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- PDB-5kd4: Crystal Structure of Murine MHC-I H-2Dd in complex with Murine Be... -

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Basic information

Entry
Database: PDB / ID: 5kd4
TitleCrystal Structure of Murine MHC-I H-2Dd in complex with Murine Beta2-Microglobulin and a Variant of Peptide (PVI10) of HIV gp120 MN Isolate (IGPGRAFYVI)
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-D alpha chain
  • Peptide of HIV gp120 MN isolate, PVI10 (IGPGRAFYVI)
KeywordsIMMUNE SYSTEM / MAJOR HISTOMPATIBILITY COMPLEX CLASS I / MHC-I / H2-Dd / H-2Dd / HIV peptide / PVI10 / GLYCOPROTEIN / IMMUNE RESPONSE
Function / homology
Function and homology information


Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Dectin-2 family / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / positive regulation of plasma membrane raft polarization ...Endosomal/Vacuolar pathway / DAP12 interactions / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / DAP12 signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Dectin-2 family / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / cellular defense response / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / Neutrophil degranulation / host cell endosome membrane / lumenal side of endoplasmic reticulum membrane / cellular response to iron(III) ion / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / iron ion transport / 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 / MHC class I protein complex / 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 / negative regulation of epithelial cell proliferation / sensory perception of smell / positive regulation of cellular senescence / T cell differentiation in thymus / negative regulation of neuron projection development / protein refolding / protein homotetramerization / clathrin-dependent endocytosis of virus by host cell / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / viral protein processing / fusion of virus membrane with host plasma membrane / external side of plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / Golgi apparatus / protein homodimerization activity / extracellular space / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 ...Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / MHC class I, alpha chain, C-terminal / MHC_I C-terminus / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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 / H-2 class I histocompatibility antigen, D-D alpha chain / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesMus musculus (house mouse)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsJiang, J. / Natarajan, K. / Margulies, D.
CitationJournal: J. Immunol. / Year: 2018
Title: Effects of Cross-Presentation, Antigen Processing, and Peptide Binding in HIV Evasion of T Cell Immunity.
Authors: Frey, B.F. / Jiang, J. / Sui, Y. / Boyd, L.F. / Yu, B. / Tatsuno, G. / Billeskov, R. / Solaymani-Mohammadi, S. / Berman, P.W. / Margulies, D.H. / Berzofsky, J.A.
History
DepositionJun 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 28, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 27, 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
Revision 1.4Nov 20, 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: H-2 class I histocompatibility antigen, D-D alpha chain
B: Beta-2-microglobulin
P: Peptide of HIV gp120 MN isolate, PVI10 (IGPGRAFYVI)
C: H-2 class I histocompatibility antigen, D-D alpha chain
D: Beta-2-microglobulin
Q: Peptide of HIV gp120 MN isolate, PVI10 (IGPGRAFYVI)


Theoretical massNumber of molelcules
Total (without water)90,3016
Polymers90,3016
Non-polymers00
Water00
1
A: H-2 class I histocompatibility antigen, D-D alpha chain
B: Beta-2-microglobulin
P: Peptide of HIV gp120 MN isolate, PVI10 (IGPGRAFYVI)


Theoretical massNumber of molelcules
Total (without water)45,1513
Polymers45,1513
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-23 kcal/mol
Surface area19230 Å2
MethodPISA
2
C: H-2 class I histocompatibility antigen, D-D alpha chain
D: Beta-2-microglobulin
Q: Peptide of HIV gp120 MN isolate, PVI10 (IGPGRAFYVI)


Theoretical massNumber of molelcules
Total (without water)45,1513
Polymers45,1513
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-22 kcal/mol
Surface area18990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.130, 90.300, 120.070
Angle α, β, γ (deg.)90.00, 113.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein H-2 class I histocompatibility antigen, D-D alpha chain / H-2D(D)


Mass: 32265.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01900
#2: Protein Beta-2-microglobulin


Mass: 11791.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: PET2D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887
#3: Protein/peptide Peptide of HIV gp120 MN isolate, PVI10 (IGPGRAFYVI)


Mass: 1093.299 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Mutations / Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: ENV / Production host: synthetic construct (others) / References: UniProt: P05877*PLUS
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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 15% PEG 20000, 0.1M Sodium Cacodylate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0333 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 25, 2015
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0333 Å / Relative weight: 1
ReflectionResolution: 3.05→47.1 Å / Num. obs: 17628 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 59.9 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.189 / Net I/σ(I): 13
Reflection shellResolution: 3.05→3.16 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.6 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ECB

3ecb


Resolution: 3.05→47.088 Å / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.22
RfactorNum. reflection% reflection
Rfree0.2237 886 5.03 %
Rwork0.1836 --
obs0.1858 17628 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 51 Å2
Refinement stepCycle: LAST / Resolution: 3.05→47.088 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6278 0 0 0 6278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076466
X-RAY DIFFRACTIONf_angle_d1.1678770
X-RAY DIFFRACTIONf_dihedral_angle_d15.6522394
X-RAY DIFFRACTIONf_chiral_restr0.047888
X-RAY DIFFRACTIONf_plane_restr0.0051148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0501-3.24120.28821450.2472751X-RAY DIFFRACTION94
3.2412-3.49130.26571460.20692773X-RAY DIFFRACTION94
3.4913-3.84250.2521460.19242768X-RAY DIFFRACTION94
3.8425-4.3980.24851470.17562786X-RAY DIFFRACTION94
4.398-5.53930.17321470.15292800X-RAY DIFFRACTION95
5.5393-43.36940.18881510.18282861X-RAY DIFFRACTION94

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