9H2D | pdb_00009h2d

Human IFT172 C-terminal U-box domain crystal structure

• PDB DOI: https://doi.org/10.2210/pdb9H2D/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-11 Released: 2024-12-04 
• Deposition Author(s): Lorentzen, E., Zacharia, N.K., Bhogaraju, S.
• Funding Organization(s): Novo Nordisk Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.238 (Depositor), 0.238 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: in silico

Literature

Intraflagellar transport protein IFT172 contains a C-terminal ubiquitin-binding U-box-like domain involved in ciliary signaling

Lorentzen, E., Zacharia, N.K., Bhogaraju, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 61.55 kDa 
• Atom Count: 4,401 
• Modeled Residue Count: 529 
• Deposited Residue Count: 544 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Intraflagellar transport protein 172 homolog	A, B	272	Homo sapiens	Mutation(s): 0  Gene Names: IFT172, KIAA1179
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UG01 (Homo sapiens) Explore Q9UG01  Go to UniProtKB:  Q9UG01
PHAROS:  Q9UG01 GTEx:  ENSG00000138002

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EPE (Subject of Investigation/LOI)	C [auth A], E [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C8 H18 N2 O4 S JKMHFZQWWAIEOD-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.238 (Depositor), 0.238 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.967	α = 90
b = 90.507	β = 97.42
c = 67.423	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-12-04 
Deposition Author(s): Lorentzen, E., Zacharia, N.K., Bhogaraju, S.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF23OC0085823

Revision History  

• Version 1.0: 2024-12-04
  Type: Initial release