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- PDB-4nqx: Crystal Structure of HLA A*0101 in complex with NP44-S7N, an 9-me... -

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Basic information

Entry
Database: PDB / ID: 4nqx
TitleCrystal Structure of HLA A*0101 in complex with NP44-S7N, an 9-mer influenza epitope
Components
  • Beta-2-microglobulin
  • HLA class I histocompatibility antigen, A-1 alpha chain
  • NP44-S7N mutant peptide, CTELKLNDY
KeywordsImmune System/Viral Protein / immune system / presenting viral epitope / T cell receptor / Immune System-Viral Protein complex
Function / homology
Function and homology information


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 / helical viral capsid / CD8 receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I ...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 / helical viral capsid / 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 / viral penetration into host nucleus / 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 / host cell / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / viral nucleocapsid / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / defense response to Gram-positive bacterium / immune response / endoplasmic reticulum lumen / ribonucleoprotein complex / Amyloid fiber formation / signaling receptor binding / Golgi membrane / lysosomal membrane / innate immune response / external side of plasma membrane / focal adhesion / Neutrophil degranulation / symbiont entry into host cell / endoplasmic reticulum membrane / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity
Similarity search - Function
Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / 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 / : ...Influenza virus nucleoprotein (NP) / Influenza virus nucleoprotein / 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
HLA class I histocompatibility antigen, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin / Nucleoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
H7N9 subtype (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRossjohn, J. / Gras, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Preexisting CD8+ T-cell immunity to the H7N9 influenza A virus varies across ethnicities.
Authors: Quinones-Parra, S. / Grant, E. / Loh, L. / Nguyen, T.H. / Campbell, K.A. / Tong, S.Y. / Miller, A. / Doherty, P.C. / Vijaykrishna, D. / Rossjohn, J. / Gras, S. / Kedzierska, K.
History
DepositionNov 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Sep 20, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HLA class I histocompatibility antigen, A-1 alpha chain
B: Beta-2-microglobulin
C: HLA class I histocompatibility antigen, A-1 alpha chain
D: Beta-2-microglobulin
E: HLA class I histocompatibility antigen, A-1 alpha chain
F: Beta-2-microglobulin
G: HLA class I histocompatibility antigen, A-1 alpha chain
H: Beta-2-microglobulin
I: HLA class I histocompatibility antigen, A-1 alpha chain
J: Beta-2-microglobulin
K: HLA class I histocompatibility antigen, A-1 alpha chain
L: Beta-2-microglobulin
M: NP44-S7N mutant peptide, CTELKLNDY
N: NP44-S7N mutant peptide, CTELKLNDY
O: NP44-S7N mutant peptide, CTELKLNDY
P: NP44-S7N mutant peptide, CTELKLNDY
Q: NP44-S7N mutant peptide, CTELKLNDY
R: NP44-S7N mutant peptide, CTELKLNDY


Theoretical massNumber of molelcules
Total (without water)274,09018
Polymers274,09018
Non-polymers00
Water14,394799
1
A: HLA class I histocompatibility antigen, A-1 alpha chain
B: Beta-2-microglobulin
M: NP44-S7N mutant peptide, CTELKLNDY


Theoretical massNumber of molelcules
Total (without water)45,6823
Polymers45,6823
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-16 kcal/mol
Surface area19340 Å2
MethodPISA
2
C: HLA class I histocompatibility antigen, A-1 alpha chain
D: Beta-2-microglobulin
N: NP44-S7N mutant peptide, CTELKLNDY


Theoretical massNumber of molelcules
Total (without water)45,6823
Polymers45,6823
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-17 kcal/mol
Surface area19210 Å2
MethodPISA
3
E: HLA class I histocompatibility antigen, A-1 alpha chain
F: Beta-2-microglobulin
O: NP44-S7N mutant peptide, CTELKLNDY


