7M3Q | pdb_00007m3q

Structure of the Smurf2 HECT Domain with a High Affinity Ubiquitin Variant (UbV)

• PDB DOI: https://doi.org/10.2210/pdb7M3Q/pdb

• Classification: SIGNALING PROTEIN/TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-03-18 Released: 2021-04-21 
• Deposition Author(s): Chowdhury, A., Singer, A.U., Ogunjimi, A.A., Teyra, J., Zhang, W., Sicheri, F., Sidhu, S.S.
• Funding Organization(s): Ontario Research Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.235 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Structure of the Smurf2 HECT Domain with a High Affinity Ubiquitin Variant (UbV)

Chowdhury, A., Singer, A.U., Ogunjimi, A.A., Teyra, J., Chung, J., Wrana, J.L., Zhang, W., Sicheri, F., Sachdev, S.S.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 57.44 kDa 
• Atom Count: 3,738 
• Modeled Residue Count: 447 
• Deposited Residue Count: 485 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase SMURF2	A	387	Homo sapiens	Mutation(s): 0  Gene Names: SMURF2 EC: 2.3.2.26
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HAU4 (Homo sapiens) Explore Q9HAU4  Go to UniProtKB:  Q9HAU4
PHAROS:  Q9HAU4 GTEx:  ENSG00000108854

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin variant	B	98	Homo sapiens	Mutation(s): 9  Gene Names: UBA52, UBCEP2
UniProt & NIH Common Fund Data Resources
Find proteins for P62987 (Homo sapiens) Explore P62987  Go to UniProtKB:  P62987
PHAROS:  P62987 GTEx:  ENSG00000221983

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTT	M [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	N [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.235 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 201.53	α = 90
b = 72.068	β = 94.607
c = 48.813	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-04-21 
Deposition Author(s): Chowdhury, A., Singer, A.U., Ogunjimi, A.A., Teyra, J., Zhang, W., Sicheri, F., Sidhu, S.S.

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Funding Organization	Location	Grant Number
Ontario Research Fund	Canada	72056614

Revision History  

• Version 1.0: 2021-04-21
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary