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- PDB-4p5t: 14.C6 TCR complexed with MHC class II I-Ab/3K peptide -

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Basic information

Entry
Database: PDB / ID: 4p5t
Title14.C6 TCR complexed with MHC class II I-Ab/3K peptide
Components
  • H-2 class II histocompatibility antigen, A-B alpha chain
  • Human nkt tcr beta chain
  • TRA protein
  • protein of 3K peptide (FEAQKAKANKAVD),Linker region - GGGGSLVPRGSGGGG,H-2 class II histocompatibility antigen, A beta chain,H-2 class II histocompatibility antigen, A beta chain
KeywordsIMMUNE SYSTEM / MHC / TCR / immune receptor / Ig-like domain
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 / protein antigen binding / antigen processing and presentation of peptide antigen / B cell affinity maturation / positive regulation of T cell differentiation / response to type II interferon / antigen processing and presentation / toxic substance binding ...positive regulation of antigen processing and presentation / positive regulation of alpha-beta T cell activation / positive regulation of T-helper 1 type immune response / protein antigen binding / antigen processing and presentation of peptide antigen / B cell affinity maturation / positive regulation of T cell differentiation / response to type II interferon / antigen processing and presentation / toxic substance binding / negative regulation of T cell proliferation / multivesicular body / cellular response to type II interferon / peptide antigen assembly with MHC class II protein complex / MHC class II protein complex / peptide antigen binding / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / positive regulation of T cell activation / MHC class II protein complex binding / late endosome membrane / adaptive immune response / lysosome / early endosome / immune response / lysosomal membrane / external side of plasma membrane / ubiquitin protein ligase binding / protein-containing complex binding / Golgi apparatus / cell surface / 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 / MHC classes I/II-like antigen recognition protein ...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 / Immunoglobulins / Roll / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
H-2 class II histocompatibility antigen, A-B alpha chain / H-2 class II histocompatibility antigen, A beta chain
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.263 Å
AuthorsTrenh, P. / Stadinski, B. / Huseby, E.S. / Stern, L.J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of HealthR01-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 19, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 28, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRA protein
B: Human nkt tcr beta chain
C: H-2 class II histocompatibility antigen, A-B alpha chain
D: protein of 3K peptide (FEAQKAKANKAVD),Linker region - GGGGSLVPRGSGGGG,H-2 class II histocompatibility antigen, A beta chain,H-2 class II histocompatibility antigen, A beta chain
E: TRA protein
F: Human nkt tcr beta chain
G: H-2 class II histocompatibility antigen, A-B alpha chain
H: protein of 3K peptide (FEAQKAKANKAVD),Linker region - GGGGSLVPRGSGGGG,H-2 class II histocompatibility antigen, A beta chain,H-2 class II histocompatibility antigen, A beta chain


Theoretical massNumber of molelcules
Total (without water)191,5038
Polymers191,5038
Non-polymers00
Water00
1
A: TRA protein
B: Human nkt tcr beta chain


Theoretical massNumber of molelcules
Total (without water)50,1872
Polymers50,1872
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-25 kcal/mol
Surface area19340 Å2
MethodPISA
2
C: H-2 class II histocompatibility antigen, A-B alpha chain
D: protein of 3K peptide (FEAQKAKANKAVD),Linker region - GGGGSLVPRGSGGGG,H-2 class II histocompatibility antigen, A beta chain,H-2 class II histocompatibility antigen, A beta chain


Theoretical massNumber of molelcules
Total (without water)45,5652
Polymers45,5652
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-29 kcal/mol
Surface area17270 Å2
MethodPISA
3
E: TRA protein
F: Human nkt tcr beta chain


Theoretical massNumber of molelcules
Total (without water)50,1872
Polymers50,1872
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-25 kcal/mol
Surface area18520 Å2
MethodPISA
4
G: H-2 class II histocompatibility antigen, A-B alpha chain
H: protein of 3K peptide (FEAQKAKANKAVD),Linker region - GGGGSLVPRGSGGGG,H-2 class II histocompatibility antigen, A beta chain,H-2 class II histocompatibility antigen, A beta chain


