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- PDB-5wes: Crystal Structure H2-Dd with disulfide-linked 5mer peptide -

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Basic information

Entry
Database: PDB / ID: 5wes
TitleCrystal Structure H2-Dd with disulfide-linked 5mer peptide
Components
  • Beta-2-microglobulin
  • H-2 class I histocompatibility antigen, D-D alpha chain
  • Surface protein gp120
KeywordsIMMUNE SYSTEM / Antigen presentation / peptide editing / MAJOR HISTOMPATIBILITY COMPLEX CLASS I / MHC-I / TAPBPR / H2-Dd / H-2DD / TAPASIN / Peptide Loading Complex / PLC / 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 erythrocyte differentiation / regulation of iron ion transport / HFE-transferrin receptor complex / MHC class I peptide loading complex / response to molecule of bacterial origin / 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 / membrane / plasma membrane / cytosol
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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 ...Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / 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
GLYCINE / LEUCINE / 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 type 1 group M subtype B
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.706 Å
AuthorsJiang, J.S. / Natarajan, K. / Boyd, L.F. / Margulies, D.H.
CitationJournal: Science / Year: 2017
Title: Crystal structure of a TAPBPR-MHC I complex reveals the mechanism of peptide editing in antigen presentation.
Authors: Jiang, J. / Natarajan, K. / Boyd, L.F. / Morozov, G.I. / Mage, M.G. / Margulies, D.H.
History
DepositionJul 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class I histocompatibility antigen, D-D alpha chain
B: Beta-2-microglobulin
P: Surface protein gp120
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5075
Polymers44,3013
Non-polymers2062
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-15 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.507, 63.029, 91.978
Angle α, β, γ (deg.)90.00, 105.41, 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: 32150.770 Da / Num. of mol.: 1 / Fragment: residues 26-301 / Mutation: S73C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-D1 / Plasmid: PET21-B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01900
#2: Protein Beta-2-microglobulin


Mass: 11660.350 Da / Num. of mol.: 1 / Fragment: residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: B2m / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01887
#3: Protein/peptide Surface protein gp120 / Envelope glycoprotein gp160 / Env polyprotein


Mass: 489.570 Da / Num. of mol.: 1 / Fragment: V3 domain residues 316-320 / Mutation: R5C / Source method: obtained synthetically
Source: (synth.) Human immunodeficiency virus type 1 group M subtype B
References: UniProt: P03377
#4: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
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: 3.02 Å3/Da / Density % sol: 59.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 10-15% PEG 20000, 0.1M MES

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.033 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.69→88.72 Å / Num. obs: 14293 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 29.7 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.201 / Rpim(I) all: 0.085 / Net I/σ(I): 12.8
Reflection shellResolution: 2.69→2.79 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 1067 / CC1/2: 0.923 / Rpim(I) all: 0.22 / % possible all: 71.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.706→37.05 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 26.71
RfactorNum. reflection% reflectionSelection details
Rfree0.2457 714 5 %RANDOM
Rwork0.1949 ---
obs0.1976 14279 98.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31 Å2
Refinement stepCycle: LAST / Resolution: 2.706→37.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3095 0 13 0 3108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043200
X-RAY DIFFRACTIONf_angle_d0.7044345
X-RAY DIFFRACTIONf_dihedral_angle_d15.511906
X-RAY DIFFRACTIONf_chiral_restr0.045438
X-RAY DIFFRACTIONf_plane_restr0.005570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7058-2.91460.32761340.26292543X-RAY DIFFRACTION94
2.9146-3.20780.30981430.24062726X-RAY DIFFRACTION100
3.2078-3.67160.28571450.20182754X-RAY DIFFRACTION100
3.6716-4.62440.2081450.16332755X-RAY DIFFRACTION100
4.6244-37.05370.18881470.1722787X-RAY DIFFRACTION99

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