8F14

Structure of the STUB1 TPR domain in complex with H201, an all-D Helicon Polypeptide

• PDB DOI: https://doi.org/10.2210/pdb8F14/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-11-04 Released: 2023-02-15 
• Deposition Author(s): Li, K., Callahan, A.J., Travaline, T.L., Tokareva, O.S., Swiecicki, J.-M., Verdine, G.L., Pentelute, B.L., McGee, J.H.
• Funding Organization(s): Other private, German Research Foundation (DFG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.236 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 

Starting Model: experimental

Literature

Single-Shot Flow Synthesis of D-Proteins for Mirror-Image Phage Display

Callahan, A.J., Gandhesiri, S., Travaline, T.L., Lozano Salazar, L, Hanna, S., Lee, Y.-C., Li, K., Tokareva, O.S., Swiecicki, J.-M., Loas, A., Verdine, G.L., McGee, J.H., Pentelute, B.L.

(2023) ChemRxiv 

• DOI: https://doi.org/10.26434/chemrxiv-2023-x86xp

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: surface plasmon resonance

Macromolecule Content

• Total Structure Weight: 17.72 kDa 
• Atom Count: 1,422 
• Modelled Residue Count: 148 
• Deposited Residue Count: 151 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase CHIP	A	134	Homo sapiens	Mutation(s): 0  Gene Names: STUB1, CHIP, PP1131 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNE7 (Homo sapiens) Explore Q9UNE7  Go to UniProtKB:  Q9UNE7
PHAROS:  Q9UNE7 GTEx:  ENSG00000103266

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
all-D Helicon Polypeptide H201	B	17	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WHL	G [auth B]	N,N'-(1,4-phenylene)diacetamide C10 H12 N2 O2 KVEDKKLZCJBVNP-UHFFFAOYSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002512	B	all-D Helicon Polypeptide FP40914	Peptide-like / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.236 
• R-Value Work: 0.197 
• R-Value Observed: 0.198 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.158	α = 90
b = 90.115	β = 90
c = 92.333	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-15 
Deposition Author(s): Li, K., Callahan, A.J., Travaline, T.L., Tokareva, O.S., Swiecicki, J.-M., Verdine, G.L., Pentelute, B.L., McGee, J.H.

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Funding Organization	Location	Grant Number
Other private		FOG Pharmaceuticals
Other private		MIT School of Science Fellowship in Cancer Research
German Research Foundation (DFG)	Germany	LE 4224/1-1

Revision History  

• Version 1.0: 2023-02-15
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-11-13
  Changes: Structure summary