Theoretical massNumber of molelcules
Total (without water)45,5652
Polymers45,5652
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-28 kcal/mol
Surface area17200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.007, 74.142, 259.289
Angle α, β, γ (deg.)90.000, 92.000, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain C and ((resseq 1:85))) or (chain D and ((resseq -26:94)))
21(chain G and ((resseq 1:85))) or (chain H and ((resseq -26:94)))
12(chain C and ((resseq 86:300)))
22(chain G and ((resseq 86:300)))
13(chain D and ((resseq 95:300)))
23(chain H and ((resseq 95:300)))
14(chain A and ((resseq 0:110))) or (chain B and ((resseq 0:110)))
24(chain E and ((resseq 0:110))) or (chain F and ((resseq 0:110)))
15(chain A and ((resseq 111:500)))
25(chain E and ((resseq 111:500)))
16(chain B and ((resseq 111:500)))
26(chain F and ((resseq 111:500)))

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEILEILE(chain C and ((resseq 1:85))) or (chain D and ((resseq -26:94)))CC01
21ILEILEILEILE(chain G and ((resseq 1:85))) or (chain H and ((resseq -26:94)))GG01
12ILEILEILEILE(chain C and ((resseq 86:300)))CC01
22ILEILEILEILE(chain G and ((resseq 86:300)))GG01
13PHEPHEPHEPHE(chain D and ((resseq 95:300)))DD-251
23PHEPHEPHEPHE(chain H and ((resseq 95:300)))HH-251
14GLNGLNGLNGLN(chain A and ((resseq 0:110))) or (chain B and ((resseq 0:110)))AA12
24GLNGLNGLNGLN(chain E and ((resseq 2:110))) or (chain F and ((resseq 2:110)))EE23
15GLNGLNGLNGLN(chain A and ((resseq 111:500)))AA12
25GLNGLNGLNGLN(chain E and ((resseq 111:500)))EE23
16ALAALAALAALA(chain B and ((resseq 111:500)))BB12
26ALAALAALAALA(chain F and ((resseq 111:500)))FF12

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(-0.999889, 0.002487, -0.014665), (-0.004468, 0.890161, 0.455625), (0.014187, 0.45564, -0.890051)-2.72864, 26.994801, -113.047997
2given(-0.999982, -0.003743, -0.004653), (-0.005449, 0.890694, 0.454571), (0.002443, 0.454588, -0.890698)-1.95339, 26.8573, -113.269997
3given(-0.999989, -6.41439, -0.004653), (0.002085, 0.884716, 0.466126), (-0.004095, 0.46613, -0.884707)-1.15265, 27.923, -112.904999
4given(-0.996138, 0.066941, -0.05682), (0.033572, 0.888324, 0.457989), (0.081133, 0.454313, -0.88714)-7.37682, 26.994301, -113.191002
5given(-0.972269, 0.172708, -0.157687), (0.096747, 0.910892, 0.401142), (0.212916, 0.374762, -0.902341)-22.315701, 18.7353, -116.149002
6given(-0.97627, 0.166714, -0.138218), (0.091124, 0.895237, 0.436173), (0.196454, 0.413228, -0.889184)-19.4205, 23.7596, -114.869003
Detailsbiological unit is the same as asym.

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Components

#1: Antibody TRA protein


Mass: 23183.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRA@ / Production host: Escherichia coli (E. coli)
#2: Protein Human nkt tcr beta chain


Mass: 27002.885 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, HDCMA22P / Production host: Escherichia coli (E. coli)
#3: Protein H-2 class II histocompatibility antigen, A-B alpha chain / IAalpha


Mass: 20597.957 Da / Num. of mol.: 2 / Fragment: Residues 27-208
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
#4: Protein protein of 3K peptide (FEAQKAKANKAVD),Linker region - GGGGSLVPRGSGGGG,H-2 class II histocompatibility antigen, A beta chain,H-2 class II histocompatibility antigen, A beta chain


Mass: 24966.844 Da / Num. of mol.: 2 / Fragment: Residues 30-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Ab1, H2-iabeta / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P14483

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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: 3.31 Å3/Da / Density % sol: 62.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 100mM sodium cacodylate, 200mM sodium citrate, 10% PEG 4000, 0.5% n-octyl-beta-D-glucoside

