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- PDB-5d2l: Crystal structure of TCR C7 in complex with HCMV NLV epitope pres... -

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Basic information

Entry
Database: PDB / ID: 5d2l
TitleCrystal structure of TCR C7 in complex with HCMV NLV epitope presented by HLA-A2
Components
  • ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL
  • Beta-2-microglobulin
  • C7 TCR alpha chain
  • C7 TCR beta chain
  • HLA class I histocompatibility antigen, A-2 alpha chain
KeywordsIMMUNE SYSTEM / TCR / HCMV / HLA-A2 / Complex
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 / antibacterial humoral response / positive regulation of cellular senescence / 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
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: 3.511 Å
AuthorsGao, M. / Mariuzza, R.A.
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 1.1Aug 23, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.type / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 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 1.5Sep 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 1.6Nov 6, 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
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
I: C7 TCR alpha chain
J: C7 TCR beta chain
Q: ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL
G: HLA class I histocompatibility antigen, A-2 alpha chain
H: Beta-2-microglobulin
K: C7 TCR alpha chain
L: C7 TCR beta chain
U: ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL
M: HLA class I histocompatibility antigen, A-2 alpha chain
N: Beta-2-microglobulin
O: C7 TCR alpha chain
P: C7 TCR beta chain
T: ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL
C: HLA class I histocompatibility antigen, A-2 alpha chain
D: Beta-2-microglobulin
E: C7 TCR alpha chain
F: C7 TCR beta chain
R: ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL


Theoretical massNumber of molelcules
Total (without water)381,15920
Polymers381,15920
Non-polymers00
Water97354
1
A: HLA class I histocompatibility antigen, A-2 alpha chain
B: Beta-2-microglobulin
I: C7 TCR alpha chain
J: C7 TCR beta chain
Q: ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL


Theoretical massNumber of molelcules
Total (without water)95,2905
Polymers95,2905
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: HLA class I histocompatibility antigen, A-2 alpha chain
H: Beta-2-microglobulin
K: C7 TCR alpha chain
L: C7 TCR beta chain
U: ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL


Theoretical massNumber of molelcules
Total (without water)95,2905
Polymers95,2905
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
M: HLA class I histocompatibility antigen, A-2 alpha chain
N: Beta-2-microglobulin
O: C7 TCR alpha chain
P: C7 TCR beta chain
T: ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL


Theoretical massNumber of molelcules
Total (without water)95,2905
Polymers95,2905
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: HLA class I histocompatibility antigen, A-2 alpha chain
D: Beta-2-microglobulin
E: C7 TCR alpha chain
F: C7 TCR beta chain
R: ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL


Theoretical massNumber of molelcules
Total (without water)95,2905
Polymers95,2905
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.760, 366.643, 151.948
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11G-305-

HOH

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Components

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Protein , 4 types, 16 molecules AGMCBHNDIKOEJLPF

#1: Protein
HLA class I histocompatibility antigen, A-2 alpha chain / MHC class I antigen A*2


Mass: 31985.398 Da / Num. of mol.: 4 / Fragment: UNP residues 25-299
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HLA-A, HLAA / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P01892, UniProt: P04439*PLUS
#2: Protein
Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 4 / Fragment: UNP residues 21-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P61769
#3: Protein
C7 TCR alpha chain


Mass: 22930.268 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)
#4: Protein
C7 TCR beta chain


Mass: 27551.531 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)

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Protein/peptide / Non-polymers , 2 types, 58 molecules QUTR

#5: Protein/peptide
ASN-LEU-VAL-PRO-MET-VAL-ALA-THR-VAL


Mass: 943.161 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Cytomegalovirus / References: UniProt: P18139*PLUS
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 30% PEG 400, 0.1M Tris-HCl pH 8.5, 0.2M MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / 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
ReflectionResolution: 3.5→50 Å / Num. obs: 53000 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 86.74 Å2 / Rmerge(I) obs: 0.203 / Rpim(I) all: 0.079 / Rrim(I) all: 0.208 / Χ2: 1.067 / Net I/av σ(I): 10.917 / Net I/σ(I): 4.2 / Num. measured all: 399727
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
3.5-3.567.60.93726180.8760.3640.807100
3.56-3.637.60.85525910.9020.3320.8161000.917
3.63-3.697.60.80126160.8820.3110.8371000.86
3.69-3.777.60.64126530.920.2490.8351000.688
3.77-3.857.60.58925920.9370.2280.8821000.632
3.85-3.947.60.49726240.9510.1920.8721000.533
3.94-4.047.60.40926360.9660.1590.8981000.439
4.04-4.157.60.35826370.9790.1390.9271000.384
4.15-4.277.60.29926210.9790.1160.9841000.321
4.27-4.417.60.25126260.9850.0981.0381000.27
4.41-4.577.60.22226370.9850.0861.0651000.238
4.57-4.757.60.19226400.9890.0751.1051000.207
4.75-4.977.60.18126460.990.071.1831000.195
4.97-5.237.60.18526480.9890.0721.1951000.199
5.23-5.557.60.18526620.9890.0721.251000.199
5.55-5.987.50.18226480.9870.0711.2531000.195
5.98-6.587.50.15526870.9910.0611.1781000.167
6.58-7.537.50.10726850.9970.0421.1711000.115
7.53-9.487.40.06727130.9980.0261.3891000.072
9.48-5070.04928200.9990.021.6699.60.053

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PHASERphasing
Cootmodel building
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GSN, 4OZF

3gsn

4ozf


Resolution: 3.511→49.512 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3546 2699 5.1 %Random selection
Rwork0.2697 50201 --
obs0.2739 52900 99.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 194.07 Å2 / Biso mean: 80.2544 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 3.511→49.512 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25218 0 0 54 25272
Biso mean---78 -
Num. residues----3198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00925892
X-RAY DIFFRACTIONf_angle_d1.58535141
X-RAY DIFFRACTIONf_chiral_restr0.0713727
X-RAY DIFFRACTIONf_plane_restr0.0094595
X-RAY DIFFRACTIONf_dihedral_angle_d18.1549187
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.511-3.57490.37381340.30242369250390
3.5749-3.64360.38971350.31725872722100
3.6436-3.7180.38811510.306826202771100
3.718-3.79880.37331220.305826772799100
3.7988-3.88710.34311460.305926022748100
3.8871-3.98430.38311450.292626402785100
3.9843-4.09190.361610.287726042765100
4.0919-4.21230.37961380.282826552793100
4.2123-4.34820.35921410.262926162757100
4.3482-4.50350.31451530.257126242777100
4.5035-4.68370.31661490.243326292778100
4.6837-4.89670.33721340.241326982832100
4.8967-5.15460.28591420.243326222764100
5.1546-5.47710.3521320.272126752807100
5.4771-5.89940.39411230.268726872810100
5.8994-6.49190.40021420.298126852827100
6.4919-7.42860.36641430.284427012844100
7.4286-9.34890.34511680.259226912859100
9.3489-49.51660.36261400.242819295999

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