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- PDB-3jtt: Cystal structure of Rhesus macaque MHC class I:Mamu-A*02 -

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Basic information

Entry
Database: PDB / ID: 3jtt
TitleCystal structure of Rhesus macaque MHC class I:Mamu-A*02
Components
  • Beta-2-microglobulin
  • MHC class I Mamu-A*02
  • peptide of Protein Nef
KeywordsIMMUNE SYSTEM / ALPHA HELIX / BETA SHEET / BETA BARREL / Immune response / MHC I / Membrane / Transmembrane / Disease mutation / Disulfide bond / Glycation / Glycoprotein / Immunoglobulin domain / Pyrrolidone carboxylic acid / Secreted
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 / 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 ...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 / 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
MHC class I Mamu-A*02 / Beta-2-microglobulin / Protein Nef
Similarity search - Component
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsDai, L. / Feng, Y. / Qi, J. / Gao, G.F.
CitationJournal: To be Published
Title: Crystal structure of Rhesus macaque MHC class I:Mamu-A*02
Authors: Dai, L.
History
DepositionSep 14, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 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 1.3Nov 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: MHC class I Mamu-A*02
B: Beta-2-microglobulin
C: peptide of Protein Nef
D: MHC class I Mamu-A*02
E: Beta-2-microglobulin
F: peptide of Protein Nef
G: MHC class I Mamu-A*02
H: Beta-2-microglobulin
I: peptide of Protein Nef


Theoretical massNumber of molelcules
Total (without water)134,7359
Polymers134,7359
Non-polymers00
Water4,864270
1
A: MHC class I Mamu-A*02
B: Beta-2-microglobulin
C: peptide of Protein Nef


Theoretical massNumber of molelcules
Total (without water)44,9123
Polymers44,9123
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-17 kcal/mol
Surface area19570 Å2
MethodPISA
2
D: MHC class I Mamu-A*02
E: Beta-2-microglobulin
F: peptide of Protein Nef


Theoretical massNumber of molelcules
Total (without water)44,9123
Polymers44,9123
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-19 kcal/mol
Surface area19600 Å2
MethodPISA
3
G: MHC class I Mamu-A*02
H: Beta-2-microglobulin
I: peptide of Protein Nef


Theoretical massNumber of molelcules
Total (without water)44,9123
Polymers44,9123
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-19 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.993, 129.007, 129.026
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MHC class I Mamu-A*02 / YY9-Mamu-A*02-rb2m


Mass: 32106.320 Da / Num. of mol.: 3 / Fragment: UNP residues 17-292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: Mamu / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q30597
#2: Protein Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11791.275 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: B2M / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6V7J5
#3: Protein/peptide peptide of Protein Nef


Mass: 1014.114 Da / Num. of mol.: 3 / Fragment: UNP residues 159-167 / Source method: obtained synthetically
Details: This sequence occurs from Simian immunodeficiency virus
References: UniProt: Q9WH73
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 3.98 Å3/Da / Density % sol: 69.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M Bis-Tris pH 5.5, 2 M ammonium sulfate , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5478 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 20, 2008 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5478 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 51015 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 37.2
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 7 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 4.7 / Num. unique all: 4987 / Rsym value: 0.528 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1zvs

1zvs


Resolution: 2.8→31.293 Å / SU ML: 0.4 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0.09 / Stereochemistry target values: ML / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.2554 2579 5.06 %random
Rwork0.2138 ---
obs0.2158 51015 95.21 %-
all-53070 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.463 Å2 / ksol: 0.356 e/Å3
Displacement parametersBiso mean: 57.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.047 Å20 Å20 Å2
2---1.4671 Å2-0 Å2
3---1.5141 Å2
Refinement stepCycle: LAST / Resolution: 2.8→31.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9486 0 0 270 9756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029759
X-RAY DIFFRACTIONf_angle_d0.6613230
X-RAY DIFFRACTIONf_dihedral_angle_d16.8723564
X-RAY DIFFRACTIONf_chiral_restr0.0481314
X-RAY DIFFRACTIONf_plane_restr0.0031758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8003-2.85410.37881330.27242413X-RAY DIFFRACTION88
2.8541-2.91230.33151300.27922494X-RAY DIFFRACTION90
2.9123-2.97560.32881410.27292506X-RAY DIFFRACTION89
2.9756-3.04470.32811500.25952492X-RAY DIFFRACTION91
3.0447-3.12080.28291400.23772533X-RAY DIFFRACTION91
3.1208-3.20510.31141250.23152711X-RAY DIFFRACTION95
3.2051-3.29930.31451340.23342676X-RAY DIFFRACTION95
3.2993-3.40570.27231420.22052665X-RAY DIFFRACTION96
3.4057-3.52730.25161540.21072714X-RAY DIFFRACTION96
3.5273-3.66830.26441460.20232730X-RAY DIFFRACTION97
3.6683-3.8350.2391530.19732714X-RAY DIFFRACTION98
3.835-4.03670.25461270.19362823X-RAY DIFFRACTION98
4.0367-4.28910.24241440.18422781X-RAY DIFFRACTION98
4.2891-4.61930.20271360.17572757X-RAY DIFFRACTION98
4.6193-5.08230.21741580.172785X-RAY DIFFRACTION98
5.0823-5.81370.20871430.18622847X-RAY DIFFRACTION99
5.8137-7.30920.24881570.2182890X-RAY DIFFRACTION99
7.3092-31.29490.22041660.23922905X-RAY DIFFRACTION97

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