Overview of Protein Folds in the Immune System

Peter D. Sun1, Jeffrey C. Boyington1

1 National Institute of Allergy and Infectious Diseases, NIH, Rockville, Maryland
Publication Name:  Current Protocols in Immunology
Unit Number:  Appendix 1N
DOI:  10.1002/0471142735.ima01ns44
Online Posting Date:  November, 2001
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The rapid advancement of X‐ray crystallography and nuclear magnetic resonance techniques in recent years has resulted in the solution of macromolecular structures at an unprecedented rate. This review aims at providing a comprehensive description of structures and folds related to the function of the immune system. Focus is placed on immunologically relevant proteins such as immunoreceptors and major histocompatibility complexes. Information is also provided regarding protein structure data banks.

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Table of Contents

  • Access to the Protein Structural Data Bank
  • Immunoglobulins and the Immunoglobulin‐Like Fold
  • The MHC Peptide‐Binding Fold
  • Proteasome
  • Proteins Involved in Signal Transductions: Cytokines
  • Proteins Involved in Signal Transduction: Cell Surface Receptors
  • Signal Transduction: Modular Domains
  • Signal Transduction: Protein Kinases and Phosphatases
  • Proteins in the Complement System
  • DNA‐Binding Proteins
  • Antimicrobial Peptides: Defensins
  • Literature Cited
  • Figures
  • Tables
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  •   FigureFigure a0.1N.1 Tertiary and secondary structures of immunoglobulin fold. The coordinates used for the ribbon diagrams are taken from the PDB entries indicated. (A) V (PDB entry 3hfl), (B) C1 (PDB entry 3hfl), (C) C2 (PBD entry 1hnf) and C2(Fn) (PDB entry 1fna), (D) I type (PDB entry 1tlk), and (E) E type (PDB entry 1gof).
  •   FigureFigure a0.1N.2 Ribbon diagram of an intact mouse IgG2a (PDB entry 1igt). The heavy and light chains are shown in blue and green, respectively. The CDR loops are shown in red. The glycosylation residues associated with the Fc region are also shown.
  •   FigureFigure a0.1N.3 (A) Structure of a B7 TCR in complex with HLA‐A2 and Tax peptide (PDB entry 1bd2). The α and β chains of the TCR are shown in red and orange, respectively. HLA‐A2 heavy chain and β2m are shown in green and blue, respectively, with the bound Tax peptide in magenta. (B) The structure of a human class I HLA‐A2 molecule in complex with CD8 αα homodimer. The class I heavy chain is in green, β2m is in blue, the bound peptide is shown in magenta, and the CD8 molecule is shown in red (PDB entry 1akj). (C) The structure of a human CD4 (PDB entry 1wio). (D) Killer immunoglobulin receptor 2DL2 (PDB entry 2dl2). (E) Structure of the human growth hormone receptor (in blue) in complex with growth hormone (in red) (PDB entry 3hhr). (F) Crystal structures of the N‐terminal two domains of VCAM‐1 (PDB entry 1vca) (G) ICAM‐2 (PDB entry 1zxq). The integrin binding domain is colored in yellow.
  •   FigureFigure a0.1N.4 (A) Ribbon diagram of the peptide binding domain of a class I MHC molecule in complex with a peptide (PDB entry 2clr). (B) Ribbon diagram of the peptide binding domain of a class II MHC molecule in complex with a peptide (PDB entry 1dlh). (C) Molecular surface shows the binding pockets located in the class I MHC peptide bindi ng groove (PDB entry 2clr). The peptide positions are labeled.
  •   FigureFigure a0.1N.5 The 20S proteasome from yeast (PDB entry 1ryp). (A) Side view of the barrel‐shaped complex. The α and β subunits are colored red (or darker gray) and green (or lighter gray), respectively. (B) View of the complex looking down the axis of the barrel. (C) The N‐terminal nucleophile (Ntn) fold of a single β subunit. The catalytic threonine is shown as a ball and stick model.
  •   FigureFigure a0.1N.6 The structure of (A) a long‐chain helical cytokine, G‐CSF (PDB entry 1rhg), (B) a short chain helical cytokine, IL‐4 (PDB entry 1rcb), and (C) interferon γ (PDB entry 1rfb). The two monomers of interferon γ are shown in red and purple. (D) Connectivity between helices in four‐helix bundle cytokines. The “up helices” are drawn in white and the “down helices” are in black. (E) Connectivity between helices of IFN‐γ. The block shaded regions correspond to the four‐helix bundles.
  •   FigureFigure a0.1N.7 (A) The structure of a human IL1β: a member of the β trefoil fold. (PDB entry 1hib). (B,C) Crystal structure of a human transforming growth factor‐β2 (PDB entry 2tgi). In panel B, the four strands that define the cysteine knot fold are numbered. The six knotted cysteines are shown in ball and stick model (the sulfur atoms are lighter colored). (D) Structure of IL‐8 (PDB entry 1il8). (E) The structure of a human MIP‐1β (PDB entry 1hum).
  •   FigureFigure a0.1N.8 (A) Trimer of tumor necrosis factor (in red) in complex of TNF receptor (in blue). (B) Trimer of TNF. (C) A monomer of TNF receptor. The coordinates are from PDB entry 1tnr.
  •   FigureFigure a0.1N.9 The integrin I‐domain of LFA‐1 (PDB entry 1lfa).
