7R7O

Structure of methyltransferase domain of Spb1 boudn to SAM

• PDB DOI: https://doi.org/10.2210/pdb7R7O/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-06-25 Released: 2022-06-29 
• Deposition Author(s): Cruz, V.E., Sekulski, K., Peddada, N., Erzberger, J.P.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Cancer Prevention and Research Institute of Texas (CPRIT), Robert A. Welch Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.245 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 

Literature

Post-catalytic rRNA binding by the DEAD-box ATPase Spb4 and methyltransferase Spb1 guide the late nucleolar assembly of 60S ribosomes

Cruz, V.E., Sekulski, K., Peddada, N., Sailer, C., Balasubramanian, S., Weirich, C.S., Stengel, F., Erzberger, J.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.78 kDa 
• Atom Count: 3,943 
• Modelled Residue Count: 418 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AdoMet-dependent rRNA methyltransferase SPB1	A, B	220	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: SPB1, PACBIOSEQ_LOCUS534 EC: 2.1.1
UniProt
Find proteins for P25582 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P25582  Go to UniProtKB:  P25582

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM (Subject of Investigation/LOI)	C [auth A], D [auth B]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.58 Å
• R-Value Free: 0.245 
• R-Value Work: 0.229 
• R-Value Observed: 0.230 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.714	α = 90
b = 45.497	β = 123.422
c = 92.031	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-29 
Deposition Author(s): Cruz, V.E., Sekulski, K., Peddada, N., Erzberger, J.P.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM135617-01
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RR150074
Robert A. Welch Foundation	United States	I-1897

Revision History  

• Version 1.0: 2022-06-29
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description