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- PDB-4p46: J809.B5 Y31A TCR bound to IAb3K -

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Basic information

Entry
Database: PDB / ID: 4p46
TitleJ809.B5 Y31A TCR bound to IAb3K
Components
  • 3K Peptide,H-2 class II histocompatibility antigen, A beta chain
  • H-2 class II histocompatibility antigen, A-B alpha chain
  • J809.B5 TCR Y31A alpha chain (Va2.8)
  • J809.B5 TCR beta chain (Vb8.2)
KeywordsIMMUNE SYSTEM / TCR MHCII
Function / homology
Function and homology information


positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / positive regulation of T-helper 1 type immune response / antigen processing and presentation of peptide antigen / B cell affinity maturation / protein antigen binding / alpha-beta T cell receptor complex / positive regulation of T cell differentiation / antigen processing and presentation / Translocation of ZAP-70 to Immunological synapse ...positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / positive regulation of T-helper 1 type immune response / antigen processing and presentation of peptide antigen / B cell affinity maturation / protein antigen binding / alpha-beta T cell receptor complex / positive regulation of T cell differentiation / antigen processing and presentation / Translocation of ZAP-70 to Immunological synapse / Phosphorylation of CD3 and TCR zeta chains / alpha-beta T cell activation / Generation of second messenger molecules / Co-inhibition by PD-1 / response to type II interferon / toxic substance binding / multivesicular body / MHC class II protein complex / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptide antigen binding / cellular response to type II interferon / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Downstream TCR signaling / T cell receptor signaling pathway / adaptive immune response / early endosome / lysosome / immune response / external side of plasma membrane / ubiquitin protein ligase binding / Golgi apparatus / membrane / plasma membrane
Similarity search - Function
Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / : ...Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 / MHC class II, beta chain, N-terminal / Class II histocompatibility antigen, beta domain / Class II histocompatibility antigen, beta domain / MHC class II, alpha chain, N-terminal / Class II histocompatibility antigen, alpha domain / Class II histocompatibility antigen, alpha domain / MHC class II, alpha/beta chain, N-terminal / : / 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
T cell receptor beta constant 1 / H-2 class II histocompatibility antigen, A-B alpha chain / H-2 class II histocompatibility antigen, A beta chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Synthetic Construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.851 Å
AuthorsStadinski, B.D. / Huseby, E.S. / Trenh, P. / Stern, L.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of HealthRO1-DK095077 United States
National Institutes of HealthR01-AI-38996 United States
National Institutes of HealthT32 AI 007349 United States
CitationJournal: J Immunol. / Year: 2014
Title: Effect of CDR3 Sequences and Distal V Gene Residues in Regulating TCR-MHC Contacts and Ligand Specificity.
Authors: Stadinski, B.D. / Trenh, P. / Duke, B. / Huseby, P.G. / Li, G. / Stern, L.J. / Huseby, E.S.
History
DepositionMar 11, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Other
Revision 1.3Jan 31, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 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: H-2 class II histocompatibility antigen, A-B alpha chain
D: 3K Peptide,H-2 class II histocompatibility antigen, A beta chain
A: J809.B5 TCR Y31A alpha chain (Va2.8)
B: J809.B5 TCR beta chain (Vb8.2)


Theoretical massNumber of molelcules
Total (without water)94,3014
Polymers94,3014
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11010 Å2
ΔGint-54 kcal/mol
Surface area35800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.123, 73.429, 65.680
Angle α, β, γ (deg.)90.000, 90.340, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein H-2 class II histocompatibility antigen, A-B alpha chain / IAalpha


Mass: 20242.615 Da / Num. of mol.: 1 / Fragment: Residues 27-205
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Aa / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14434
#2: Protein 3K Peptide,H-2 class II histocompatibility antigen, A beta chain


Mass: 25094.973 Da / Num. of mol.: 1 / Fragment: Residues 30-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synthetic Construct (others), (gene. exp.) Mus musculus (house mouse)
Gene: H2-Ab1, H2-iabeta / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14483
#3: Protein J809.B5 TCR Y31A alpha chain (Va2.8)


Mass: 22277.682 Da / Num. of mol.: 1 / Mutation: Va2.8 Y31A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#4: Protein J809.B5 TCR beta chain (Vb8.2)


