6BGA

2B4 I-Ek TCR-MHC complex with affinity-enhancing Velcro peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.307 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Stress-testing the relationship between T cell receptor/peptide-MHC affinity and cross-reactivity using peptide velcro.

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.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: E7369-E7378

  • DOI: 10.1073/pnas.1802746115

  • PubMed Abstract: 
  • T cell receptors (TCRs) bind to peptide-major histocompatibility complex (pMHC) with low affinity ( <i>K </i> <sub>d </sub> ∼ μM), which is generally assumed to facilitate cross-reactive TCR "scanning" of ligands. To understand the relationship betwe ...

    T cell receptors (TCRs) bind to peptide-major histocompatibility complex (pMHC) with low affinity ( K d ∼ μM), which is generally assumed to facilitate cross-reactive TCR "scanning" of ligands. To understand the relationship between TCR/pMHC affinity and cross-reactivity, we sought to engineer an additional weak interaction, termed "velcro," between the TCR and pMHC to probe the specificities of TCRs at relatively low and high affinities. This additional interaction was generated through an eight-amino acid peptide library covalently linked to the N terminus of the MHC-bound peptide. Velcro was selected through an affinity-based isolation and was subsequently shown to enhance the cognate TCR/pMHC affinity in a peptide-dependent manner by ∼10-fold. This was sufficient to convert a nonstimulatory ultra-low-affinity ligand into a stimulatory ligand. An X-ray crystallographic structure revealed how velcro interacts with the TCR. To probe TCR cross-reactivity, we screened TCRs against yeast-displayed pMHC libraries with and without velcro, and found that the peptide cross-reactivity profiles of low-affinity ( K d > 100 μM) and high-affinity ( K d ∼ μM) TCR/pMHC interactions are remarkably similar. The conservation of recognition of the TCR for pMHC across affinities reveals the nature of low-affinity ligands for which there are important biological functions and has implications for understanding the specificities of affinity-matured TCRs.


