Integrative Models of Molecular Machines: ChimeraX Demo

Tom Goddard
November 8, 2016
NIH site-visit

This ChimeraX demonstration exploring nuclear pore architecture will highlight recent developments related to Technology Research and Development (TR&D) projects 1 and 2, and two driving biological projects (DBP 1 and 3) and a collaborative project (CSP 1) described in the grant proposal.

Collaborations highlighted in this demo

Technologies highlighted in this demo

Related Core TR&D projects

Nuclear pore electron microscopy

Human nuclear pore EM, 23 Angstroms resolution (Beck lab). Ambient occlusion lighting shadows crevices. Simple lighting used by current generation visualization programs, hard to perceive depth. Ribosome size compared to nuclear pore.

Nuclear pore atomic model

  • 736 copies of 20 proteins, 4 million atoms composing about half the mass of nuclear pore fit to electron microscopy (Hoelz lab, 2016).
  • Hierarchical organization: inner and outer rings, spokes, and Y-complex. Asymmetric unit has 92 proteins.
  • Copies of Y-complex form scaffold for outer rings. Look in detail at integrative model of Y-complex.

Integrative hybrid model of Y-complex

  • 7 protein Y-complex (also called nup84) forms scaffold for nuclear pore outer rings.
  • Model built from many data sources:
    • 2 protein X-ray models
    • 5 comparative models, 16 template structures and sequence alignments
    • 300 chemical crosslinks resolved by mass-spectroscopy, 2 different linkers
    • 2D electron microscopy constraints model projection
    • Disordered regions modeled with beads representing 10 residue segements
  • Results
    • Coarse grain models, one or more residues per bead.
    • Ensemble of several thousand models, grouped in two clusters.
    • Localization density maps summarize variation in protein localization.
  • Data is saved in an mmCIF Integrated Hybrid Model format being developed in collaboration with RCSB for archiving at PDB.

Sequence alignments and templates for comparative models

Models from IHM file Template sequence alignments for one protein. Superimposed template models on comparative model.

Model ensemble from sampling and scoring restraints

  • Integrated Modeling Platform (IMP) software (Sali lab) computes ensembles of thousands of models scored based on restraints.
  • Two clusters for two conformations each of contain 1000 models.
  • Playing ensemble like dynamics trajectory shows variation within ensemble.
  • Localization density maps for each protein in ensemble also shows variability.

Crosslink analysis

Crosslink network shows most crosslinks are intra-protein.
Lengths of 286 crosslinks for best model
Length of one long crosslink for 1259 ensemble models.
Is violated crosslink satisfied in any ensemble model?

Pull in additional protein-protein interface data using BLAST web service

BLAST PDB nup133 sequence 3ikr aligned to nup84 (aka nup107) 3ikr (light blue) bridging nup84/nup133