, J.X. / Price, D.A. / Gao, G.F.
CitationJournal: J.Immunol. / Year: 2011
Title: Structural basis of diverse peptide accommodation by the rhesus macaque MHC class I molecule Mamu-B*17: insights into immune protection from simian immunodeficiency virus
Authors: Wu, Y. / Gao, F. / Liu, J. / Qi, J.X. / Gostick, E. / Price, D.A. / Gao, G.F.
History
DepositionMay 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 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: Major histocompatibility complex class I
B: Beta-2-microglobulin
C: Nef IW11 peptide from Protein Nef
D: Major histocompatibility complex class I
E: Beta-2-microglobulin
F: Nef IW11 peptide from Protein Nef


Theoretical massNumber of molelcules
Total (without water)90,3086
Polymers90,3086
Non-polymers00
Water9,116506
1
A: Major histocompatibility complex class I
B: Beta-2-microglobulin
C: Nef IW11 peptide from Protein Nef


Theoretical massNumber of molelcules
Total (without water)45,1543
Polymers45,1543
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-19 kcal/mol
Surface area18880 Å2
MethodPISA
2
D: Major histocompatibility complex class I
E: Beta-2-microglobulin
F: Nef IW11 peptide from Protein Nef


Theoretical massNumber of molelcules
Total (without water)45,1543
Polymers45,1543
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-16 kcal/mol
Surface area18910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.219, 69.025, 81.001
Angle α, β, γ (deg.)96.45, 88.79, 89.94
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Major histocompatibility complex class I


Mass: 32025.082 Da / Num. of mol.: 2 / Fragment: residues 24-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: MHCI-B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GJ77
#2: Protein Beta-2-microglobulin


Mass: 11660.079 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: Q6V7J5
#3: Protein/peptide Nef IW11 peptide from Protein Nef


Mass: 1468.742 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthtic peptide / Source: (synth.) Simian immunodeficiency virus / References: UniProt: Q5QGG3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 506 / Source method: isolated from a natural source / Formula: H2O
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: 2.78 Å3/Da / Density % sol: 55.77 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorDate: Jun 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 28767 / Biso Wilson estimate: 26.49 Å2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6.4_486) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BVO

2bvo


Resolution: 2.602→27.276 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.782 / SU ML: 0.38 / σ(F): 1.98 / Phase error: 29.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2772 1450 5.04 %
Rwork0.2279 --
obs0.2304 28745 96.28 %
all-28767 -
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 17.317 Å2 / ksol: 0.321 e/Å3
Displacement parametersBiso max: 81.77 Å2 / Biso mean: 29.153 Å2 / Biso min: 7.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.0927 Å20.4429 Å2-0.1191 Å2
2---0.3253 Å2-0.237 Å2
3---0.418 Å2
Refinement stepCycle: LAST / Resolution: 2.602→27.276 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6378 0 0 506 6884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046814
X-RAY DIFFRACTIONf_angle_d0.4538920
X-RAY DIFFRACTIONf_chiral_restr0.033872
X-RAY DIFFRACTIONf_plane_restr0.0011186
X-RAY DIFFRACTIONf_dihedral_angle_d11.8362438
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6021-2.6950.35551420.30482533267589
2.695-2.80280.37181500.28812704285496
2.8028-2.93020.33371420.27532717285996
2.9302-3.08450.30771470.26332704285196
3.0845-3.27750.32511570.25312748290596
3.2775-3.530.28131460.23762759290597
3.53-3.88440.27541340.21832764289898
3.8844-4.44440.23931520.18462765291798
4.4444-5.59150.22771400.17992808294898
5.5915-27.27790.21391400.21362793293399

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