3ICU

Protease-associated domain of the E3 ligase grail

• PDB DOI: https://doi.org/10.2210/pdb3ICU/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2009-07-18 Released: 2009-09-29 
• Deposition Author(s): Walker, J.R., Yermekbayeva, L., Seitova, A., Weigelt, J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Models: experimental

Literature

PA Domain of the E3 Ligase Grail

Walker, J.R., Yermekbayeva, L., Seitova, A., Weigelt, J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S.

To be published.

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: 21.27 kDa 
• Atom Count: 1,475 
• Modelled Residue Count: 171 
• Deposited Residue Count: 194 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RNF128	A	194	Homo sapiens	Mutation(s): 0  Gene Names: GRAIL, RNF128 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TEB7 (Homo sapiens) Explore Q8TEB7  Go to UniProtKB:  Q8TEB7
PHAROS:  Q8TEB7 GTEx:  ENSG00000133135
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q8TEB7-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.795	α = 90
b = 65.795	β = 90
c = 136.524	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-29 
Deposition Author(s): Walker, J.R., Yermekbayeva, L., Seitova, A., Weigelt, J., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Dhe-Paganon, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-09-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.5: 2024-10-16
  Changes: Structure summary