6MBL

SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, Second P212121 Crystal Form

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

SETD3 is an actin histidine methyltransferase that prevents primary dystocia.

Wilkinson, A.W., Diep, J., Dai, S., Liu, S., Ooi, Y.S., Song, D., Li, T.M., Horton, J.R., Zhang, X., Liu, C., Trivedi, D.V., Ruppel, K.M., Vilches-Moure, J.G., Casey, K.M., Mak, J., Cowan, T., Elias, J.E., Nagamine, C.M., Spudich, J.A., Cheng, X., Carette, J.E., Gozani, O.

(2019) Nature 565: 372-376

  • DOI: 10.1038/s41586-018-0821-8
  • Primary Citation of Related Structures:  
    6MBJ, 6MBL, 6MBK

  • PubMed Abstract: 

    • For more than 50 years, the methylation of mammalian actin at histidine 73 has been known to occur 1 . Despite the pervasiveness of His73 methylation, which we find is conserved in several model animals and plants, its function remains unc ...

    For more than 50 years, the methylation of mammalian actin at histidine 73 has been known to occur 1 . Despite the pervasiveness of His73 methylation, which we find is conserved in several model animals and plants, its function remains unclear and the enzyme that generates this modification is unknown. Here we identify SET domain protein 3 (SETD3) as the physiological actin His73 methyltransferase. Structural studies reveal that an extensive network of interactions clamps the actin peptide onto the surface of SETD3 to orient His73 correctly within the catalytic pocket and to facilitate methyl transfer. His73 methylation reduces the nucleotide-exchange rate on actin monomers and modestly accelerates the assembly of actin filaments. Mice that lack SETD3 show complete loss of actin His73 methylation in several tissues, and quantitative proteomics analysis shows that actin His73 methylation is the only detectable physiological substrate of SETD3. SETD3-deficient female mice have severely decreased litter sizes owing to primary maternal dystocia that is refractory to ecbolic induction agents. Furthermore, depletion of SETD3 impairs signal-induced contraction in primary human uterine smooth muscle cells. Together, our results identify a mammalian histidine methyltransferase and uncover a pivotal role for SETD3 and actin His73 methylation in the regulation of smooth muscle contractility. Our data also support the broader hypothesis that protein histidine methylation acts as a common regulatory mechanism.

    Organizational Affiliation: 

    Department of Biology, Stanford University, Stanford, CA, USA. ogozani@stanford.edu.



Macromolecules
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Actin PeptideY15Homo sapiensMutation(s): 0 
Gene Names: ACTB
Find proteins for P60709 (Homo sapiens)
Explore P60709 
Go to UniProtKB:  P60709
NIH Common Fund Data Resources
PHAROS  P60709
GTEx  ENSG00000075624
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase setd3A599Homo sapiensMutation(s): 0 
Gene Names: SETD3, C14orf154
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.85 (UniProt)
Find proteins for Q86TU7 (Homo sapiens)
Explore Q86TU7 
Go to UniProtKB:  Q86TU7
NIH Common Fund Data Resources
PHAROS  Q86TU7
GTEx  ENSG00000183576
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH
Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N		 Ligand Interaction
EDO
Query on EDO
Download CCD File 
A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.557α = 90
b = 92.83β = 90
c = 111.635γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM049245-23

Revision History 

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2019-01-16
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-13
    Changes: Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence