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- PDB-4nhu: The M33 TCR p3M33l/H-2 Ld Complex -

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Basic information

Entry
Database: PDB / ID: 4nhu
TitleThe M33 TCR p3M33l/H-2 Ld Complex
Components
  • 2C m33 alpha VmCh chimera
  • 2C m33 beta VmCh chimera
  • H-2 class I histocompatibility antigen, L-D alpha chain
KeywordsIMMUNE SYSTEM / Ig / TCR / MHC / antigen
Function / homology
Function and homology information


positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation ...positive regulation of antibody-dependent cellular cytotoxicity / regulation of natural killer cell mediated immunity / positive regulation of TRAIL production / antigen processing and presentation of exogenous peptide antigen via MHC class Ib / MHC class Ib protein complex / positive regulation of natural killer cell mediated immunity / positive regulation of natural killer cell cytokine production / natural killer cell tolerance induction / natural killer cell lectin-like receptor binding / negative regulation of natural killer cell activation / positive regulation of natural killer cell activation / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / positive regulation of natural killer cell proliferation / T cell receptor complex / positive regulation of immunoglobulin production / 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 / positive regulation of interleukin-4 production / MHC class I protein binding / protection from natural killer cell mediated cytotoxicity / beta-2-microglobulin binding / T cell receptor binding / negative regulation of T cell proliferation / 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 / lumenal side of endoplasmic reticulum membrane / defense response / MHC class I protein complex / positive regulation of T cell mediated cytotoxicity / phagocytic vesicle membrane / peptide antigen binding / positive regulation of tumor necrosis factor production / protein-folding chaperone binding / antibacterial humoral response / adaptive immune response / cell surface receptor signaling pathway / defense response to Gram-positive bacterium / immune response / external side of plasma membrane / signaling receptor binding / Golgi apparatus / cell surface / endoplasmic reticulum / extracellular space / plasma membrane
Similarity search - Function
Domain of unknown function (DUF1968) / 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 / Immunoglobulin V-Type / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily ...Domain of unknown function (DUF1968) / 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 / Immunoglobulin V-Type / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / Immunoglobulin V-set domain / MHC classes I/II-like antigen recognition protein / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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
T-cell receptor alpha chain V region PHDS58 / H-2 class I histocompatibility antigen, L-D alpha chain / T-cell receptor beta chain V region C5
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsBirnbaum, M.E. / Adams, J.J. / Garcia, K.C.
CitationJournal: To be Published
Title: Interrogating TCR Signal Strength and Cross-Reactivity by Yeast Display of pMHC
Authors: Birnbaum, M.E. / Adams, J.J. / Garcia, K.C.
History
DepositionNov 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 2C m33 alpha VmCh chimera
B: 2C m33 beta VmCh chimera
E: H-2 class I histocompatibility antigen, L-D alpha chain
C: 2C m33 alpha VmCh chimera
D: 2C m33 beta VmCh chimera
G: H-2 class I histocompatibility antigen, L-D alpha chain


Theoretical massNumber of molelcules
Total (without water)150,8896
Polymers150,8896
Non-polymers00
Water0
1
A: 2C m33 alpha VmCh chimera
B: 2C m33 beta VmCh chimera
G: H-2 class I histocompatibility antigen, L-D alpha chain


Theoretical massNumber of molelcules
Total (without water)75,4453
Polymers75,4453
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: H-2 class I histocompatibility antigen, L-D alpha chain
C: 2C m33 alpha VmCh chimera
D: 2C m33 beta VmCh chimera


Theoretical massNumber of molelcules
Total (without water)75,4453
Polymers75,4453
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.760, 92.800, 94.950
Angle α, β, γ (deg.)112.29, 103.57, 102.37
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody 2C m33 alpha VmCh chimera


Mass: 24279.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P01738*PLUS
#2: Protein 2C m33 beta VmCh chimera


Mass: 28051.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P04213*PLUS
#3: Protein H-2 class I histocompatibility antigen, L-D alpha chain


Mass: 23113.705 Da / Num. of mol.: 2 / Mutation: N30D, A49V, I66V, W97R, K131R, W167A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-L / Production host: Escherichia coli (E. coli) / References: UniProt: P01897
Sequence detailsRESIDUES 181-194 IN CHAINS E,G ARE ENGINEERED TETHER TO PHYSICALLY LINK THE THE PRESENTED PEPTIDE ...RESIDUES 181-194 IN CHAINS E,G ARE ENGINEERED TETHER TO PHYSICALLY LINK THE THE PRESENTED PEPTIDE ANTIGEN (RESIDUES 195-203) TO THE MHC FOLD.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Crystals grown in 20% PEG 3350 and 200mM Ammonium Nitrate and micro seeded into 20% PEG 3350 and 200mM Ammonium phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 25, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→82.31 Å / Num. all: 31872 / Num. obs: 31171 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.9→3.06 Å / % possible all: 95.8

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→47.859 Å / SU ML: 0.39 / σ(F): 2.02 / Phase error: 28.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2604 1568 5.03 %random
Rwork0.229 ---
obs0.2306 31159 97.79 %-
all-31863 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→47.859 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9829 0 0 0 9829
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00210105
X-RAY DIFFRACTIONf_angle_d0.57713718
X-RAY DIFFRACTIONf_dihedral_angle_d12.4663617
X-RAY DIFFRACTIONf_chiral_restr0.0411428
X-RAY DIFFRACTIONf_plane_restr0.0031803
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.99360.3311430.3152594X-RAY DIFFRACTION95
2.9936-3.10060.3571270.30862725X-RAY DIFFRACTION98
3.1006-3.22470.37241470.29142625X-RAY DIFFRACTION98
3.2247-3.37140.30441360.27452730X-RAY DIFFRACTION98
3.3714-3.54910.28321450.25482723X-RAY DIFFRACTION98
3.5491-3.77140.29421600.24742648X-RAY DIFFRACTION98
3.7714-4.06240.27731350.23462681X-RAY DIFFRACTION98
4.0624-4.4710.2341400.19162738X-RAY DIFFRACTION98
4.471-5.11730.22111540.17962689X-RAY DIFFRACTION98
5.1173-6.44480.2031240.21332745X-RAY DIFFRACTION99
6.4448-47.86580.21971570.19992693X-RAY DIFFRACTION98
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)
13.45711.7748-0.64426.0308-1.22534.2034-0.0147-0.0366-0.2965-0.05540.00160.02550.8774-0.1425-0.0010.4495-0.0309-0.00950.29-0.04110.21944.12856.197737.8708
23.5265-1.0580.02782.7141-0.87950.3769-0.01920.3306-0.079-0.5185-0.13050.51830.5552-1.0010.01460.8098-0.24190.03560.77310.02670.531319.779-5.43557.1129
33.578-2.3302-0.51998.4713.5044.2541-0.12410.4132-0.634-0.2913-0.21591.10360.4819-0.39480.2640.9328-0.23490.01560.49860.0360.508219.2293-8.118257.7448
44.02281.2342-1.63094.0749-0.85576.530.3007-0.2814-0.18291.51980.42460.2184-1.3322-0.1894-0.1710.2426-0.0051-0.03380.3341-0.04430.270440.138725.338958.0826
54.5220.779-1.91564.9627-0.5796.63370.198-0.0878-0.01120.0549-0.05340.0615-0.5890.0394-0.23520.24560.0304-0.01360.2407-0.0440.217342.952627.50247.4839
63.1494-1.57941.49885.27270.36954.2514-0.05840.18460.1377-0.16640.2657-0.3411-0.61840.6604-0.23060.32490.0754-0.0020.3001-0.10840.286146.221918.639248.9595
71.07721.4163-0.92191.8065-0.91043.6306-0.10720.56691.01720.622-0.85311.3087-0.5843-0.4842-0.19540.40150.22880.0090.72840.0453-0.258424.68923.16661.3981
83.3376-0.4891-0.81015.16381.85754.41790.23460.3139-0.0153-0.5452-0.06730.40290.4996-0.4799-0.14610.3613-0.08-0.03620.44340.01520.305225.66890.934964.8881
91.66122.05250.07525.0749-0.76193.56471.1358-0.4155-0.03941.3725-0.079-0.24440.6582-1.0355-0.20580.5459-0.06690.18560.1794-0.11490.344530.8099-1.153574.9018
102.8226-0.3921-0.32822.1794-1.87013.00420.1278-0.26050.35520.2256-0.0074-0.20090.1112-0.2638-0.07150.2864-0.03860.00790.3450.0170.238826.663516.903472.7901
112.99570.40540.58794.0892-2.27411.6308-0.1447-0.20160.2520.23660.01760.0280.0656-0.27460.08450.17980.0535-0.01280.5070.03250.209132.8716-39.459718.8926
125.0057-3.43651.28515.061-0.72481.73560.0177-0.11930.30680.4227-0.1882-0.79610.07370.36390.19110.3043-0.0779-0.02980.38360.09020.350339.9192-37.204419.5084
134.0679-3.46361.82556.6002-0.51593.16510.1329-0.4940.12311.6492-0.10720.832-0.271-0.3660.27970.1136-0.165-0.33050.37930.11580.114725.1984-35.57114.1826
14-0.0512-0.31970.42010.6437-1.28983.109-0.10440.4683-0.428-0.1927-0.19560.24250.0647-0.43580.16420.2304-0.0834-0.04840.4455-0.05960.414928.1121-42.66753.6756
154.1399-3.7598-0.3318.4046-0.07362.60560.1172-0.0315-0.0709-0.2873-0.1435-0.01080.0253-0.09480.05940.2113-0.03410.05480.26330.01340.22335.005-36.83493.7837
164.47472.1254-1.24753.2552-4.33727.61720.14030.53470.3114-0.04180.1479-0.3997-0.3580.0431-0.2190.5699-0.0690.12550.2182-0.09890.285853.9679-12.9131-11.3889
173.0673.11451.62573.83152.6242.7505-0.34960.0005-0.0883-0.2220.3729-0.38740.23950.1272-0.14540.25460.10070.03140.21890.04050.306845.4172-19.5218-2.9019
183.8023-0.96971.45792.06840.97666.5381-0.1294-0.09830.5306-0.2392-0.2080.0659-0.8774-0.41130.2410.47770.02870.05530.2358-0.01980.292345.7254-8.24530.0485
193.6251-0.23811.56222.5141.3645.33570.22880.00690.23320.0193-0.29190.6228-0.4212-0.96020.15940.29360.12060.1010.32930.07620.588638.5191-17.3447-9.6837
207.7933.65341.01977.39712.11185.5456-0.5405-0.30850.9529-0.4030.48860.546-0.3603-0.24570.00940.3646-0.0596-0.05250.3887-0.04560.255847.8269-7.9744-11.9513
210.3115-0.19760.41930.0986-0.40790.50830.02320.0308-0.3392-0.57080.121-0.68050.0304-0.18840.02560.34750.07010.10750.2292-0.08960.28948.164-18.86771.9229
224.88195.2526-4.49479.2539-4.36595.63980.00280.90140.4026-1.77190.7683-0.5313-0.36760.4017-0.0641.0353-0.2970.32780.41310.11380.336360.41092.702-17.2572
231.2194-0.0833-1.25194.86310.47816.3734-0.1360.05560.3569-0.66150.3771-1.6789-0.47361.5279-0.17240.5898-0.09670.11170.76080.03230.895777.228214.6551-5.8984
245.06040.31210.11758.16172.67534.93340.0721-0.0387-0.562-0.44190.2275-1.48050.4810.8307-0.42650.6245-0.04040.18920.5506-0.1110.760273.7812-0.2602-12.5534
257.64871.80463.21152.23290.12816.8941-0.3099-0.01560.0137-0.29480.13770.1507-0.2753-0.16790.18260.69520.02770.06340.5398-0.09510.297963.86587.1617-9.0438
262.0139-2.33889.28442.2761-0.82237.92620.17671.3974-0.3929-0.3202-0.32-0.7913-0.031.12210.03870.6243-0.04860.33070.66580.02610.653768.78047.3738-9.3736
272.3740.062.90212.3042-2.43476.307-0.07641.54330.0317-0.2583-0.707-1.5962-0.52751.29290.69740.790.00210.15181.33110.19020.920585.85777.2043-7.6213
281.61381.8957-1.1422.2133-1.21392.00350.1090.3862-0.5128-1.47750.7389-0.76050.05371.4828-0.86080.99110.05260.03261.0367-0.29611.055276.90725.9865-19.6962
294.62041.6832-0.04053.6679-0.04444.2274-0.007-0.05140.11410.3469-0.0536-0.1521-0.3805-0.04980.08270.25440.0183-0.03130.2473-0.07710.242652.1984-14.257817.8428
305.8452-3.55233.20884.10210.7646.25920.1286-0.15780.34680.4692-0.42980.37760.4689-0.43770.35340.28970.0451-0.0690.4204-0.07310.282547.3146-11.175110.5474
311.60892.7772-1.50015.9871-1.96991.67820.28560.1715-0.61930.1261-0.4936-1.2669-0.40830.45090.33660.4586-0.0639-0.21470.536-0.07240.623370.9361-4.247816.6749
326.0257-1.77333.14333.00611.63054.5371-0.28220.48850.1481-0.14610.1728-0.6618-0.39220.7059-0.11350.3053-0.05980.02790.3094-0.010.483568.73312.4202-1.0731
333.8987-1.36481.72978.8771-0.7454.86330.12350.067-1.0120.0909-0.3237-0.36070.92040.41970.21570.50390.01310.18730.39120.03390.508167.85933.3972.4581