Theoretical massNumber of molelcules
Total (without water)45,6823
Polymers45,6823
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-12 kcal/mol
Surface area18900 Å2
MethodPISA
4
G: HLA class I histocompatibility antigen, A-1 alpha chain
H: Beta-2-microglobulin
P: NP44-S7N mutant peptide, CTELKLNDY


Theoretical massNumber of molelcules
Total (without water)45,6823
Polymers45,6823
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-17 kcal/mol
Surface area19450 Å2
MethodPISA
5
I: HLA class I histocompatibility antigen, A-1 alpha chain
J: Beta-2-microglobulin
Q: NP44-S7N mutant peptide, CTELKLNDY


Theoretical massNumber of molelcules
Total (without water)45,6823
Polymers45,6823
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-16 kcal/mol
Surface area19600 Å2
MethodPISA
6
K: HLA class I histocompatibility antigen, A-1 alpha chain
L: Beta-2-microglobulin
R: NP44-S7N mutant peptide, CTELKLNDY


Theoretical massNumber of molelcules
Total (without water)45,6823
Polymers45,6823
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-15 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)264.610, 81.411, 140.290
Angle α, β, γ (deg.)90.000, 121.820, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
HLA class I histocompatibility antigen, A-1 alpha chain / MHC class I antigen A*1


Mass: 32703.156 Da / Num. of mol.: 6 / Fragment: UNP residues 25-308
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Production host: Escherichia coli (E. coli) / References: UniProt: P30443, UniProt: P04439*PLUS
#2: Protein
Beta-2-microglobulin / Beta-2-microglobulin form pI 5.3


Mass: 11879.356 Da / Num. of mol.: 6 / 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) / References: UniProt: P61769
#3: Protein/peptide
NP44-S7N mutant peptide, CTELKLNDY


Mass: 1099.235 Da / Num. of mol.: 6 / Fragment: NP44, 9-mer influenza epitope / Mutation: S7N mutation against the epitope in related 4NQV / Source method: obtained synthetically / Source: (synth.) H7N9 subtype (virus) / References: UniProt: Q07FI1*PLUS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 799 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE 9-MER PEPTIDE NP44 IS INFLUENZA EPITOPE, WITH S7N MUTATION AGAINST THE EPITOPE IN RELATED 4NQV. ...THE 9-MER PEPTIDE NP44 IS INFLUENZA EPITOPE, WITH S7N MUTATION AGAINST THE EPITOPE IN RELATED 4NQV. BUT THE EPITOPE IS SHARED BY MANY STRAINS, THUS IT IS NOT APPROPRIATE TO ASSIGN A UNP REFERENCE OF SPECIFIC STRAIN.

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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: 47.49 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 5.6
Details: 0.2M MgCl, 0.1M Na-citrate pH 5.6, 15-20% PEG 6K, EVAPORATION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→119.207 Å / Num. all: 165625 / Num. obs: 165625 / % possible obs: 97.1 % / Redundancy: 6.8 % / Biso Wilson estimate: 38.65 Å2 / Rsym value: 0.082 / Net I/σ(I): 14

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
PHASERphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NQV

