RNA in 3D�How does it work?
RNA in 3D�How does it work?
What is RNA 3D structure?
How do we study RNA 3D structure?
Discovery
Design
GUUUUUAAACGGGUUUGCGGUGUAAGUGCAGCCCGUCUUACACCGUGCGGCACAGGCAGUAGUACUGAUGUCGUAUACAGGGCUUUUG
GUUUUUAAACGGGUUUGCGGUGUAAGUGCAGCCCGUCUUACACCGUGCGGCACAGGCAGUAGUACUGAUGUCGUAUACAGGGCUUUUG
Discovery & Design
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GCUCAAAUACACAAGAAAGGCAUUUCAAACGGUCUUCCGUCCGGGGAGUAAAAUUUCUUUUUAACCUUGAUGAUCAGAUAUGUUAUGGGUAGUGUGACUGCGGCGGACCCUGGGUUCUCGUAUUUCCACAUUCUCGCGACCGCUGGGAGCGUGGGACAACGAUUGAGUGCUCAGCCGCAGUACCUCAUCGUAUCGAGCUAGGUGGGUUAAACGUUCGUCUGCAGUAGAGUGUCAAUGGUAAGGGACCUAACGGUUCCCCCGUUCACCACAGGAAACUGGAUGUGGUAACGUACACGGUAAAAACAGUAAUGGGAGGCAACUCGAUGAGGAGCUGUAUGCGAAAGCCAGACUUCAGAACUGUGGUUGAGAAAGCGACCUUCGCUCGGAGUGCUGCCGUGGUCUAUUUUCCAUUGAGACGUCUGUAAUGCAAUGAGGGUGAUAGCAUGUUGCACAGGUAGACUCCCCCUAAUACUCGCGUCCUAUGUCAUUGACGGUGAAAGUGUGCUUGUGAUCACAGCUGAGUUAUCACGCGUCUGUAGUU�GUUUUUAAACGGGUUUGCGGUGUAAGUGCAGCCCGUCUUACACCGUGCGGCACAGGCAGUAGUACUGAUGUCGUAUACAGGGCUUUUG�AUACACAAUUCCUGCCUACACAAGGGAUUAGGUUGAAGAUUAAGACUGCUUAAGUUUAUUAUUAUGACUCUCGUACAAAACUCGCAGUGGUUGGCUUGUGAGAACUGGAUCAUUAACAUUAAAGUCGGCCCAAUAGCAUGACCCCAAGUUAAGGGGACCCACUAUCAGGCCUACCUGUAGAUACAUGCACGCUACAUAAACACGCACUUAGAGAACACGAGUCAAAUCCAAAGUGCUGGCACCAUACGCUGCAAUAAAGGCAACCGACAGGCCUAAUCGCGCAGACAAGCGAAACAGAGCAGACGCCGGCUUUGGUACCGGCUAAACUCUCAAGUUUAAAGCUCCCUACCGCCAUGUGAUGUGCGCGUUACUUUCAUAAAACCCGCCCAGUCCACCCAUAAACCGCUGCCCUCGUGUAGUCCCCGGGCACUUCGGUAAACAGAAAUACCCCUGCGAACC
GUUUUUAAACGGGUUUGCGGUGUAAGUGCAGCCCGUCUUACACCGUGCGGCACAGGCAGUAGUACUGAUGUCGUAUACAGGGCUUUUG
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Key takes away
2D links and constrains 3D – knowing 2D can help!!
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Levels of RNA shape
2D stacks in 3D
Base stacking can orient stacks
Pseudoknots!
More than just base pairs and stacks
How we solve 3D shapes and where you can find them
The number of 3D RNA shapes is unknown!
RNA in 3D
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Levels of RNA shape
2D stacks in 3D
Base stacking can orient stacks
Pseudoknots!
More than just base pairs and stacks
How we solve 3D shapes and where you can find them
The number of 3D RNA shapes is unknown!
RNA in 3D
8
Putting on our structural biologist lens
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Putting on our structural biologist lens
Red hat
Brown shoes
Blue eyes
Blue overalls
Black mustache
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Putting on our structural biologist lens
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Putting on our structural biologist lens
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Putting on our structural biologist lens
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Putting on our structural biologist lens
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Putting on our structural biologist lens
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The scene
= cell
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The scene
The cast
= cell
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Biology happens when “macromolecules” interact in a cell
The scene
= macromolecules
The cast
= cell
How does it work?
How can we stop it working?
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Recall our structural biology lens
Red hat
Brown shoes
Blue eyes
Blue overall
Black mustache
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Recall our structural biology lens
Red hat
Brown shoes
Blue eyes
Blue overall
Black mustache
GUUUUUAAACGGGUUUGCGGUGUAAGUGCAGCCCGUCUUACACCGUGCGGCACAGGCAGUAGUACUGAUGUCGUAUACAGGGCUUUUG
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Levels of RNA shape
2D stacks in 3D
Base stacking can orient stacks
Pseudoknots!
More than just base pairs and stacks
How we solve 3D shapes and where you can find them
The number of 3D RNA shapes is unknown!
RNA in 3D
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PDB: 1MT4
“Stem” or “Helix”
RNA 3D structure
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Levels of RNA shape
2D stacks in 3D
Base stacking can orient stacks
Pseudoknots!
More than just base pairs and stacks
How we solve 3D shapes and where you can find them
The number of 3D RNA shapes is unknown!
RNA in 3D
2nbx
27
Levels of RNA shape
2D stacks in 3D
Base stacking can orient stacks
Pseudoknots!
More than just base pairs and stacks
How we solve 3D shapes and where you can find them
The number of 3D RNA shapes is unknown!
RNA in 3D
29
Levels of RNA shape
2D stacks in 3D
Base stacking can orient stacks
Pseudoknots!
More than just base pairs and stacks
How we solve 3D shapes and where you can find them
The number of 3D RNA shapes is unknown!
RNA in 3D
30
Lot’s more RNA interactions that can constain 3D shape
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Don’t forget RNA is not alone!
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Levels of RNA shape
2D stacks in 3D
Base stacking can orient stacks
Pseudoknots!
More than just base pairs and stacks
How we solve 3D shapes and where you can find them
RNA in 3D
33
Expiremental methods for 3D structures
Looking at PDB entry
Multiple copies
Multiple models
Resolution
Validation
Change to relevant structure
Find PK
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The number of 3D RNA shapes is unknown!
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Science is a community effort
Chiu lab and S2C2:
Htet Khan
Yan (Amy) Liu
Greg Pintilie
Lily Xu
Xueting Zhou
Patrick Mitchell
Lydia-Marie Joubert
Chensong Zhang
Guan-chin Su
Gong-her Wu
Chih-ta Chien
Rahel Woldeyes
Yanyan Zhoa
Stefan Oliver
Corey Hecksel
Anton Jackson-Smith
David Chmielewski
Jesus Galaz-Montoya
Yee Ting Li
Patrick Pascual
Muyuan Chen
Peter Dahlberg
JoAnn Polizzi
Lisa Dunn
Michael Schmid
Wah Chiu
Das lab:
Ramya Rangan
Ved Topkar
Christian Cole
Grace Nye
Kailee Yoshimura
Philip Pham
Lisa Sharp
Rhiju Das
Kalli Kappel
Ivan (Vanya) Zheludev
Kaiming Zhang
Zhoaming Su
Andrew Watkins
Shashan Li
Wipapat Kladwang
Michael Palo
Hannah Wayment-Steele