9B5R

Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (singly Ub-loaded) - cluster 3 map and model (ATP/Mg)

• PDB DOI: https://doi.org/10.2210/pdb9B5R/pdb
• EM Map EMD-44222: EMDB EMDataResource

• Classification: LIGASE
• Organism(s): Schizosaccharomyces pombe 972h-
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2024-03-22 Released: 2024-06-05 
• Deposition Author(s): Kochanczyk, T., Lima, C.D.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.95 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structural basis for transthiolation intermediates in the ubiquitin pathway

Kochanczyk, T., Hann, Z.S., Lux, M.C., Reyes, A.M.V.D., Ji, C., Tan, D.S., Lima, C.D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy, gel filtration

Macromolecule Content

• Total Structure Weight: 138.22 kDa 
• Atom Count: 8,935 
• Modelled Residue Count: 1,133 
• Deposited Residue Count: 1,233 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-activating enzyme E1 1	A	1,001	Schizosaccharomyces pombe 972h-	Mutation(s): 0  Gene Names: ptr3, SPBC1604.21c, SPBC211.09 EC: 6.2.1.45
UniProt
Find proteins for O94609 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore O94609  Go to UniProtKB:  O94609

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 4	B [auth C]	153	Schizosaccharomyces pombe 972h-	Mutation(s): 2  Gene Names: ubc4, SPBC119.02 EC: 2.3.2.23
UniProt
Find proteins for P46595 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore P46595  Go to UniProtKB:  P46595

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	C [auth D]	79	Schizosaccharomyces pombe 972h-	Mutation(s): 0  Gene Names: uep1, ubi2, SPAC1805.12c
UniProt
Find proteins for P0CH07 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore P0CH07  Go to UniProtKB:  P0CH07

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	F [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
A1AIV (Subject of Investigation/LOI)	G [auth D]	4-aminobutanenitrile C4 H8 N2 XGYKKVTZDQDYJQ-UHFFFAOYSA-N
MG	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.95 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-05 
Deposition Author(s): Kochanczyk, T., Lima, C.D.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM118080

Revision History  

• Version 1.0: 2024-06-05
  Type: Initial release