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- PDB-6bga: 2B4 I-Ek TCR-MHC complex with affinity-enhancing Velcro peptide -

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Basic information

Entry
Database: PDB / ID: 6bga
Title2B4 I-Ek TCR-MHC complex with affinity-enhancing Velcro peptide
Components
  • (T cell receptor 2B4 ...) x 2
  • 2B4 peptide,MHC I-Ek B chain
  • H-2 class II histocompatibility antigen, E-K alpha chain
  • Velcro peptide
KeywordsIMMUNE SYSTEM / Complex / engineered peptide
Function / homology
Function and homology information


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 / lysosomal 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
PHOSPHATE ION / H-2 class II histocompatibility antigen, E-K alpha chain / MHC class II antigen IEk-beta
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.307 Å
AuthorsGee, M.H. / Sibener, L.V. / Birnbaum, M.E. / Jude, K.M. / Garcia, K.C.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI103867 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI045757 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI057229 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Stress-testing the relationship between T cell receptor/peptide-MHC affinity and cross-reactivity using peptide velcro.
Authors: Gee, M.H. / Sibener, L.V. / Birnbaum, M.E. / Jude, K.M. / Yang, X. / Fernandes, R.A. / Mendoza, J.L. / Glassman, C.R. / Garcia, K.C.
History
DepositionOct 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Aug 8, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: H-2 class II histocompatibility antigen, E-K alpha chain
B: 2B4 peptide,MHC I-Ek B chain
C: T cell receptor 2B4 alpha chain
D: T cell receptor 2B4 beta chain
E: Velcro peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,08413
Polymers104,6255
Non-polymers1,4588
Water7,782432
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.107, 58.851, 224.619
Angle α, β, γ (deg.)90.00, 91.71, 90.00
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11B-509-

HOH

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein H-2 class II histocompatibility antigen, E-K alpha chain


Mass: 23618.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P04224
#2: Protein 2B4 peptide,MHC I-Ek B chain


Mass: 26586.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: H2-Eb1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q31163

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T cell receptor 2B4 ... , 2 types, 2 molecules CD

#3: Protein T cell receptor 2B4 alpha chain


Mass: 24104.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper)
#4: Protein T cell receptor 2B4 beta chain


Mass: 29007.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper)

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Protein/peptide , 1 types, 1 molecules E

#5: Protein/peptide Velcro peptide


Mass: 1308.354 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Trichoplusia ni (cabbage looper)

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Sugars , 2 types, 4 molecules

#6: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 436 molecules

#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.5 Å3/Da / Density % sol: 50.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 18-20% PEG 3350, 20 mM Na/K phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.307→50 Å / Num. obs: 44671 / % possible obs: 97.24 % / Redundancy: 3.6 % / Biso Wilson estimate: 34.38 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.1416 / Rpim(I) all: 0.08509 / Rrim(I) all: 0.1658 / Net I/σ(I): 8.52
Reflection shellResolution: 2.307→2.39 Å / Redundancy: 3.56 % / Rmerge(I) obs: 1.043 / Mean I/σ(I) obs: 1.19 / Num. unique obs: 4264 / CC1/2: 0.481 / Rpim(I) all: 0.6306 / Rrim(I) all: 1.223 / % possible all: 93.69

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSJanuary 10, 2014data reduction
Aimless0.1.26data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P2O