    Organizational Affiliation

    Sprint Bioscience , 141 57 Huddinge , Sweden.,Infectious Diseases Discovery , GlaxoSmithKline , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States.,College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, People's Republic of China. Electronic address: zhouwh@nankai.edu.cn.,Antibody and Vaccine Group, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK.,Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305.,Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH 44106, USA.,Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, Grenoble, France.,Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore.,Pohang Accelerator Laboratory, Pohang, Gyeongbuk, Republic of Korea.,Protein Core Facility, University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK.,European Synchrotron Radiation Facility, 38043 Grenoble, France.,Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom. Electronic address: stuart.conway@chem.ox.ac.uk.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305; kcgarcia@stanford.edu.,Scripps Research, United States.,School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom.,Charnwood Molecular , Loughborough LE11 5DA , U.K.,Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom.,Neuroscience, IMED Biotech Unit , AstraZeneca , Cambridge CB21 6GH , U.K.,Department of Hematology and Oncology, Center for Cancer Immune Therapy, Herlev Hospital, University of Copenhagen, Herlev, Denmark.,Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K.,Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.,Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas, 66047.,The Gut Health and Food Safety Programme, Quadram Bioscience Institute, NR4 7UA Norwich, United Kingdom.,Epigenetic Regulation of Chromatin Function Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.,Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Pohang Accelerator Laboratory, Pohang, Gyeongbuk, Republic of Korea. jaehyun.park@postech.ac.kr.,Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, I-40127 Bologna, Italy. stefano.ciurli@unibo.it.,Polgenix Inc., Cleveland, OH 44106, USA.,The Gut Health and Food Safety Programme, Quadram Bioscience Institute, NR4 7UA Norwich, United Kingdom; c.dong@uea.ac.uk nathalie.juge@quadram.ac.uk.,Departments of Biophysics, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, 75390.,BioMedical Research Centre, University of East Anglia, NR4 7TJ Norwich, United Kingdom; c.dong@uea.ac.uk nathalie.juge@quadram.ac.uk.,Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.,Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.,Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37232-0146 , United States.,College of Life Sciences, College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, People's Republic of China.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, 112, Taiwan.,BioMedical Research Centre, University of East Anglia, NR4 7TJ Norwich, United Kingdom.,Department of Biochemistry, National University of Singapore, Singapore.,Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan.,Immunocore LTD, Oxford, United Kingdom.,School of Pharmacy, University of East Anglia, NR4 7TJ Norwich, United Kingdom.,Antibody and Vaccine Group, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK.,Antibody and Vaccine Group, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK. Electronic address: ann.white@ucb.com.,Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan tendo@cc.kyoto-su.ac.jp.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305.,Max Planck Institute of Biophysics, Frankfurt am Main, Germany.,Japan Science and Technology Agency/Core Research for Evolutional Science and Technology, Nagoya University, Nagoya, Japan.,College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, People's Republic of China.,Cardiovascular and Metabolic Diseases, IMED Biotech Unit , AstraZeneca , 141 57 Huddinge , Sweden.,Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.,Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7LD, U.K.,Department of Molecular Biology and Biochemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada.,Boehringer Ingelheim RCV GmbH & Co. KG , Doktor-Boehringer-Gasse 5-11 , 1120 Vienna , Austria.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan.,CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, United Kingdom.,Department of Chemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada . Email: dvocadlo@sfu.ca.,Institute of Biochemistry, ETH Zürich, Zürich, Switzerland.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305.,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China.,School of Chemistry and Biochemistry , The University of Western Australia (M313) , 35 Stirling Highway , Crawley , WA 6009 , Australia.,Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.,Department of Food Science, National (Taiwan) Ocean University, Keelung, 202, Taiwan.,Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS, 66045.,Hamburg Centre for Ultrafast Imaging & Institute for Nanostructure and Solid State Physics, University of Hamburg, 20146 Hamburg, Germany.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 3TA, United Kingdom.,Department of Biology, Faculty of Science, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China. Electronic address: tangrp99@iccas.ac.cn.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore.,Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7LD, UK.,Discovery Sciences, IMED Biotech Unit , AstraZeneca , S-43183 Mölndal , Sweden.,Japan Science and Technology Agency/Core Research for Evolutional Science and Technology, Kyoto Sangyo University, Kyoto, Japan.,Discovery Safety, Drug Safety and Metabolism, IMED Biotech Unit , AstraZeneca , Waltham , Massachusetts 02451 , United States.,Medicines Discovery Institute , Cardiff University , Main Building, Park Place , Cardiff CF10 3AT , United Kingdom.,Division of Biotechnology, Korea University, Seoul, Republic of Korea. structures@korea.ac.kr.,Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China. Electronic address: zhmin07@ahu.edu.cn.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore.,College of Life Sciences, Tianjin University, Tianjin, 300071, People's Republic of China.,Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom.,Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan. Electronic address: muto.tsuyoshi.zu@daiichisankyo.co.jp.,Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany.,Biotechnology Center, National Chung Hsing University, Taichung City, 402, Taiwan.,Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom; Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.,Institute of Life Science and Natural Resources, Korea University, Seoul, Republic of Korea. structures@korea.ac.kr.,Research Center for Materials Science, Nagoya University, Nagoya, Japan.,Botnar Research Centre, Oxford Biomedical Research Unit, Oxford OX3 7LD, U.K.,Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage Hertfordshire SG1 2NY, United Kingdom.,Department of Life Science, POSTECH, Pohang, Gyeongbuk, Republic of Korea.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.,Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan.,Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, 66045.,Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, United States; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, United States; Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109-2216, United States.,York Structural Biology Laboratory , Department of Chemistry , The University of York , YO10 5DD , UK.,Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047.,VA Tennessee Valley Healthcare System , 1310 24th Avenue S. , Nashville , Tennessee 37212 , United States.,Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany.,University of Puerto Rico at Humacao, Humacao, PR, USA.,Departments of Microbiology, 5323 Harry Hines Blvd., Dallas, Texas, 75390.,Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata, Japan.,Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506.,Molecular Medicine, Scripps Research, United States.,National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, NY 11973, USA.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, OX3 7FZ, UK.,T-Cell Modulation Group, Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom.,Research Service, Louis Stokes Cleveland VA Medical Center, Cleveland, OH 44106, USA.,IMCA-CAT, Hauptman-Woodward Medical Research Institute, Argonne, Illinois, 60439.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Department of Biological and Food Engineering, Bozhou University, 2266 Tangwang Road, Bozhou, Anhui, China.,Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K.,Oncology Chemistry, IMED Biotech Unit , AstraZeneca , Cambridge CB4 0WG , U.K.,Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan. Electronic address: murafuji.hidenobu.bj@daiichisankyo.co.jp.,Department of Biochemistry, National Centre of Competence in Research Chemical Biology, University of Geneva, Geneva, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
H-2 class II histocompatibility antigen, E-K alpha chain
A
204Mus musculusMutation(s): 0 
Find proteins for P04224 (Mus musculus)
Go to UniProtKB:  P04224
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
2B4 peptide,MHC I-Ek B chain
B
233N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
T cell receptor 2B4 alpha chain
C
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
T cell receptor 2B4 beta chain
D
255N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Velcro peptide
E
15N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
B, C
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.307 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • Space Group: I 1 2 1
  • Diffraction Data DOI: 
    10.15785/SBGRID/515 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 79.107α = 90.00
b = 58.851β = 91.71
c = 224.619γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI103867
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI045757
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI057229

Revision History 

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2018-08-01
    Type: Data collection, Database references
  • Version 1.2: 2018-08-08
    Type: Data collection, Database references
  • Version 1.3: 2019-02-20
    Type: Author supporting evidence, Data collection