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- PDB-6am5: Crystal structure of DMF5 TCR bound to HLA-A2 presenting syntheti... -

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Basic information

Entry
Database: PDB / ID: 6am5
TitleCrystal structure of DMF5 TCR bound to HLA-A2 presenting synthetic peptide SMLGIGIVPV
Components
  • Beta-2-microglobulin
  • DMF5 TCR alpha chain
  • DMF5 TCR beta chain
  • HLA class I histocompatibility antigen, A-2 alpha chain
  • SER-MET-LEU-GLY-ILE-GLY-ILE-VAL-PRO-VAL
KeywordsIMMUNE SYSTEM / TCR / MHC
Function / homology
Function and homology information


T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / 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 / endoplasmic reticulum exit site ...T cell mediated cytotoxicity directed against tumor cell target / positive regulation of memory T cell activation / TAP complex binding / positive regulation of CD8-positive, alpha-beta T cell activation / CD8-positive, alpha-beta T cell activation / Golgi medial cisterna / 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 / endoplasmic reticulum exit site / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent / TAP binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / detection of bacterium / 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 / negative regulation of receptor binding / DAP12 interactions / 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 / 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 / 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 / regulation of erythrocyte differentiation / peptide antigen assembly with MHC class I protein complex / ER to Golgi transport vesicle membrane / regulation of iron ion transport / response to molecule of bacterial origin / MHC class I peptide loading complex / HFE-transferrin receptor complex / T cell mediated cytotoxicity / 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 / positive regulation of receptor-mediated endocytosis / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / specific granule lumen / recycling endosome membrane / phagocytic vesicle membrane / positive regulation of type II interferon production / peptide antigen binding / positive regulation of cellular senescence / negative regulation of epithelial cell proliferation / antigen processing and presentation of exogenous peptide antigen via MHC class II / 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 / positive regulation of T cell activation / Interferon alpha/beta signaling / sensory perception of smell / negative regulation of neuron projection development / positive regulation of protein binding / tertiary granule lumen / DAP12 signaling / E3 ubiquitin ligases ubiquitinate target proteins / MHC class II protein complex binding / late endosome membrane / T cell receptor signaling pathway / iron ion transport / antibacterial humoral response / ER-Phagosome pathway / early endosome membrane / T cell differentiation in thymus / protein refolding / protein homotetramerization / intracellular iron ion homeostasis / amyloid fibril formation / learning or memory / defense response to Gram-positive bacterium / immune response / Amyloid fiber formation / endoplasmic reticulum lumen / external side of plasma membrane / Golgi membrane / lysosomal membrane / innate immune response / signaling receptor binding / focal adhesion / Neutrophil degranulation / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / Golgi apparatus / cell surface / endoplasmic reticulum
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 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, A alpha chain / HLA class I histocompatibility antigen, A alpha chain / Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.394 Å
AuthorsRiley, T.P. / Baker, B.M.
CitationJournal: To Be Published
Title: Crystal structure of DMF5 TCR bound to HLA-A2 presenting synthetic peptide SMLGIGIVPV
Authors: Riley, T.P. / Baker, B.M.
History
DepositionAug 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2018Provider: repository / Type: Initial release

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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
C: SER-MET-LEU-GLY-ILE-GLY-ILE-VAL-PRO-VAL
D: DMF5 TCR alpha chain
E: DMF5 TCR beta chain


Theoretical massNumber of molelcules
Total (without water)92,1865
Polymers92,1865
Non-polymers00
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10840 Å2
ΔGint-55 kcal/mol
Surface area36970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)228.106, 49.900, 92.455
Angle α, β, γ (deg.)90.00, 95.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 4 types, 4 molecules ABDE

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


Mass: 31854.203 Da / Num. of mol.: 1
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: P01892, UniProt: P04439*PLUS
#2: Protein Beta-2-microglobulin


Mass: 11879.356 Da / Num. of mol.: 1 / 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
#4: Protein DMF5 TCR alpha chain


Mass: 20828.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#5: Protein DMF5 TCR beta chain


Mass: 26637.748 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Protein/peptide / Non-polymers , 2 types, 213 molecules C

#3: Protein/peptide SER-MET-LEU-GLY-ILE-GLY-ILE-VAL-PRO-VAL


Mass: 985.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.1 / Details: 13% PEG3350, 0.25 M magnesium chloride, 0.1 M Tris

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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 23, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 40458 / % possible obs: 98 % / Redundancy: 3.8 % / Biso Wilson estimate: 23.94 Å2 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.037 / Rrim(I) all: 0.072 / Χ2: 1.119 / Net I/σ(I): 8.7 / Num. measured all: 152065
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.443.70.53319930.8520.3220.6240.6398.5
2.44-2.493.80.45420390.9080.2690.5290.62598.5
2.49-2.533.90.41919900.8970.2460.4860.61998.6
2.53-2.593.80.34919840.9320.2060.4050.65798.5
2.59-2.643.90.2920740.9530.1710.3370.64898.5
2.64-2.73.80.25719570.9550.1530.2990.78198.5
2.7-2.773.90.20820520.9710.1230.2420.75598.7
2.77-2.853.80.17220190.9750.1020.20.82898.7
2.85-2.933.80.14520220.9790.0870.1690.84298.8
2.93-3.023.80.11620270.9860.0690.1350.89999
3.02-3.133.80.09920180.990.0590.1160.9898.9
3.13-3.263.80.08520380.9920.0510.0991.11699
3.26-3.413.80.07220460.9920.0440.0841.13898.9
3.41-3.583.60.06620110.9930.0410.0781.3297.5
3.58-3.813.50.05819510.9940.0360.0691.48594
3.81-4.13.30.05319440.990.0340.0631.81594.2
4.1-4.523.80.04720560.9960.0280.0551.9199
4.52-5.173.80.04220530.9960.0260.051.92698.8
5.17-6.513.80.04220940.9970.0250.0491.78798.6
6.51-503.60.03620900.9970.0220.0431.86295.9

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data scaling
HKL-2000data collection
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.394→38.754 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2437 1919 4.95 %
Rwork0.2011 --
obs0.2033 38731 93.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.394→38.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6484 0 0 212 6696
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026658
X-RAY DIFFRACTIONf_angle_d0.5759046
X-RAY DIFFRACTIONf_dihedral_angle_d18.2462427
X-RAY DIFFRACTIONf_chiral_restr0.049953
X-RAY DIFFRACTIONf_plane_restr0.0031185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3941-2.4540.30631190.26652227X-RAY DIFFRACTION81
2.454-2.52030.30541260.25652436X-RAY DIFFRACTION87
2.5203-2.59450.30281280.24292480X-RAY DIFFRACTION89
2.5945-2.67820.32471330.23852542X-RAY DIFFRACTION91
2.6782-2.77390.30461390.22422598X-RAY DIFFRACTION93
2.7739-2.88490.22811380.21962604X-RAY DIFFRACTION95
2.8849-3.01620.27731360.21772718X-RAY DIFFRACTION97
3.0162-3.17510.271400.22042728X-RAY DIFFRACTION98
3.1751-3.37390.26631430.20772740X-RAY DIFFRACTION98
3.3739-3.63430.24351370.20142604X-RAY DIFFRACTION93
3.6343-3.99970.19411400.18242685X-RAY DIFFRACTION95
3.9997-4.57760.22231450.1582804X-RAY DIFFRACTION99
4.5776-5.76430.19481460.16532797X-RAY DIFFRACTION99
5.7643-38.75920.21181490.19512849X-RAY DIFFRACTION97
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)
12.0186-0.25690.48491.83710.38471.83540.13440.33280.3396-0.0367-0.0260.1320.02230.1978-0.0130.12130.00040.0095-0.0081-0.05080.2341-39.0177-14.9235-2.9002
21.6568-0.23991.51490.75430.11582.68440.15331.05390.6789-0.31990.0620.1424-0.38790.2799-0.09080.38120.05370.09560.66990.34180.5069-41.9601-10.9005-26.9342
30.6807-1.12950.6311.9668-0.76621.28010.02440.86951.5115-0.22990.0294-0.0504-0.98910.06370.20570.84920.02560.02090.82710.63691.2068-51.51050.3959-32.2063
41.5882-1.0989-0.47213.31361.69555.77010.07560.07830.48070.11870.1678-0.0531-0.12980.0620.01370.08920.0293-0.03530.14490.14980.4348-58.6734-9.1835-13.4275
52.6620.64491.76121.71390.52481.17170.00351.19510.0332-1.25490.10310.05190.14060.002-0.14730.59210.03480.00930.96930.05810.1747-57.1557-20.7814-36.1397
63.2420.12150.62133.95781.18893.36650.23510.67260.0856-0.56730.0980.13130.00870.0953-0.19510.21290.0586-0.03460.2720.08680.2034-56.5305-16.9454-21.6553
75.56443.62825.8636.14266.39568.70220.1153-0.03980.25040.2018-0.00370.16220.4917-0.3033-0.270.1669-0.0246-0.00160.14280.1060.2623-61.783-18.4948-12.5962
85.1282-0.65231.76275.01610.96956.11950.25110.3683-0.3605-0.1685-0.05670.38410.8929-0.4427-0.30040.2906-0.074-0.12940.23310.04510.2972-63.9175-26.8166-19.9403
94.16220.28121.83583.95731.47635.31730.11120.45080.078-0.14820.2122-0.21450.18320.1861-0.36690.14960.03820.01430.09860.08870.2245-52.0836-16.335-15.4595
104.10670.45420.552.31830.2721.41670.2531.0053-0.0361-1.0419-0.1830.9110.0416-0.9753-0.07020.7871-0.0016-0.32160.98340.0610.5424-69.4123-21.8035-34.3118
112.82840.02841.2313.37411.75075.79540.01620.14530.24150.0744-0.16350.50370.2208-0.4854-0.01720.1125-0.0138-0.01580.22370.14660.3643-66.9824-14.7859-13.1312
123.4303-1.12210.28374.81141.87015.08960.21140.87230.4283-0.9693-0.12970.235-0.328-0.07210.18050.3780.0529-0.18320.50950.29220.4459-65.5778-12.4994-27.4542
132.19460.85110.11821.6821-0.1360.95170.1030.075-0.11960.1348-0.0995-0.0009-0.04820.0676-0.08130.1228-0.03830.01390.0133-0.11570.3255-33.5998-16.58151.6079
142.2104-0.4203-0.30850.3736-0.43070.867-0.03890.1886-0.4036-0.0303-0.1012-0.14180.3310.5922-0.62040.41370.3717-0.0380.6754-0.26540.3829-7.176-32.73882.7483
151.0473-0.3255-0.79640.3940.16690.62060.10030.0939-0.0180.0125-0.0954-0.11170.1020.7216-0.2540.11280.2480.19270.6942-0.18380.1743-11.8773-24.8952-0.4877
161.7905-0.1095-0.29441.1578-0.94591.3410.1969-0.07720.24060.0108-0.3455-0.3139-0.08981.00270.0020.09540.02690.02870.6217-0.07730.2151-11.8818-21.91156.0654
172.6104-1.04170.56851.0219-0.25110.6566-0.2327-0.3538-0.42650.5028-0.083-0.1356-0.09111.19310.10150.51820.1465-0.05181.39730.25410.35215.288-37.547423.4569
186.5192-0.50810.13344.11490.00272.1376-0.23260.6331-1.06670.0938-0.1853-0.20570.19671.43230.43460.930.1039-0.031.7062-0.22080.73019.5731-44.800418.3082
195.59630.0079-0.18454.468-0.51552.2707-0.3640.0945-0.20.30890.0038-0.3352-0.45061.48080.38880.7774-0.103-0.06951.31290.08170.34396.7456-35.613225.4914
208.4536-0.1837-0.19674.12860.77891.9782-0.42790.2206-1.63290.0287-0.07260.01160.60621.40250.45410.92890.24630.39281.6264-0.14951.035313.0428-51.662324.1952
213.8963-1.51040.43744.06-0.30833.0980.2167-0.5227-0.56590.37750.09360.24550.37340.3965-0.2340.26250.0226-0.04160.1356-0.13250.1442-26.7516-33.424618.4912
222.6898-0.55270.58753.2118-0.03152.34820.2714-0.219-0.45620.0570.02570.42680.44020.1838-0.20070.22140.0078-0.05910.1314-0.06150.2054-29.5512-32.82114.4956
235.9653-2.47683.98821.9398-1.73896.74560.4949-0.4463-1.0774-0.07770.0160.38540.69850.4087-0.35230.67580.0871-0.10760.54820.16810.413-18.7125-49.332427.9612
242.7934-0.3251.12921.0865-0.45233.41930.08290.1162-0.2459-0.0589-0.0806-0.1961-0.39871.1698-0.13780.65890.0149-0.03251.33580.09050.12760.7118-38.415833.6247
256.60372.92550.61272.7159-1.07914.55320.2011-1.0816-0.96760.4466-0.11370.74460.4155-0.376-0.37030.73570.04380.0091.07430.19670.5824-21.8313-48.716336.886
261.2946-0.02321.32321.5349-0.22325.5933-0.1993-0.15060.02750.29110.0221-0.3512-0.2891.13120.13120.7518-0.0225-0.00831.21910.06810.12691.9052-38.312244.1007
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 162 )
2X-RAY DIFFRACTION2chain 'A' and (resid 163 through 198 )
3X-RAY DIFFRACTION3chain 'A' and (resid 199 through 275 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 12 )
5X-RAY DIFFRACTION5chain 'B' and (resid 13 through 20 )
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 31 )
7X-RAY DIFFRACTION7chain 'B' and (resid 32 through 42 )
8X-RAY DIFFRACTION8chain 'B' and (resid 43 through 52 )
9X-RAY DIFFRACTION9chain 'B' and (resid 53 through 72 )
10X-RAY DIFFRACTION10chain 'B' and (resid 73 through 78 )
11X-RAY DIFFRACTION11chain 'B' and (resid 79 through 91 )
12X-RAY DIFFRACTION12chain 'B' and (resid 92 through 100 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 10 )
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 13 )
15X-RAY DIFFRACTION15chain 'D' and (resid 14 through 31 )
16X-RAY DIFFRACTION16chain 'D' and (resid 32 through 96 )
17X-RAY DIFFRACTION17chain 'D' and (resid 97 through 135 )
18X-RAY DIFFRACTION18chain 'D' and (resid 136 through 150 )
19X-RAY DIFFRACTION19chain 'D' and (resid 151 through 175 )
20X-RAY DIFFRACTION20chain 'D' and (resid 176 through 190 )
21X-RAY DIFFRACTION21chain 'E' and (resid 1 through 49 )
22X-RAY DIFFRACTION22chain 'E' and (resid 50 through 106 )
23X-RAY DIFFRACTION23chain 'E' and (resid 107 through 121 )
24X-RAY DIFFRACTION24chain 'E' and (resid 122 through 212 )
25X-RAY DIFFRACTION25chain 'E' and (resid 213 through 230 )
26X-RAY DIFFRACTION26chain 'E' and (resid 231 through 242 )

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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