5K7N | pdb_00005k7n

MicroED structure of tau VQIVYK peptide at 1.1 A resolution

• PDB DOI: https://doi.org/10.2210/pdb5K7N/pdb
• EM Map EMD-8216: EMDB EMDataResource

• Classification: PROTEIN FIBRIL
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2016-05-26 Released: 2017-04-05 
• Deposition Author(s): de la Cruz, M.J., Hattne, J., Shi, D., Seidler, P., Rodriguez, J., Reyes, F.E., Sawaya, M.R., Cascio, D., Eisenberg, D., Gonen, T.
• Funding Organization(s): National Institutes of Health/National Institute on Aging (NIH/NIA)

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 1.10 Å
• R-Value Free: 
  0.223 (Depositor) 
• R-Value Work: 
  0.210 (Depositor) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED.

de la Cruz, M.J., Hattne, J., Shi, D., Seidler, P., Rodriguez, J., Reyes, F.E., Sawaya, M.R., Cascio, D., Weiss, S.C., Kim, S.K., Hinck, C.S., Hinck, A.P., Calero, G., Eisenberg, D., Gonen, T.

(2017) Nat Methods 14: 399-402

• PubMed: 28192420 
• DOI: https://doi.org/10.1038/nmeth.4178
• Primary Citation Related Structures: 
  5K7N, 5K7O, 5K7P, 5K7Q, 5K7R, 5K7S, 5K7T, 5TY4


• PubMed Abstract: 
  

  Traditionally, crystallographic analysis of macromolecules has depended on large, well-ordered crystals, which often require significant effort to obtain. Even sizable crystals sometimes suffer from pathologies that render them inappropriate for high-resolution structure determination. Here we show that fragmentation of large, imperfect crystals into microcrystals or nanocrystals can provide a simple path for high-resolution structure determination by the cryoEM method MicroED and potentially by serial femtosecond crystallography.

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Organizational Affiliation: 
• Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia, USA.
Howard Hughes Medical Institute, UCLA-DOE Institute, Departments of Biological Chemistry, Chemistry &Biochemistry, and Molecular Biology Institute, UCLA, Los Angeles, California, USA.
Department of Structural Biology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 9-mer - A9 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 0.75 kDa 
• Atom Count: 55 
• Modeled Residue Count: 6 
• Deposited Residue Count: 6 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
VQIVYK	A [auth Z]	6	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P10636 (Homo sapiens) Explore P10636  Go to UniProtKB:  P10636
PHAROS:  P10636 GTEx:  ENSG00000186868

Experimental Data & Validation

Experimental Data

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 1.10 Å
• R-Value Free:  0.223 (Depositor) 
• R-Value Work:  0.210 (Depositor) 
• R-Value Observed: 0.211 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/284

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.42	α = 90
b = 4.99	β = 111.55
c = 37.17	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	BUSTER	2.10.0

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-04-05 
Deposition Author(s): de la Cruz, M.J., Hattne, J., Shi, D., Seidler, P., Rodriguez, J., Reyes, F.E., Sawaya, M.R., Cascio, D., Eisenberg, D., Gonen, T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)	United States	1R01-AG029430

Revision History  

• Version 1.0: 2017-04-05
  Type: Initial release
  
• Version 1.1: 2017-04-12
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence
• Version 1.3: 2018-08-22
  Changes: Data collection, Database references
• Version 1.4: 2019-12-18
  Changes: Author supporting evidence
• Version 1.5: 2024-02-28
  Changes: Data collection, Database references