Structure of the FANCI-FANCD2 Complex: Insights into the Fanconi Anemia DNA Repair Pathway
Woo Joo1,*,
Guozhou Xu2,*,
Nicole S. Persky1,3,*,
Agata Smogorzewska4,5,
Derek G. Rudge1,3,
Olga Buzovetsky1,3,
Stephen J. Elledge3,4, and
Nikola P. Pavletich1,3,
1 Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
2 Sloan-Kettering Division, Joan and Sanford I. Weill Graduate School of Medical Sciences, Cornell University, New York, NY 10065, USA.
3 Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.
4 Department of Genetics, Harvard Medical School, Division of Genetics, Brigham and Women’s Hospital, Boston, MA 02115, USA.
5 Laboratory of Genome Maintenance, The Rockefeller University, New York, NY 10065, USA.
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Fig. 1. The overall structure of the ID complex. (A) View looking into the interior of the troughlike structure. The FANCI (light blue) and FANCD2 (pink) solenoid (S1 to S4), HD1, and HD2 domains are labeled near their centers. The ubiquitination-site lysine side chains are shown in yellow and outlined in black. The FANCD2 Lys559 (K559) side chain is poorly ordered. (B) View orthogonal to (A) looking down the left end. Only the segments closest to the viewer are labeled. (C) View orthogonal to (A) looking down the right end.
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Fig. 2. The I-D interface. (A) Portion of the ID structure (gray) showing space-filling representations of side chains within intermolecular-contact distance. Boxes indicate clusters of contacts with their respective segments labeled. (B) Close-up view of the FANCD2 cap–solenoid 1 and FANCI solenoid 2–HD2 segments showing side chains from (A) (24). Green dotted lines indicate heteroatoms within hydrogen bonding distance and geometry. Top panel orientation is similar to (A), with the bottom panel rotated ~180° about the horizontal axis. The approximate boundaries of segments are labeled. (C) Reciprocal end of the interface formed by the FANCI cap–solenoid 1 and FANCD2 solenoid 2–HD2 segments.
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Fig. 3. Monoubiquitination and phosphorylation sites of the ID complex. (A) Surface representation of the solvent-accessible tunnel harboring the FANCI Lys522 (K522) ubiquitination site, looking from the interface center. The surface portion above the figure plane is clipped, and the surface interior is gray. The approximate distances from the lysine to the tunnel exits are indicated. The free ubiquitin (Ub) structure (green) was manually docked with its tail approaching from either the "top" or "bottom" exits of the tunnel. (B) Surface representation of the FANCD2 Lys559 tunnel. As in (A), two ubiquitin molecules were docked approaching from either tunnel exit. (C) The FANCI Ser555, Thr558, and Thr564 phosphorylation sites map to an HD2 segment that undergoes a conformational change between free FANCI (purple) and FANCD2-bound FANCI (light blue). In free FANCI, the three sites map to a disordered loop (dotted purple line). FANCD2 is shown in pink. (D) The hydrogen bond network centered on the phosphorylation sites, also showing neighboring residues that may interact with the phosphorylated residues. Orange dotted lines denote heteroatoms within hydrogen bonding distance.
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Fig. 4. Electron-density map of the Y DNA-FANCI crystals reveals bound dsDNA and ssDNA segments. (A) 7.8 Å resolution Fo map, contoured at 1.2 , calculated with molecular-replacement phases that were improved by threefold noncrystallographic symmetry and multicrystal averaging (Fo, observed structure factors). The manually positioned model of ideal B-type DNA is shown in cartoon representation (green), and the tubular density of ssDNA is marked by a black line. Orientation is similar to that shown in Fig. 1A. (B) View looking down the blunt end of the Y DNA. (C) Electrostatic potential of the ID molecular surface showing the dsDNA cartoon and ssDNA path (yellow spheres) from the Y DNA–FANCI maps, as well as their models on FANCD2, positioned by superimposing solenoids 3 and 4 of the two paralogs. The electrostatic potential was calculated with Adaptive Poisson-Boltzmann Solver (APBS) (25) and illustrated (–8 to +8 kT) with PyMOL (26).
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