Mass: 26685.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P01850*PLUS
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: 3.15 Å3/Da / Density % sol: 60.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4 / Details: 100mM NaCitrate, 100mM NaCacodylate, 8% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.86→44 Å / Num. obs: 27043 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 56.34 Å2 / Rmerge(I) obs: 0.137 / Χ2: 0.965 / Net I/av σ(I): 11.589 / Net I/σ(I): 8.4 / Num. measured all: 180378
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.86-2.916.60.5313460.70899.7
2.91-2.966.30.43213340.75100
2.96-3.026.50.40813410.7799.9
3.02-3.086.90.35213340.799100
3.08-3.156.80.30613610.955100
3.15-3.226.90.26913161.064100
3.22-3.36.60.2413641.143100
3.3-3.396.40.20213401.151100
3.39-3.496.80.18313411.097100
3.49-3.66.90.16513381.163100
3.6-3.736.60.15713491.044100
3.73-3.886.50.14613601.031100
3.88-4.066.90.13813411.011100
4.06-4.276.80.12613471.029100
4.27-4.546.50.1213500.977100
4.54-4.896.90.11613760.952100
4.89-5.386.50.1113470.942100
5.38-6.166.90.1113660.979100
6.16-7.756.60.10513690.971100
7.75-446.40.09314230.7499.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKLdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RDT

