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- PDB-3rwc: Crystal structure of rhesus macaque MHC class I molecule Mamu-B*17-IW9 -

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Basic information

Entry
Database: PDB / ID: 3rwc
TitleCrystal structure of rhesus macaque MHC class I molecule Mamu-B*17-IW9
Components
  • Beta-2-microglobulin
  • Major histocompatibility complex class I
  • Nef IW9 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 / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / ER to Golgi transport vesicle membrane / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane ...antigen processing and presentation of peptide antigen via MHC class I / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / lumenal side of endoplasmic reticulum membrane / ER to Golgi transport vesicle membrane / MHC class I protein complex / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / early endosome membrane / receptor-mediated endocytosis of virus by host cell / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / virus-mediated perturbation of host defense response / GTP binding / extracellular space / extracellular region
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 / Immunoglobulins / Immunoglobulin-like fold / 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: 2.502 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

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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 IW9 peptide from Protein Nef
D: Major histocompatibility complex class I
E: Beta-2-microglobulin
F: Nef IW9 peptide from Protein Nef


Theoretical massNumber of molelcules
Total (without water)89,7096
Polymers89,7096
Non-polymers00
Water7,620423
1
A: Major histocompatibility complex class I
B: Beta-2-microglobulin
C: Nef IW9 peptide from Protein Nef


Theoretical massNumber of molelcules
Total (without water)44,8553
Polymers44,8553
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-16 kcal/mol
Surface area18930 Å2
MethodPISA
2
D: Major histocompatibility complex class I
E: Beta-2-microglobulin
F: Nef IW9 peptide from Protein Nef


Theoretical massNumber of molelcules
Total (without water)44,8553
Polymers44,8553
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-16 kcal/mol
Surface area18940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.233, 68.558, 81.754
Angle α, β, γ (deg.)83.79, 89.13, 89.98
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 IW9 peptide from Protein Nef


Mass: 1169.374 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.: 423 / 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: 2.81 Å3/Da / Density % sol: 56.21 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorDetector: IMAGE PLATE / Date: Jun 6, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 32603 / Biso Wilson estimate: 28.72 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: 2.502→27.012 Å / Occupancy max: 1 / Occupancy min: 0.32 / FOM work R set: 0.809 / SU ML: 0.41 / σ(F): 1.97 / Phase error: 26.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2494 1642 5.04 %
Rwork0.1965 --
obs0.1993 32603 96.84 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.044 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso max: 126.51 Å2 / Biso mean: 30.8969 Å2 / Biso min: 3.47 Å2
Baniso -1Baniso -2Baniso -3
1-1.1125 Å20.8656 Å2-1.7733 Å2
2---3.0812 Å2-0.3085 Å2
3---1.9686 Å2
Refinement stepCycle: LAST / Resolution: 2.502→27.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6334 0 0 423 6757
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056792
X-RAY DIFFRACTIONf_angle_d0.5588885
X-RAY DIFFRACTIONf_chiral_restr0.04869
X-RAY DIFFRACTIONf_plane_restr0.0021185
X-RAY DIFFRACTIONf_dihedral_angle_d11.4032443
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 (%)
2.5022-2.59160.40891790.2972950312994
2.5916-2.69530.34591530.26093080323396
2.6953-2.81780.32011580.24383122328096
2.8178-2.96620.29811530.22853049320296
2.9662-3.15180.3151430.22433137328097
3.1518-3.39470.29631640.22393086325097
3.3947-3.73550.25681840.20013115329998
3.7355-4.27430.20681590.15853130328998
4.2743-5.37810.16621760.13453135331199
5.3781-27.01350.18221730.17383157333099
Refinement TLS params.Method: refined / Origin x: -0.9029 Å / Origin y: -8.7053 Å / Origin z: -19.3753 Å
111213212223313233
T0.0755 Å20.0034 Å2-0.005 Å2-0.0239 Å20.0122 Å2--0.0429 Å2
L0.0719 °20.0274 °2-0.013 °2--0.1454 °20.2062 °2--0.1147 °2
S-0.0223 Å °-0.006 Å °0.0048 Å °-0.0002 Å °0.0096 Å °0.0452 Å °-0.0214 Å °-0.0229 Å °0.0276 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 276
2X-RAY DIFFRACTION1ALLA277 - 415
3X-RAY DIFFRACTION1ALLC1 - 9
4X-RAY DIFFRACTION1ALLC42 - 421
5X-RAY DIFFRACTION1ALLB1 - 99
6X-RAY DIFFRACTION1ALLB100 - 412
7X-RAY DIFFRACTION1ALLE1 - 99
8X-RAY DIFFRACTION1ALLE100 - 417
9X-RAY DIFFRACTION1ALLD1 - 276
10X-RAY DIFFRACTION1ALLD277 - 423
11X-RAY DIFFRACTION1ALLF1 - 9
12X-RAY DIFFRACTION1ALLF93 - 422

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