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- PDB-3rwf: Rhesus macaque MHC class I molecule Mamu-B*17-QW9 -

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Basic information

Entry
Database: PDB / ID: 3rwf
TitleRhesus macaque MHC class I molecule Mamu-B*17-QW9
Components
  • Beta-2-microglobulin
  • Major histocompatibility complex class I
  • Nef QW9 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 / 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 ...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 / 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 / phagocytic vesicle membrane / recycling endosome membrane / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / immune response / lysosomal membrane / external side of plasma 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: 2.6 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major histocompatibility complex class I
B: Beta-2-microglobulin
C: Nef QW9 peptide from Protein Nef


Theoretical massNumber of molelcules
Total (without water)44,9793
Polymers44,9793
Non-polymers00
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4600 Å2
ΔGint-11 kcal/mol
Surface area19350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.689, 95.689, 129.029
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Major histocompatibility complex class I


Mass: 32025.082 Da / Num. of mol.: 1 / 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: 11791.275 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 (E. coli) / References: UniProt: Q6V7J5
#3: Protein/peptide Nef QW9 peptide from Protein Nef


Mass: 1162.164 Da / Num. of mol.: 1 / 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.: 135 / 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: 2.53 Å3/Da / Density % sol: 51.34 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 13578 / Biso Wilson estimate: 38.78 Å2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.6.2_432) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BVO

2bvo


Resolution: 2.6→24.639 Å / Occupancy max: 1 / Occupancy min: 0.49 / FOM work R set: 0.799 / SU ML: 0.42 / σ(F): 1.99 / Phase error: 27.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2462 671 4.96 %
Rwork0.1891 --
obs0.1921 13540 99.93 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.132 Å2 / ksol: 0.335 e/Å3
Displacement parametersBiso max: 132.48 Å2 / Biso mean: 43.295 Å2 / Biso min: 6.44 Å2
Baniso -1Baniso -2Baniso -3
1--3.7952 Å20 Å20 Å2
2---3.7952 Å20 Å2
3---7.5903 Å2
Refinement stepCycle: LAST / Resolution: 2.6→24.639 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3174 0 0 135 3309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053391
X-RAY DIFFRACTIONf_angle_d0.5834446
X-RAY DIFFRACTIONf_chiral_restr0.043434
X-RAY DIFFRACTIONf_plane_restr0.003594
X-RAY DIFFRACTIONf_dihedral_angle_d11.5171220
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.6003-2.80090.38371410.294925732714
2.8009-3.08220.33511460.233725632709
3.0822-3.52710.24611150.202926022717
3.5271-4.43960.21821330.161525672700
4.4396-24.63990.1971360.156125642700
Refinement TLS params.Method: refined / Origin x: -26.3939 Å / Origin y: -7.4902 Å / Origin z: -0.1929 Å
111213212223313233
T0.0555 Å2-0.0079 Å2-0.0179 Å2-0.045 Å2-0.0254 Å2--0.0247 Å2
L0.6153 °20.3161 °2-0.2841 °2-0.9435 °2-0.0763 °2--0.2197 °2
S0.0382 Å °0.0363 Å °-0.0272 Å °0.0329 Å °-0.0344 Å °0.0583 Å °-0.0237 Å °0.007 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 276
2X-RAY DIFFRACTION1ALLA277 - 361
3X-RAY DIFFRACTION1ALLC1 - 9
4X-RAY DIFFRACTION1ALLC38 - 134
5X-RAY DIFFRACTION1ALLB0 - 99
6X-RAY DIFFRACTION1ALLB100 - 144

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