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- PDB-3rwj: Rhesus macaque MHC class I molecule Mamu-B*17-HW8 -

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Basic information

Entry
Database: PDB / ID: 3rwj
TitleRhesus macaque MHC class I molecule Mamu-B*17-HW8
Components
  • Beta-2-microglobulin
  • Major histocompatibility complex class I
  • Vif HW8 peptide from Virion infectivity factor
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 / viral life cycle / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion ...antigen processing and presentation of peptide antigen via MHC class I / viral life cycle / : / : / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / negative regulation of receptor binding / DAP12 interactions / cellular response to iron ion / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / 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 / 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 / virion component / cellular response to nicotine / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of cellular senescence / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / Interferon gamma signaling / MHC class II protein complex binding / positive regulation of protein binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / iron ion transport / T cell differentiation in thymus / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / host cell cytoplasm / learning or memory / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / Golgi membrane / external side of plasma membrane / lysosomal membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Retroviral Vif (Viral infectivity) protein / Retroviral Vif (Viral infectivity) 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 / : ...Retroviral Vif (Viral infectivity) protein / Retroviral Vif (Viral infectivity) 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 / Virion infectivity factor / Major histocompatibility complex class I
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
Homo sapiens (human)
Simian immunodeficiency virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 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

Downloads & links

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Assembly

Deposited unit
A: Major histocompatibility complex class I
B: Beta-2-microglobulin
C: Vif HW8 peptide from Virion infectivity factor


Theoretical massNumber of molelcules
Total (without water)44,9373
Polymers44,9373
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4510 Å2
ΔGint-18 kcal/mol
Surface area19330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.960, 44.600, 80.630
Angle α, β, γ (deg.)90.00, 96.94, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-317-

HOH

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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: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#3: Protein/peptide Vif HW8 peptide from Virion infectivity factor


Mass: 1032.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthtic peptide / Source: (synth.) Simian immunodeficiency virus / References: UniProt: Q89490
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.7 Å3/Da / Density % sol: 54.43 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.26→54.96 Å / Num. obs: 13484 / Biso Wilson estimate: 36.65 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: 2.7→22.487 Å / Occupancy max: 1 / Occupancy min: 0.44 / FOM work R set: 0.81 / SU ML: 0.37 / σ(F): 1.37 / Phase error: 25.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2561 696 5.18 %
Rwork0.2101 --
obs0.2126 13430 99.64 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.302 Å2 / ksol: 0.399 e/Å3
Displacement parametersBiso max: 123.97 Å2 / Biso mean: 38.3046 Å2 / Biso min: 2.28 Å2
Baniso -1Baniso -2Baniso -3
1-1.0039 Å2-0 Å2-0.0841 Å2
2---1.4401 Å20 Å2
3---0.4363 Å2
Refinement stepCycle: LAST / Resolution: 2.7→22.487 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3172 0 0 124 3296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043405
X-RAY DIFFRACTIONf_angle_d0.4434454
X-RAY DIFFRACTIONf_chiral_restr0.032438
X-RAY DIFFRACTIONf_plane_restr0.002594
X-RAY DIFFRACTIONf_dihedral_angle_d11.3421222
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7001-2.90820.38121360.312425152651100
2.9082-3.20010.31231330.257925442677100
3.2001-3.66140.281320.203725382670100
3.6614-4.60650.21261520.167425332685100
4.6065-22.48810.21581430.19722604274799
Refinement TLS params.Method: refined / Origin x: -24.8737 Å / Origin y: -0.3847 Å / Origin z: -19.2352 Å
111213212223313233
T0.0259 Å2-0.0254 Å20.0092 Å2-0.0524 Å2-0.0248 Å2--0.0167 Å2
L0.3077 °20.3196 °20.1807 °2-0.3705 °20.2655 °2--0.424 °2
S0.0147 Å °-0.132 Å °0.0119 Å °-0.0183 Å °-0.1364 Å °0.0337 Å °-0.0371 Å °-0.1089 Å °0.0912 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 276
2X-RAY DIFFRACTION1ALLA277 - 358
3X-RAY DIFFRACTION1ALLC1 - 8
4X-RAY DIFFRACTION1ALLC37 - 81
5X-RAY DIFFRACTION1ALLB0 - 99
6X-RAY DIFFRACTION1ALLB100 - 140

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