3rdt


Resolution: 2.851→41.937 Å / FOM work R set: 0.8058 / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 26.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2467 1267 4.97 %random selection
Rwork0.1813 24244 --
obs0.1846 25511 93.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 173.08 Å2 / Biso mean: 60.05 Å2 / Biso min: 21.21 Å2
Refinement stepCycle: final / Resolution: 2.851→41.937 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6273 0 0 0 6273
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086453
X-RAY DIFFRACTIONf_angle_d1.1768806
X-RAY DIFFRACTIONf_chiral_restr0.079968
X-RAY DIFFRACTIONf_plane_restr0.0051151
X-RAY DIFFRACTIONf_dihedral_angle_d13.8812220
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8511-2.96520.34251290.23452498262788
2.9652-3.10010.30751390.22122704284395
3.1001-3.26350.27641450.21182689283495
3.2635-3.46790.28981410.19682673281494
3.4679-3.73550.2731390.18542675281494
3.7355-4.11110.25731440.17822722286694
4.1111-4.70530.21061340.14972714284895
4.7053-5.92550.19511400.15792750289096
5.9255-41.94150.23351560.192819297596
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)
14.033-1.6437-1.33895.23311.54114.7103-0.356-0.2714-0.98870.28760.0920.22150.6520.17550.2660.29790.01990.05180.28740.01020.485846.3554-41.8872-13.5614
28.6905-2.679-7.90471.90311.17618.6141-0.07970.9342-0.9504-0.51310.8484-0.84350.60590.508-0.71990.6439-0.27380.11020.8768-0.39760.957962.21-47.0576-29.4272
36.26190.2414-0.26387.13011.35567.13980.47060.1496-0.6547-0.26270.0449-0.17270.3919-0.0754-0.44780.57980.155-0.06560.4826-0.03110.608977.6586-40.8226-30.8857
44.95640.6512-2.30732.04460.00862.27490.1079-0.49420.36290.03520.2027-0.4066-0.42140.7028-0.27590.3712-0.10450.05010.3981-0.15210.399852.3171-19.1146-9.3047
54.8332-2.43880.81156.11680.67923.93880.599-0.03960.0642-0.8913-0.3223-0.0521-0.12270.15-0.2410.5095-0.05830.01560.2747-0.0480.541872.2165-25.2902-31.7339
63.42192.9658-2.88226.6034-4.69845.30010.0055-0.0123-0.10230.1229-0.2220.0796-0.0043-0.33620.10430.29140.0587-0.01360.467-0.0730.265620.4296-24.06066.7435
73.90761.02470.2293.5388-1.46422.91990.1461-0.5728-0.42010.4182-0.0205-0.0236-0.3944-0.5453-0.12520.41860.1298-0.02270.34990.0860.29626.3446-24.552212.1509
80.9676-0.7224-1.75812.8309-0.76865.4705-0.2328-0.9107-0.1390.51790.3047-0.2388-0.29390.9978-0.0750.37410.136-0.08070.60050.060.412334.9507-27.045215.0823
90.89090.9554-0.69291.0150.24543.38320.15110.32730.3567-0.3323-0.09410.1601-0.7274-0.437-0.04360.51560.1450.05780.46420.14770.33923.7762-13.2817-1.5293
106.09742.70340.50067.87580.92759.07180.1309-1.1940.68150.6889-0.06690.53970.7732-0.205-0.07240.29960.11880.07830.4824-0.02140.342817.1678-18.462233.8371
111.32650.031-0.62843.9894-2.88498.63590.0144-0.33840.26470.4108-0.04540.1886-0.944-0.85790.02210.28170.05380.05410.4216-0.0510.278119.989-12.241722.5601
122.012-7.07981.99722.0147.42092.01830.1365-0.53361.01680.402-0.65110.1594-0.8567-0.1820.57490.6382-0.06350.06420.5874-0.15330.895226.8913-7.175732.2739
137.07491.39382.27345.55260.75837.5499-0.1449-0.42390.0284-0.0312-0.16910.1314-0.4298-1.1030.35640.23130.02550.01470.47210.01110.270218.3942-17.95112.6059
142.3052-0.4051-0.09363.1974-2.35338.06680.0707-0.65980.50560.7705-0.02650.316-1.44880.0843-0.04970.56970.03220.08790.5679-0.09720.391619.5351-8.348128.2818
152.863-0.0436-1.60124.89390.70713.21890.0270.20590.0008-0.1023-0.3377-0.0010.2491-0.64050.26370.3179-0.0125-0.06150.3945-0.01130.171423.9149-24.64630.7816
161.72770.2709-0.52524.61730.28943.7974-0.22080.62740.00250.14980.23540.33480.283-0.89460.02710.21440.0321-0.01480.6293-0.03240.350715.2539-27.9078-2.6517
179.4973-3.5048-4.66112.00078.59197.86630.73380.3967-0.585-0.6917-0.36060.8928-0.6983-0.738-0.33480.46540.1469-0.00880.6130.13880.347418.3464-22.2936-13.688
186.5539-1.85410.21618.1653-5.46472.0182-0.1970.32820.34690.2872-0.63-0.54870.9556-0.52530.71260.4436-0.01250.01710.481-0.09310.284524.8106-34.308-8.1713
191.10460.1548-0.49570.0551-0.02947.8312-0.1091-0.1669-0.52080.5767-0.02650.03030.87170.58330.20620.5770.15730.05910.42770.10860.431825.3184-39.186514.8371
205.9999-0.9121-3.93532.97280.92028.5918-0.2189-1.3891-0.0240.25220.02380.16480.04550.74270.20680.34820.0275-0.01340.64140.07910.31078.3056-30.092440.476
213.5581-1.06220.80211.99492.2133.76690.2959-0.2614-1.08590.7451-0.32660.09620.03440.17930.05210.43940.0063-0.10750.3072-0.01610.4977-1.7281-34.76639.4762
222.9780.0668-0.93871.65140.01363.29410.53830.39710.5181-0.08170.13690.0379-0.3937-0.1136-0.61240.27160.039-0.00390.44360.11270.270511.8975-27.100930.5386
232.4568-0.8064-1.24143.84750.73663.7853-0.3388-1.0271-1.08720.5009-0.42450.60981.5144-0.21510.75610.6533-0.03350.17480.8890.18270.51278.3063-37.904542.7792
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 104 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 105 through 118 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 119 through 201 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 119 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 120 through 239 )B0
6X-RAY DIFFRACTION6chain 'C' and (resid 0 through 18 )C0
7X-RAY DIFFRACTION7chain 'C' and (resid 19 through 35 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 36 through 55 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 56 through 87 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 88 through 101 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 102 through 123 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 124 through 133 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 134 through 146 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 147 through 178 )C0
15X-RAY DIFFRACTION15chain 'D' and (resid -25 through 18 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 19 through 51 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 52 through 64 )D0
18X-RAY DIFFRACTION18chain 'D' and (resid 65 through 77 )D0
19X-RAY DIFFRACTION19chain 'D' and (resid 78 through 98 )D0
20X-RAY DIFFRACTION20chain 'D' and (resid 99 through 134 )D0
21X-RAY DIFFRACTION21chain 'D' and (resid 135 through 145 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 146 through 165 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 166 through 191 )D0

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