4P22 | pdb_00004p22

Crystal Structure of N-terminal Fragments of E1

• PDB DOI: https://doi.org/10.2210/pdb4P22/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-02-28 Released: 2015-02-25 
• Deposition Author(s): Xie, S.-T.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.264 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.208 (Depositor) 

Literature

Expression, purification, and crystal structure of N-terminal domains of human ubiquitin-activating enzyme (E1).

Xie, S.T.

(2014) Biosci Biotechnol Biochem 78: 1542-1549

• PubMed: 25209502 
• DOI: https://doi.org/10.1080/09168451.2014.923301
• Primary Citation Related Structures: 
  4P22


• PubMed Abstract: 
  

  Ubiquitin-activating enzyme (E1) is a key regulator in protein ubiquitination, which lies on the upstream of the ubiquitin-related pathways and determines the activation of the downstream enzyme cascade. Thus far, no structural information about the human ubiquitin-activating enzyme has been reported. We expressed and purified the N-terminal domains of human E1 and determined their crystal structures, which contain inactive adenylation domain (IAD) and the first catalytic cysteine half-domain (FCCH). This study presents the crystal structure of human E1 fragment for the first time. The main structure of both IAD and FCCH superimposed well with their corresponding domains in yeast Uba1, but their relative positions vary significantly. This work provides new structural insights in understanding the mechanisms of ubiquitin activation in humans.

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Organizational Affiliation: 
• a MOE Key Laboratory of Protein Sciences and Tsinghua-Peking Center for Life Sciences , School of Life Sciences, Tsinghua University , Beijing , China.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 96.92 kDa 
• Atom Count: 5,848 
• Modeled Residue Count: 745 
• Deposited Residue Count: 892 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-like modifier-activating enzyme 1	A, B	446	Homo sapiens	Mutation(s): 1  Gene Names: UBA1, A1S9T, UBE1 EC: 6.2.1.45
UniProt & NIH Common Fund Data Resources
Find proteins for P22314 (Homo sapiens) Explore P22314  Go to UniProtKB:  P22314
PHAROS:  P22314 GTEx:  ENSG00000130985

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.264 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.208 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.126	α = 90
b = 186.812	β = 90
c = 135.222	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-02-25 
Deposition Author(s): Xie, S.-T.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	31070643
National Natural Science Foundation of China (NSFC)	China	31130062

Revision History  

• Version 1.0: 2015-02-25
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy
• Version 1.2: 2020-01-08
  Changes: Author supporting evidence
• Version 1.3: 2023-12-27
  Changes: Data collection, Database references, Refinement description