341.2428-0.0524-0.35293.9718-1.35791.8956-0.2472-0.15680.24030.35140.2531-0.5753-0.2616-0.04970.08360.4951-0.0047-0.1040.336-0.02850.486267.848213.16728.1153
356.36-0.23174.57894.229-1.23048.05820.259-0.5706-0.28660.38080.565-0.4815-0.0988-0.006-0.33030.23840.0413-0.0490.297-0.09250.322259.653738.214926.7979
368.6114-0.15446.7965.2586-1.82419.2231-0.2779-0.16920.41420.99510.2685-0.4607-1.08990.13710.03060.37520.0576-0.11690.1905-0.03660.42154.104944.206728.5997
372.7014-1.02620.62784.477-1.532.0878-0.0942-0.2146-0.0771-0.04070.23740.11450.0549-0.1332-0.12360.3371-0.01970.070.2759-0.0110.190258.463831.803524.7283
384.4124-0.37311.92135.2198-0.99233.4114-0.17350.2639-0.4821-0.26780.14940.360.4899-0.1181-0.05320.42-0.13180.11610.3231-0.02530.228255.62923.266620.2837
392.05110.9711-0.03250.728-0.76622.4372-0.4505-0.19160.3463-0.7212-0.0405-0.2341-0.3811-0.14440.2750.58170.0585-0.10040.4966-0.06520.253453.639626.522626.3414
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 105 )
2X-RAY DIFFRACTION2chain 'A' and (resid 106 through 157 )
3X-RAY DIFFRACTION3chain 'A' and (resid 158 through 199 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 25 )
5X-RAY DIFFRACTION5chain 'B' and (resid 26 through 86 )
6X-RAY DIFFRACTION6chain 'B' and (resid 87 through 104 )
7X-RAY DIFFRACTION7chain 'B' and (resid 105 through 119 )
8X-RAY DIFFRACTION8chain 'B' and (resid 120 through 197 )
9X-RAY DIFFRACTION9chain 'B' and (resid 198 through 210 )
10X-RAY DIFFRACTION10chain 'B' and (resid 211 through 239 )
11X-RAY DIFFRACTION11chain 'E' and (resid 1 through 28 )
12X-RAY DIFFRACTION12chain 'E' and (resid 29 through 84 )
13X-RAY DIFFRACTION13chain 'E' and (resid 85 through 103 )
14X-RAY DIFFRACTION14chain 'E' and (resid 104 through 137 )
15X-RAY DIFFRACTION15chain 'E' and (resid 138 through 203 )
16X-RAY DIFFRACTION16chain 'C' and (resid 2 through 20 )
17X-RAY DIFFRACTION17chain 'C' and (resid 21 through 38 )
18X-RAY DIFFRACTION18chain 'C' and (resid 39 through 49 )
19X-RAY DIFFRACTION19chain 'C' and (resid 50 through 71 )
20X-RAY DIFFRACTION20chain 'C' and (resid 72 through 85 )
21X-RAY DIFFRACTION21chain 'C' and (resid 86 through 105 )
22X-RAY DIFFRACTION22chain 'C' and (resid 106 through 118 )
23X-RAY DIFFRACTION23chain 'C' and (resid 119 through 137 )
24X-RAY DIFFRACTION24chain 'C' and (resid 138 through 152 )
25X-RAY DIFFRACTION25chain 'C' and (resid 153 through 167 )
26X-RAY DIFFRACTION26chain 'C' and (resid 168 through 177 )
27X-RAY DIFFRACTION27chain 'C' and (resid 178 through 187 )
28X-RAY DIFFRACTION28chain 'C' and (resid 188 through 200 )
29X-RAY DIFFRACTION29chain 'D' and (resid 2 through 86 )
30X-RAY DIFFRACTION30chain 'D' and (resid 87 through 104 )
31X-RAY DIFFRACTION31chain 'D' and (resid 105 through 119 )
32X-RAY DIFFRACTION32chain 'D' and (resid 120 through 157 )
33X-RAY DIFFRACTION33chain 'D' and (resid 158 through 183 )
34X-RAY DIFFRACTION34chain 'D' and (resid 184 through 239 )
35X-RAY DIFFRACTION35chain 'G' and (resid 1 through 28 )
36X-RAY DIFFRACTION36chain 'G' and (resid 29 through 44 )
37X-RAY DIFFRACTION37chain 'G' and (resid 45 through 137 )
38X-RAY DIFFRACTION38chain 'G' and (resid 138 through 171 )
39X-RAY DIFFRACTION39chain 'G' and (resid 172 through 203 )

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