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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 9, 2012
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.25→50 Å / Num. obs: 39106 / % possible obs: 99.1 % / Redundancy: 6.6 % / Biso Wilson estimate: 49.44 Å2 / Rmerge(I) obs: 0.155 / Net I/σ(I): 12.92
Reflection shellResolution: 3.25→3.31 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3.8 / % possible all: 97.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.09 Å48.79 Å
Translation3.09 Å48.79 Å

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Processing

Software
NameVersionClassification
PHASER2.3.0phasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.14data extraction
Coot0.7.1model building
HKLdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 3RDT

3rdt


Resolution: 3.263→47.051 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2362 1956 5.01 %Random selection
Rwork0.1863 37124 --
obs0.1888 39080 98.96 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.3 Å2 / Biso mean: 65.3614 Å2 / Biso min: 17.18 Å2
Refinement stepCycle: final / Resolution: 3.263→47.051 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12366 0 0 0 12366
Num. residues----1608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312722
X-RAY DIFFRACTIONf_angle_d0.66617377
X-RAY DIFFRACTIONf_chiral_restr0.0271921
X-RAY DIFFRACTIONf_plane_restr0.0032268
X-RAY DIFFRACTIONf_dihedral_angle_d14.0724324
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11C1493X-RAY DIFFRACTIONPOSITIONAL0.562
12G1493X-RAY DIFFRACTIONPOSITIONAL0.562
21C720X-RAY DIFFRACTIONPOSITIONAL0.549
22G720X-RAY DIFFRACTIONPOSITIONAL0.549
31D743X-RAY DIFFRACTIONPOSITIONAL0.629
32H743X-RAY DIFFRACTIONPOSITIONAL0.629
41A1660X-RAY DIFFRACTIONPOSITIONAL0.76
42E1660X-RAY DIFFRACTIONPOSITIONAL0.76
51A576X-RAY DIFFRACTIONPOSITIONAL0.01
52E576X-RAY DIFFRACTIONPOSITIONAL0.01
61B892X-RAY DIFFRACTIONPOSITIONAL0.011
62F892X-RAY DIFFRACTIONPOSITIONAL0.011
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2631-3.34470.29371250.22312609273497
3.3447-3.43510.27021340.19342612274698
3.4351-3.53610.24161430.19042648279199
3.5361-3.65020.28441210.18292607272899
3.6502-3.78060.25411500.19342606275699
3.7806-3.93190.24721590.1832642280199
3.9319-4.11080.2081560.172649280599
4.1108-4.32740.21851290.16682628275799
4.3274-4.59830.2071380.15632634277299
4.5983-4.95290.19611220.16112681280399
4.9529-5.45070.23371550.18162641279699
5.4507-6.23790.26851280.215427182846100
6.2379-7.85320.23921510.22172672282399
7.8532-47.05590.22521450.20322777292299
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)
12.6034-0.1967-0.81440.47630.00170.98840.10070.2623-0.0225-0.038-0.0632-0.11520.00490.1554-0.01220.2478-0.0084-0.09240.2974-0.02330.280715.8926-11.6083-42.327
22.14390.2594-1.38530.3943-0.20291.29080.12380.4668-0.12830.06690.02750.0696-0.1316-0.2909-0.09690.42290.018-0.00840.88350.20410.5277-17.2984-2.1554-80.7023
30.7464-0.0571-0.64621.0931-0.0831.2989-0.0582-0.1249-0.03070.14580.0225-0.0112-0.05030.09450.02960.3081-0.0095-0.15730.08150.01230.2987-21.2823-7.61760.2131
41.26090.3123-1.20740.8544-0.51151.2050.14450.0755-0.0658-0.0988-0.0897-0.3473-0.21890.041-0.06350.79260.00050.25110.91980.05680.714222.185818.6789-114.5873
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'C' ) or (chain 'D' )C0
2X-RAY DIFFRACTION2(chain 'H' ) or (chain 'G' )H0
3X-RAY DIFFRACTION3(chain 'A' ) or (chain 'B' )A0
4X-RAY DIFFRACTION4(chain 'E' ) or (chain 'F' )E0

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