TABLE 1:

Restraints used for integrative structure modeling of the SPB core.

Restraints	Restrained feature	Functional form and parameters	Ref.a
Bayesian FRET	Distances between termini of SPB proteins and Spc110 coiled-coil	See Bonomi et al., 2014	1
Cryo-EM density	Position of Spc42	See Velazquez-Muriel et al., 2012; Materials and Methods	3
Unit-cell size and shape	Dimensions of the rhomboid primitive unit cell	Uniform distribution with bounds 9 to 13.5 nm	3
Planar Spc42	Position of Spc42	Harmonic bound on the z-axis distance between every pair of N-terminal beads (and separately, every pair of C-terminal beads) of Spc42 copies, with mean 0 nm and spring constant 1 kBT	3, 6
Coiled-coil angle	Orientations of coiled-coil domains of Spc42, Spc110, and Cnm67	Harmonic upper bound on the tilt angle between the coiled-coil domain and the z-axis, with threshold of 0° for Spc110 and Cnm67 and 20° for Spc42; spring constant 100 kBT	3, 6
CP-layer localization	Position of CP layer protein domains	Likelihood: Uniform distribution with bounds 0 and z min nm Prior: Uniform distribution for z min from −28.6 to −30 nm	2, 3, 4
SAXS shape	Structure of the Spc110-Cmd1 dimer	Harmonic bound on the minimum distance between all pairs of beads representing calmodulins in the unit cell Harmonic bound on the z-axis distance between beads representing residue 900 of Spc110 Same as (2) between beads representing residue 940 of Spc110 Mean 0 nm and spring constant 1 kBT in all cases.	1
Distance restraints for unstructured domains	Length of Spc29 distance of C-terminus of Spc42 from its coiled-coil	Likelihood: Lognormal distribution with mean d and width 0.001 Prior: Uniform distribution for d between 13-17.3 nm (Spc29) and 0–6.44 nm (Spc42)	1
Yeast two-hybrid	Proximities between interacting SPB protein domains	Harmonic bounds on the minimum distances between all pairs of the beads representing the two interacting domains, with mean 0 nm and spring constant of 1 kBT	4, 5
Cnm67-Spc42 binding site	Proximity between Cnm67 C-terminus and Spc42	Harmonic bound on the minimum distance between all pairs of beads representing Spc42 and beads corresponding to residues 503–514 of Cnm67 with mean 0 nm and spring constant of 1 kBT	8
Excluded volume	Distances between SPB components	Harmonic lower bound with mean 0 nm, spring constant 0.1 kBT	1, 7
Sequence connectivity	Distances between consecutive beads of SPB components and between SPB components and FPs	Harmonic bound on the surface distance between consecutive beads, with mean 0 nm, spring constant 1 kBT	1, 7

^aReferences are as follows: 1. this study; 2. Rout and Kilmartin, 1990; 3. Bullitt et al., 1997; 4. Adams and Kilmartin, 1999; 5. Elliott et al., 1999; 6. O’Toole et al., 1999; 7. Alber, 2007a.