4p2o


Resolution: 2.307→47.21 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.8
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2163 4.84 %Random
Rwork0.1924 ---
obs0.1946 44646 97.26 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.307→47.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6699 0 93 432 7224
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026981
X-RAY DIFFRACTIONf_angle_d0.539496
X-RAY DIFFRACTIONf_dihedral_angle_d14.7614156
X-RAY DIFFRACTIONf_chiral_restr0.0441034
X-RAY DIFFRACTIONf_plane_restr0.0041242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3071-2.36070.37361290.3112679X-RAY DIFFRACTION92
2.3607-2.41980.33861310.29082823X-RAY DIFFRACTION98
2.4198-2.48520.34141560.2742810X-RAY DIFFRACTION98
2.4852-2.55830.33951330.26122718X-RAY DIFFRACTION94
2.5583-2.64090.29621480.23842842X-RAY DIFFRACTION98
2.6409-2.73520.28161420.23732847X-RAY DIFFRACTION98
2.7352-2.84470.28781430.22962835X-RAY DIFFRACTION98
2.8447-2.97420.26351680.22452841X-RAY DIFFRACTION98
2.9742-3.1310.2561120.20552786X-RAY DIFFRACTION96
3.131-3.32710.22311720.18822825X-RAY DIFFRACTION98
3.3271-3.58390.22381580.18022876X-RAY DIFFRACTION98
3.5839-3.94440.21781330.16312907X-RAY DIFFRACTION99
3.9444-4.51480.19231360.14072839X-RAY DIFFRACTION97
4.5148-5.68660.15961560.14482908X-RAY DIFFRACTION99
5.6866-47.22020.23021460.18372947X-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)
18.45772.0191-3.69663.1394-2.07073.0307-0.4244-1.5024-0.48450.60310.15440.02860.79620.78130.27530.27110.12620.05490.5013-0.02460.2991-24.8071-16.44424.3643
25.0246-4.81172.97675.8301-3.62095.13650.070.41460.06790.2787-0.2814-0.3062-0.3010.45190.21690.2598-0.0708-0.00920.22760.00120.2648-28.32892.2229-14.8387
33.349-1.02241.41641.0908-0.18292.4557-0.05840.24030.0742-0.04140.047-0.14210.05420.41120.02470.1945-0.01370.03540.237-0.00030.2467-22.794-2.4972-16.917
43.77220.75072.46110.71370.57732.3684-0.222-0.19460.6146-0.12220.01740.1533-0.1941-0.21110.20480.26560.0193-0.03210.2715-0.01720.3665-21.964613.7874-2.8953
53.30.9110.06522.4660.72531.3138-0.15330.02110.6888-0.0285-0.00080.2257-0.22230.0790.14820.26550.009-0.05370.2721-0.0070.371-17.656115.3595-1.6237
65.7576-3.9456-1.37564.79721.22633.23250.13250.2649-0.1277-0.1007-0.21220.28780.1911-0.15140.04040.1868-0.0690.04080.16450.04830.2089-37.7437-3.2415-18.6616
71.43730.14270.33240.726-0.2521.3305-0.0652-0.0654-0.05260.10790.05090.05350.1394-0.0150.02250.21780.02340.03140.2192-0.01220.2323-36.4806-7.7139-10.7342
82.5778-0.66320.28811.99720.74546.337-0.0013-0.54660.12720.56260.1462-0.19570.1537-0.0798-0.1240.31430.015-0.05440.4097-0.03440.2884-14.1215-0.383618.993
91.48761.05340.56623.35811.47562.6097-0.04470.1355-0.1547-0.04590.1596-0.00950.34860.0719-0.12540.3320.04490.00970.282-0.00720.2712-35.4502-30.6355-30.9377
107.41190.9429-1.78967.9711-0.04032.3365-0.09160.4438-0.4622-1.05740.14270.00841.3310.24620.07670.73750.0678-0.05260.4056-0.12920.435-43.1769-47.882-61.7421
110.88652.7169-2.58268.3116-8.01188.4795-0.6803-0.3391-0.71310.3657-0.0676-1.530.38171.28240.74030.7920.4905-0.03261.2031-0.11350.8266-27.2804-44.2816-63.9869
128.52861.2264-3.31673.76271.32827.92920.13330.39060.271-0.62620.19350.00721.00260.2086-0.39370.69730.11110.02390.2730.01150.4085-42.1716-43.3139-58.1305
133.4353.1262.74646.6079-0.96625.26520.64770.2336-0.7879-1.1096-0.3142-0.87880.03340.1117-0.37431.04390.16590.06230.7032-0.12120.6618-37.483-54.8942-62.7308
143.1034-1.59751.56525.59512.31633.9027-0.4370.1194-0.7003-0.5488-0.08970.14280.18130.42310.23080.3082-0.068-0.04960.370.05830.1349-36.6272-14.3216-50.2878
152.02870.4876-0.88921.06930.71464.6921-0.15790.3535-0.021-0.19480.1811-0.0708-0.15050.2733-0.03690.2316-0.00870.02020.31050.01520.2225-32.2555-11.174-42.4401
161.74731.4499-0.12835.2144-0.35853.7906-0.1480.4321-0.2329-0.34660.4660.09290.48170.155-0.27860.37930.0176-0.05740.3619-0.05380.2782-44.8238-34.1835-62.1284
175.84993.55552.16247.3419-2.06863.00310.59111.27281.8369-1.71070.3042-0.8325-1.97681.092-0.89011.0958-0.32190.2490.98050.1030.6849-31.8402-10.7151-69.3307
184.56453.08771.44116.9960.75943.6533-0.47540.77340.2856-1.04140.74250.61120.48070.0829-0.29330.6482-0.051-0.10770.54220.09840.2875-46.5232-27.5313-69.6861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:5)
2X-RAY DIFFRACTION2(chain A and resid 6:25)
3X-RAY DIFFRACTION3(chain A and resid 26:74)
4X-RAY DIFFRACTION4(chain A and resid 75:126)
5X-RAY DIFFRACTION5(chain A and resid 127:182)
6X-RAY DIFFRACTION6(chain B and resid -26:-2)
7X-RAY DIFFRACTION7(chain B and resid -1:93)
8X-RAY DIFFRACTION8(chain B and resid 94:190)
9X-RAY DIFFRACTION9(chain C and resid 2:112)
10X-RAY DIFFRACTION10(chain C and resid 113:144)
11X-RAY DIFFRACTION11(chain C and resid 145:151)
12X-RAY DIFFRACTION12(chain C and resid 152:180)
13X-RAY DIFFRACTION13(chain C and resid 181:200)
14X-RAY DIFFRACTION14(chain D and resid 0:19)
15X-RAY DIFFRACTION15(chain D and resid 20:119)
16X-RAY DIFFRACTION16(chain D and resid 120:216)
17X-RAY DIFFRACTION17(chain D and resid 217:226)
18X-RAY DIFFRACTION18(chain D and resid 227:244)

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