Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Helical - H  (3D View)
Global Stoichiometry: Hetero 12-mer - A6B6 Pseudo Symmetry: Helical - H  (3D View)
Pseudo Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 606.62 kDa 
• Atom Count: 40506 
• Residue Count: 5124 
• Unique protein chains: 2

6DPV

Undecorated GDP microtubule

• DOI: 10.2210/pdb6DPV/pdb
• EMDataResource: EMD-7974

• Classification: CELL CYCLE
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2018-06-09 Released: 2018-07-04 
• Deposition Author(s): Zhang, R., Nogales, E.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States), Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

Literature

Separating the effects of nucleotide and EB binding on microtubule structure.

Zhang, R., LaFrance, B., Nogales, E.

(2018) Proc Natl Acad Sci U S A 115: E6191-E6200

• PubMed: 29915050 
• DOI: 10.1073/pnas.1802637115
• Primary Citation of Related Structures:  
  6DPU, 6DPW, 6DPV


• PubMed Abstract: 
  

Microtubules (MTs) are polymers assembled from αβ-tubulin heterodimers that display the hallmark behavior of dynamic instability. MT dynamics are driven by GTP hydrolysis within the MT lattice, and are highly regulated by a number of MT-associated proteins (MAPs). How MAPs affect MTs is still not fully understood, partly due to a lack of high-resolution structural data on undecorated MTs, which need to serve as a baseline for further comparisons. Here we report three structures of MTs in different nucleotide states (GMPCPP, GDP, and GTPγS) at near-atomic resolution and in the absence of any binding proteins. These structures allowed us to differentiate the effects of nucleotide state versus MAP binding on MT structure. Kinesin binding has a small effect on the extended, GMPCPP-bound lattice, but hardly affects the compacted GDP-MT lattice, while binding of end-binding (EB) proteins can induce lattice compaction (together with lattice twist) in MTs that were initially in an extended and more stable state. We propose a MT lattice-centric model in which the MT lattice serves as a platform that integrates internal tubulin signals, such as nucleotide state, with outside signals, such as binding of MAPs or mechanical forces, resulting in global lattice rearrangements that in turn affect the affinity of other MT partners and result in the exquisite regulation of MT dynamics.

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Organizational Affiliation: 

Howard Hughes Medical Institute, University of California, Berkeley, CA 94720.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1B chain	A, C, E, J, K, L	451	Sus scrofa	Mutation(s): 0  Gene Names: TUBA1B
Find proteins for Q2XVP4 (Sus scrofa) Explore Q2XVP4  Go to UniProtKB:  Q2XVP4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B, D, F, G, H, I	445	Sus scrofa	Mutation(s): 0
Find proteins for P02554 (Sus scrofa) Explore P02554  Go to UniProtKB:  P02554

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	A, C, E, J, K, L	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP	B, D, F, G, H, I	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	A, C, E, J, K, L	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.30 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-06-09 
• Released Date: 2018-07-04 
Deposition Author(s): Zhang, R., Nogales, E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM051487
National Science Foundation (NSF, United States)	United States	1106400
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History 

• Version 1.0: 2018-07-04
  Type: Initial release
  
• Version 1.1: 2018-07-18
  Changes: Data collection, Database references
• Version 1.2: 2019-11-20
  Changes: Author supporting evidence