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- PDB-5d2n: Crystal structure of C25-NLV-HLA-A2 complex -

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Basic information

Entry
Database: PDB / ID: 5d2n
TitleCrystal structure of C25-NLV-HLA-A2 complex
Components
  • ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL
  • Beta-2-microglobulin
  • C25 alpha
  • C25 beta
  • HLA class I histocompatibility antigen, A-2 alpha chain
KeywordsIMMUNE SYSTEM / TCR / NLV / HLA-A2
Function / homology
Function and homology information


viral tegument / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I ...viral tegument / positive regulation of memory T cell activation / T cell mediated cytotoxicity directed against tumor cell target / TAP complex binding / Golgi medial cisterna / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / positive regulation of CD8-positive, alpha-beta T cell proliferation / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / beta-2-microglobulin binding / endoplasmic reticulum exit site / TAP binding / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / protection from natural killer cell mediated cytotoxicity / 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 / detection of bacterium / T cell receptor binding / negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / lumenal side of endoplasmic reticulum membrane / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / 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 / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / 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 / specific granule lumen / positive regulation of type II interferon production / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Interferon alpha/beta signaling / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / antibacterial humoral response / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / T cell receptor signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / structural constituent of virion / intracellular iron ion homeostasis / host cell cytoplasm / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / cell surface / endoplasmic reticulum / Golgi apparatus
Similarity search - Function
Herpesvirus UL82/UL83 / Betaherpesvirus UL82/83 protein N terminus / dUTPase-like superfamily / 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 ...Herpesvirus UL82/UL83 / Betaherpesvirus UL82/83 protein N terminus / dUTPase-like superfamily / 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
IMIDAZOLE / HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / 65 kDa phosphoprotein / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
Cytomegalovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.099 Å
AuthorsMariuzza, R.A. / Yang, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI036900 United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Structural Basis for Clonal Diversity of the Public T Cell Response to a Dominant Human Cytomegalovirus Epitope.
Authors: Yang, X. / Gao, M. / Chen, G. / Pierce, B.G. / Lu, J. / Weng, N.P. / Mariuzza, R.A.
History
DepositionAug 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2May 8, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.3Nov 13, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: C25 alpha
F: C25 beta
H: HLA class I histocompatibility antigen, A-2 alpha chain
L: Beta-2-microglobulin
D: C25 alpha
E: C25 beta
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
G: ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL
I: ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,86313
Polymers190,65610
Non-polymers2073
Water13,799766
1
C: C25 alpha
F: C25 beta
H: HLA class I histocompatibility antigen, A-2 alpha chain
L: Beta-2-microglobulin
G: ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3976
Polymers95,3285
Non-polymers691
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10700 Å2
ΔGint-50 kcal/mol
Surface area38140 Å2
MethodPISA
2
D: C25 alpha
E: C25 beta
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
I: ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,4667
Polymers95,3285
Non-polymers1382
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10560 Å2
ΔGint-49 kcal/mol
Surface area38140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.307, 124.874, 193.843
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 6 molecules FEHALB

#2: Protein C25 beta


Mass: 27790.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#3: Protein HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31985.398 Da / Num. of mol.: 2 / Fragment: UNP residues 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01892, UniProt: P04439*PLUS
#4: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 2 / Fragment: UNP residues 21-119
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(DE3) / References: UniProt: P61769

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Antibody / Protein/peptide , 2 types, 4 molecules CDGI

#1: Antibody C25 alpha


Mass: 22729.090 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#5: Protein/peptide ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL


Mass: 943.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Cytomegalovirus / References: UniProt: P18139*PLUS

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Non-polymers , 2 types, 769 molecules

#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 766 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: PEG3000, Imidazole, Calcium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300HS / Detector: CCD / Date: Feb 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionRedundancy: 7 % / Number: 837368 / Rmerge(I) obs: 0.106 / Χ2: 1 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 119186 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
5.75010.0380.8887.2
4.525.710.0581.4227.4
3.954.5210.0772.2087.2
3.593.9510.0841.8447.3
3.333.5910.0851.3067.3
3.143.3310.0961.0147.2
2.983.1410.1180.9237.2
2.852.9810.1510.8727.2
2.742.8510.1940.8277.1
2.652.7410.2360.8147
2.562.6510.2960.7877
2.492.5610.350.7777
2.422.4910.420.7726.9
2.372.4210.4990.7556.9
2.312.3710.5660.7596.9
2.262.3110.6370.7516.9
2.222.2610.7160.7396.8
2.182.2210.8280.7426.8
2.142.1810.9610.7336.7
2.12.1410.7256.4
ReflectionResolution: 2.099→50 Å / Num. obs: 119186 / % possible obs: 99.3 % / Redundancy: 7 % / Biso Wilson estimate: 37.02 Å2 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.044 / Rrim(I) all: 0.111 / Χ2: 0.997 / Net I/av σ(I): 19.156 / Net I/σ(I): 5.7 / Num. measured all: 837368
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
2.1-2.146.458100.5670.4660.72598.6
2.14-2.186.758610.6740.3930.73398.90.961
2.18-2.226.858720.7260.3380.74298.70.8280.895
2.22-2.266.858280.7960.2910.73998.50.7160.774
2.26-2.316.958690.8240.2590.75198.50.6370.689
2.31-2.376.958440.8610.2290.75998.60.5660.612
2.37-2.426.958990.8920.2020.75598.70.4990.539
2.42-2.496.958490.920.1690.77298.60.420.453
2.49-2.56759100.940.1410.777990.350.377
2.56-2.65759240.9550.1190.78799.30.2960.319
2.65-2.74759390.9730.0950.81499.50.2360.254
2.74-2.857.159610.980.0780.82799.70.1940.209
2.85-2.987.259590.9880.060.87299.80.1510.162
2.98-3.147.260090.9920.0470.9231000.1180.127
3.14-3.337.259650.9950.0381.0141000.0960.104
3.33-3.597.360410.9950.0341.3061000.0850.091
3.59-3.957.360420.9950.0331.8441000.0840.091
3.95-4.527.260730.9960.0312.2081000.0770.083
4.52-5.77.461540.9970.0231.4221000.0580.063
5.7-507.263770.9990.0150.88899.80.0380.041

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MI5,3GSO

1mi5

3gso


Resolution: 2.099→40.697 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2527 2000 1.68 %
Rwork0.2038 117088 -
obs0.2046 119088 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.2 Å2 / Biso mean: 41.3493 Å2 / Biso min: 21.33 Å2
Refinement stepCycle: final / Resolution: 2.099→40.697 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13271 0 15 766 14052
Biso mean--49.94 42.96 -
Num. residues----1651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01413646
X-RAY DIFFRACTIONf_angle_d1.26418510
X-RAY DIFFRACTIONf_chiral_restr0.0611947
X-RAY DIFFRACTIONf_plane_restr0.0052440
X-RAY DIFFRACTIONf_dihedral_angle_d15.3894982
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0986-2.1510.28161380.2658036817496
2.151-2.20920.30981400.25778234837499
2.2092-2.27420.28791410.25088240838198
2.2742-2.34760.30241400.24598224836499
2.3476-2.43150.27491410.24128264840599
2.4315-2.52880.32351410.24418236837799
2.5288-2.64390.30691420.24198338848099
2.6439-2.78330.30361420.239883308472100
2.7833-2.95760.25481440.232684118555100
2.9576-3.18590.29951430.224784068549100
3.1859-3.50630.25651450.20984748619100
3.5063-4.01330.23661450.185884848629100
4.0133-5.05490.19611470.155985618708100
5.0549-40.70460.21791510.173888509001100

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