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- PDB-5vgd: Crystal Structure of HLA-C*0501 in complex with SAE -

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Basic information

Entry
Database: PDB / ID: 5vgd
TitleCrystal Structure of HLA-C*0501 in complex with SAE
Components
  • Beta-2-microglobulinBeta-2 microglobulin
  • HLA class I histocompatibility antigen, Cw-5 alpha chain
  • SER-ALA-GLU-PRO-VAL-PRO-LEU-GLN-LEU
KeywordsIMMUNE SYSTEM / HLA / HLA-C
Function / homology
Function and homology information


TAP 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 / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions ...TAP 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 / secretory granule membrane / positive regulation of ferrous iron binding / positive regulation of transferrin receptor binding / positive regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / negative regulation of receptor binding / lumenal side of endoplasmic reticulum membrane / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / cellular response to iron(III) ion / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / negative regulation of forebrain neuron differentiation / ER to Golgi transport vesicle membrane / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / response to molecule of bacterial origin / regulation of iron ion transport / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / cellular response to iron ion / antigen processing and presentation of endogenous peptide antigen via MHC class I / positive regulation of T cell cytokine production / MHC class I protein complex / multicellular organismal-level iron ion homeostasis / negative regulation of neurogenesis / peptide antigen assembly with MHC class II protein complex / positive regulation of receptor-mediated endocytosis / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / recycling endosome membrane / specific granule lumen / phagocytic vesicle membrane / peptide antigen binding / positive regulation of cellular senescence / antigen processing and presentation of exogenous peptide antigen via MHC class II / negative regulation of epithelial cell proliferation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / positive regulation of immune response / Modulation by Mtb of host immune system / Interferon alpha/beta signaling / sensory perception of smell / positive regulation of T cell activation / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / negative regulation of neuron projection development / MHC class II protein complex binding / late endosome membrane / T cell differentiation in thymus / ER-Phagosome pathway / iron ion transport / early endosome membrane / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / adaptive immune response / amyloid fibril formation / learning or memory / immune response / Amyloid fiber formation / lysosomal membrane / external side of plasma membrane / endoplasmic reticulum lumen / Golgi membrane / signaling receptor binding / focal adhesion / innate immune response / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane / cytosol
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 / 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 ...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
HLA class I histocompatibility antigen, C alpha chain / Beta-2-microglobulin / HLA class I histocompatibility antigen, C alpha chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.32 Å
AuthorsGras, S. / Rossjohn, J.
CitationJournal: Nat Commun / Year: 2017
Title: Structural and regulatory diversity shape HLA-C protein expression levels.
Authors: Kaur, G. / Gras, S. / Mobbs, J.I. / Vivian, J.P. / Cortes, A. / Barber, T. / Kuttikkatte, S.B. / Jensen, L.T. / Attfield, K.E. / Dendrou, C.A. / Carrington, M. / McVean, G. / Purcell, A.W. / ...Authors: Kaur, G. / Gras, S. / Mobbs, J.I. / Vivian, J.P. / Cortes, A. / Barber, T. / Kuttikkatte, S.B. / Jensen, L.T. / Attfield, K.E. / Dendrou, C.A. / Carrington, M. / McVean, G. / Purcell, A.W. / Rossjohn, J. / Fugger, L.
History
DepositionApr 11, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, Cw-5 alpha chain
B: Beta-2-microglobulin
C: SER-ALA-GLU-PRO-VAL-PRO-LEU-GLN-LEU


Theoretical massNumber of molelcules
Total (without water)44,9373
Polymers44,9373
Non-polymers00
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-15 kcal/mol
Surface area18680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.062, 80.538, 118.563
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 HLA class I histocompatibility antigen, Cw-5 alpha chain / MHC class I antigen Cw*5


Mass: 32104.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-C, HLAC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q9TNN7, UniProt: P10321*PLUS
#2: Protein Beta-2-microglobulin / Beta-2 microglobulin


Mass: 11879.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: P61769
#3: Protein/peptide SER-ALA-GLU-PRO-VAL-PRO-LEU-GLN-LEU


Mass: 953.089 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion / Details: 1.8M NaMalonate pH7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.32→47.74 Å / Num. obs: 19238 / % possible obs: 99.4 % / Redundancy: 6.9 % / Biso Wilson estimate: 42.58 Å2 / Rpim(I) all: 0.057 / Net I/σ(I): 11.5
Reflection shellResolution: 2.3→2.39 Å / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1744 / Rpim(I) all: 0.387

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.32→47.74 Å / Cor.coef. Fo:Fc: 0.8524 / Cor.coef. Fo:Fc free: 0.7608 / SU R Cruickshank DPI: 0.394 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.427 / SU Rfree Blow DPI: 0.292 / SU Rfree Cruickshank DPI: 0.29
RfactorNum. reflection% reflectionSelection details
Rfree0.2972 972 5.18 %RANDOM
Rwork0.2201 ---
obs0.2243 18775 99.07 %-
Displacement parametersBiso mean: 27.11 Å2
Baniso -1Baniso -2Baniso -3
1-7.192 Å20 Å20 Å2
2--6.9131 Å20 Å2
3----14.1051 Å2
Refine analyzeLuzzati coordinate error obs: 0.327 Å
Refinement stepCycle: 1 / Resolution: 2.3→47.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3151 0 0 150 3301
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013241HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.34400HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1124SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes92HARMONIC2
X-RAY DIFFRACTIONt_gen_planes471HARMONIC5
X-RAY DIFFRACTIONt_it3241HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.38
X-RAY DIFFRACTIONt_other_torsion21.97
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion393SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3594SEMIHARMONIC4
LS refinement shellResolution: 2.32→2.46 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.4076 145 5.02 %
Rwork0.2571 2743 -
all0.2643 2888 -
obs--99.07 %

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