  •   FigureFigure a0.1N.10 C‐type lectin structures. (A) Structure of the C‐type lectin fold of rat mannose binding protein‐A (PDB entry 1rtm). The β strands and α helices are numbered according to their order in the structure. The Ca2+ ions are represented by numbered magenta balls. Disulfide bonds are represented by an orange ball and stick model. (B) Trimeric structure of mannose binding protein‐A including the N‐terminal triple α‐helical coiled coil (PDB entry 1rtm). Each monomer is colored separately and the Ca2+ ions are represented by magenta balls. (C) The C‐type lectin domain of CD94 subunit of the CD94/NKG2 NK cell receptor (PDB entry 1b6e). Residues 102 to 112 corresponding to the second helix of the canonical C‐type lectin fold are colored purple. The β strands and α helices are numbered according to their order in the structure. Disulfide bonds are represented by an orange ball and stick model. (D) The CD94 homodimer (PDB entry 1b6e). Residues 102 to 112 are colored purple. Disulfide bonds are represented by an orange ball and stick model.
  •   FigureFigure a0.1N.11 (A) Ribbon diagram of staphylococcal enterotoxin B (SEB) (PDB entry 1se3). (B) Complex of a human MHC class II antigen HLA‐DR1 (in dark gray) with SEB (lighter gray) (PDB entry 1seb). (C) Complex of a T cell receptor β chain 14.3.d VβCβ (lighter gray) with SEC3 superantigen (darker gray) (PDB entry 1jck).
  •   FigureFigure a0.1N.12 Structures of (A) SH2 domain in complex with a phosphotyrosine peptide (PDB entry 1sha), (B) SH3 (PDB entry 1csk), and (C) PH (PDB entry 1dyn) domains.
  •   FigureFigure a0.1N.13 Protein kinase and protein phosphatase structures. (A) The structure of the inactive form of hematopoietic cell kinase of the Src family of protein kinases (PDB entry 1ad5). The SH3 and SH2 domains are colored blue‐green and magenta, respectively, and the catalytic domain is colored green and red. The phosphorylated tyrosine 572 is shown by a blue ball and stick model. (B) Low‐activity form of MAP kinase P38 from mouse (PDB entry 1p38). The MAP kinase insertion and the C‐terminal extension are shown in magenta. (C) Human SHP‐2 tyrosine kinase (PDB entry 2shp). The N‐ and C‐terminal SH2 domains are magenta and blue‐green, respectively, and the catalytic domain is colored green and red. (D) The protein serine/threonine phosphatase calcineurin (PDB entry 1aui). The calcineurin A subunit including the phosphatase domain and the calcineurin B binding helix (BBH) are shown in green and red. The calcineurin B subunit is colored blue‐green. Ca2+ cations bound to calcineurin B and the Zn2+ and Fe3+ cations bound at the active site of the phosphatase domain are represented by magenta balls. Residues 469 to 486 of the autoinhibitory element are colored blue.
  •   FigureFigure a0.1N.14 Ribbon representation of protein folds in the complement system. (A) C3d (residues 996 to 1287) (PDB entry 1c3d). Left side shows the view down the barrel axis; the right side shows the side view of the barrel. The α helices are numbered 1 to 12 and the N‐terminal 310 helix is labeled T1. The residues critical for covalent attachment to the pathogen surface, His 133, Gln 20 and Ala 17 (Cys residue in the wild‐type protein), are represented by a ball and stick model. (B) C5a (PDB entry 1kjs).The α helices are numbered from 1 to 5. (C) Complement factor D serine protease (PDB entry 1dsu). Catalytic residues His 57, Asp 102, and Ser 195 are represented by a ball and stick model. (D) Complement regulatory protein CD59 (residues 1 to 70) (PDB entry 1cdq). The β strands are numbered according to their order in the protein sequence. (E) CCP modules 15 and 16 from complement factor H (PDB entry 1hfh). The β strands for each separate CCP module are numbered according to their order in the protein sequence.
  •   FigureFigure a0.1N.15 Ribbon models of DNA‐binding proteins of immunological relevance. (A) NF‐κB p50/p50 homodimer bound to DNA (PDB entry 1svc). The N‐ and C‐terminal domains are shown in red and green, respectively. The Rel family insertion region is magenta, and the DNA in the center is represented by a blue stick model. (B) IκB ankyrin repeat domain (magenta) bound to the N‐ and C‐terminal domains of NF‐κB p65 (green) and the C‐terminal domain of NF‐κB p50 (blue), (PDB entry 1ikn). Ankyrin repeats are numbered from 1 to 6. Dotted lines indicate loops that are missing in the model. (C) Fos/Jun heterodimer (green and red, respectively) bound to DNA (PDB entry 1fos). DNA is shown by a blue stick model. (D) NFAT fragment (magenta) and Fos/Jun heterodimer (green and red respectively) bound to DNA (PDB entry 1a02). DNA is shown by a blue stick model. (E) STAT‐1 homodimer bound to DNA (PDB entry 1bf5). The coiled‐coil domain, DNA‐binding domain, linker domain, and SH2 domain are colored blue, red, green, and magenta, respectively. Dotted lines indicate loops that are missing in the crystal structure. DNA and phosphotyrosine 701 (see SH2 domain) are both represented by blue stick models. (F) Homodimer of the N‐terminal interaction domain of STAT‐4 (PDB entry 1bgf). (G) The DNA‐binding domain of IRF‐1 bound to DNA (PDB entry 1if1). β strands and α helices are green and red, respectively, and numbered according to their order in the amino acid sequence. DNA is shown by a blue stick model.
  •   FigureFigure a0.1N.16 (A) α‐defensin (PDB entry 1dfn); (B) β‐defensin (PDB entry 1bnb); (C) plant defensin (PDB entry 1ayj); (D) insect defensin (PDB entry 1ica).


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