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- PDB-3rwe: rhesus macaque MHC class I molecule Mamu-B*17-FW9 -

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Basic information

Entry
Database: PDB / ID: 3rwe
Titlerhesus macaque MHC class I molecule Mamu-B*17-FW9
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • Major histocompatibility complex class IMHC class I
  • Pol FW9 peptide from Pol protein
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 / RNA stem-loop binding / 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 / exoribonuclease H activity / MHC class I protein complex / DNA integration / peptide antigen assembly with MHC class II protein complex ...antigen processing and presentation of peptide antigen via MHC class I / RNA stem-loop binding / 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 / exoribonuclease H activity / MHC class I protein complex / DNA integration / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / positive regulation of T cell mediated cytotoxicity / viral genome integration into host DNA / recycling endosome membrane / establishment of integrated proviral latency / phagocytic vesicle membrane / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / RNA-directed DNA polymerase activity / positive regulation of immune response / RNA-DNA hybrid ribonuclease activity / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / early endosome membrane / DNA recombination / aspartic-type endopeptidase activity / symbiont entry into host cell / immune response / lysosomal membrane / external side of plasma membrane / signaling receptor binding / proteolysis / DNA binding / extracellular space / zinc ion binding / extracellular region
Similarity search - Function
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 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin / MHC class I-like antigen recognition-like ...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 / Reverse transcriptase connection / Reverse transcriptase connection domain / Beta-2-Microglobulin / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / RNase H / MHC classes I/II-like antigen recognition protein / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / DNA/RNA polymerase superfamily / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Pol protein / 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: 2.4 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: Pol FW9 peptide from Pol protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1575
Polymers44,9453
Non-polymers2122
Water4,828268
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-19 kcal/mol
Surface area19070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.808, 45.290, 81.982
Angle α, β, γ (deg.)90.00, 96.11, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein Major histocompatibility complex class I / MHC 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 / Beta-2 microglobulin


Mass: 11660.079 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 Pol FW9 peptide from Pol protein


Mass: 1259.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthtic peptide / Source: (synth.) Simian immunodeficiency virus / References: UniProt: Q5QGH9
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.83 Å3/Da / Density % sol: 56.48 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 20992 / Biso Wilson estimate: 37.66 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: 2.4→28.55 Å / Occupancy max: 1 / Occupancy min: 0.46 / FOM work R set: 0.7987 / SU ML: 0.4 / σ(F): 1.34 / Phase error: 26.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2512 1013 5.13 %
Rwork0.203 --
obs0.2056 19743 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.488 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso max: 121.3 Å2 / Biso mean: 39.0923 Å2 / Biso min: 11.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.0363 Å2-0 Å20.1035 Å2
2---0.4545 Å20 Å2
3---0.4182 Å2
Refinement stepCycle: LAST / Resolution: 2.4→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3173 0 14 268 3455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043418
X-RAY DIFFRACTIONf_angle_d0.4894460
X-RAY DIFFRACTIONf_chiral_restr0.035433
X-RAY DIFFRACTIONf_plane_restr0.002592
X-RAY DIFFRACTIONf_dihedral_angle_d11.5871228
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.52650.41430.32092612275597
2.5265-2.68470.35821390.2722616275598
2.6847-2.89180.30651430.22972660280399
2.8918-3.18240.2791490.22652651280099
3.1824-3.64210.28211330.21152695282899
3.6421-4.58560.20941560.166627022858100
4.5856-28.55220.18061500.167527942944100
Refinement TLS params.Method: refined / Origin x: 26.0119 Å / Origin y: -0.4012 Å / Origin z: 20.11 Å
111213212223313233
T0.1525 Å2-0.0015 Å2-0.0013 Å2-0.144 Å20.0152 Å2--0.122 Å2
L1.0924 °2-0.0294 °20.1211 °2-0.1963 °2-0.2096 °2--0.2919 °2
S-0.0036 Å °0.2323 Å °0.0601 Å °0.0155 Å °-0.0119 Å °0.0045 Å °0.0119 Å °0.0603 Å °0.0147 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 276
2X-RAY DIFFRACTION1ALLA278 - 430
3X-RAY DIFFRACTION1ALLA277
4X-RAY DIFFRACTION1ALLC1 - 9
5X-RAY DIFFRACTION1ALLC26 - 431
6X-RAY DIFFRACTION1ALLB1 - 99
7X-RAY DIFFRACTION1ALLB102 - 262
8X-RAY DIFFRACTION1ALLB100

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