4nqv


Resolution: 2→45.75 Å / Cor.coef. Fo:Fc: 0.9017 / Cor.coef. Fo:Fc free: 0.8928 / Occupancy max: 1 / Occupancy min: 0.24 / SU R Cruickshank DPI: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2827 8305 5.01 %RANDOM
Rwork0.2701 ---
all0.27 ---
obs0.2707 165609 96.75 %-
Displacement parametersBiso max: 150.53 Å2 / Biso mean: 46.8141 Å2 / Biso min: 14.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.1034 Å20 Å2-0.5259 Å2
2---0.4845 Å20 Å2
3---0.3811 Å2
Refine analyzeLuzzati coordinate error obs: 0.439 Å
Refinement stepCycle: LAST / Resolution: 2→45.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18859 0 0 799 19658
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d8958SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes557HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2834HARMONIC5
X-RAY DIFFRACTIONt_it19484HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2404SEMIHARMONIC5
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_contact21593SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d19484HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg26418HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion2.57
X-RAY DIFFRACTIONt_other_torsion3.33
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2372 446 4.8 %
Rwork0.2111 8839 -
all0.2123 9285 -
obs--96.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3795-0.1115-0.25562.38591.00052.7636-0.04420.0157-0.10710.17670.0798-0.02470.0857-0.0494-0.0356-0.2031-0.0204-0.0149-0.24650.0164-0.2428-63.4357-17.08857.7254
21.30010.11370.27691.44520.45432.7383-0.0102-0.01480.07950.14110.0271-0.2225-0.20480.2622-0.0168-0.0909-0.049-0.0522-0.1715-0.033-0.1203-50.2461-4.666814.105
30.72570.6834-0.022.82620.25020.9567-0.0101-0.11050.02570.165-0.0150.1439-0.1629-0.09460.0251-0.04380.06390.0024-0.21020.0324-0.3241-66.2034-22.410157.5677
41.92711.39090.39952.3230.70692.2624-0.1030.22780.0904-0.11540.13130.14110.0518-0.2207-0.0283-0.0604-0.0071-0.0046-0.12710.0401-0.2288-72.1402-28.355840.4308
50.6154-0.5616-0.12182.7707-0.36010.72620.0432-0.01150.0759-0.0673-0.0271-0.2716-0.04570.0262-0.0161-0.1831-0.00780.0431-0.2485-0.0345-0.1336-104.8327-22.0683-1.2755
61.9933-0.21550.56932.1827-0.68753.55570.0883-0.3767-0.0770.3963-0.0402-0.3292-0.03110.2108-0.048-0.1393-0.0153-0.0434-0.1911-0.0243-0.1285-97.8767-27.396215.756
72.1982-0.5893-1.62570.70210.52972.1970.09590.1412-0.0147-0.0376-0.0364-0.1885-0.2418-0.0714-0.0595-0.1182-0.0670.053-0.3196-0.0345-0.1634-135.5794-33.064629.0758
83.17750.3601-0.36650.9517-0.40731.61620.00780.1434-0.1148-0.1510.0632-0.00530.0775-0.2433-0.071-0.0351-0.00560.0254-0.1587-0.0099-0.1591-153.2721-40.180131.1059
90.83881.002-1.03625.0984-2.84693.2882-0.19150.1177-0.1031-0.4590.21210.05290.3143-0.2123-0.0206-0.26310.0266-0.0211-0.199-0.0409-0.3032-104.6879-17.363751.7322
101.5523-0.53970.14811.2998-0.78861.97550.02540.24230.1729-0.40250.09840.5747-0.106-0.1778-0.1238-0.12570.0095-0.1829-0.16680.0638-0.0804-117.7831-4.99244.5425
112.18730.4779-1.60450.8458-0.62081.533-0.24910.1395-0.2242-0.17410.0608-0.01680.1235-0.13470.1883-0.1397-0.05550.0522-0.2833-0.0276-0.1489-96.90577.6293-30.4591
123.3733-1.1445-0.23570-0.96861.6554-0.07940.1316-0.2686-0.26150.13520.12840.2843-0.3145-0.0558-0.0271-0.09-0.0088-0.1719-0.0378-0.1021-114.61750.8292-30.622
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 274
2X-RAY DIFFRACTION2{ B|* }B0 - 99
3X-RAY DIFFRACTION3{ C|* }C1 - 275
4X-RAY DIFFRACTION4{ D|* }D0 - 99
5X-RAY DIFFRACTION5{ E|* }E1 - 275
6X-RAY DIFFRACTION6{ F|* }F1 - 99
7X-RAY DIFFRACTION7{ G|* }G1 - 274
8X-RAY DIFFRACTION8{ H|* }H0 - 99
9X-RAY DIFFRACTION9{ I|* }I1 - 274
10X-RAY DIFFRACTION10{ J|* }J0 - 99
11X-RAY DIFFRACTION11{ K|* }K1 - 275
12X-RAY DIFFRACTION12{ L|* }L0 - 99

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