5TY4 | pdb_00005ty4

MicroED structure of a complex between monomeric TGF-b and its receptor, TbRII, at 2.9 A resolution

• PDB DOI: https://doi.org/10.2210/pdb5TY4/pdb
• EM Map EMD-8472: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-11-18 Released: 2017-04-26 
• Deposition Author(s): Weiss, S.C., de la Cruz, M.J., Hattne, J., Shi, D., Reyes, F.E., Callero, G., Gonen, T.

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 2.90 Å
• R-Value Free: 
  0.328 (Depositor) 
• R-Value Work: 
  0.292 (Depositor) 
• R-Value Observed: 
  0.295 (Depositor) 

Starting Model: experimental

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: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 22.87 kDa 
• Atom Count: 1,327 
• Modeled Residue Count: 166 
• Deposited Residue Count: 200 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TGF-beta receptor type-2	A	103	Homo sapiens	Mutation(s): 0  Gene Names: TGFBR2 EC: 2.7.11.30
UniProt & NIH Common Fund Data Resources
Find proteins for P37173 (Homo sapiens) Explore P37173  Go to UniProtKB:  P37173
PHAROS:  P37173 GTEx:  ENSG00000163513

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
mmTGF-b2-7m	B	97	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P61812 (Homo sapiens) Explore P61812  Go to UniProtKB:  P61812
PHAROS:  P61812 GTEx:  ENSG00000092969

Experimental Data & Validation

Experimental Data

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 2.90 Å
• R-Value Free:  0.328 (Depositor) 
• R-Value Work:  0.292 (Depositor) 
• R-Value Observed: 0.295 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.53	α = 90
b = 71.33	β = 90
c = 79.508	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.10

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-26 
Deposition Author(s): Weiss, S.C., de la Cruz, M.J., Hattne, J., Shi, D., Reyes, F.E., Callero, G., Gonen, T.

Revision History  

• Version 1.0: 2017-04-26
  Type: Initial release
  
• Version 1.1: 2017-08-09
  Changes: Data collection, Database references
• Version 1.2: 2018-07-18
  Changes: Data collection
• Version 1.3: 2018-08-22
  Changes: Data collection, Database references
• Version 1.4: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2024-11-06
  Changes: Data collection, Structure summary