6QD5

X-ray Structure of the Human Urea Channel SLC14A1/UT1

• PDB DOI: https://doi.org/10.2210/pdb6QD5/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTM


• Deposited: 2018-12-31 Released: 2019-01-09 
• Deposition Author(s): Dietz, L., Chi, G., Pike, A.C.W., Moreau, C., Man, H., Snee, M., Scacioc, A., Shrestha, L., Mukhopadhyay, S.M.M., Mckinley, G., Ellis, K., Kliszcak, M., Chalk, R., Borkowska, O., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Durr, K.L., Structural Genomics Consortium (SGC)
• Funding Organization(s): European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.225 
• R-Value Work: 0.175 
• R-Value Observed: 0.178 

Starting Model: experimental

Literature

X-ray Structure of the Human Urea Channel SLC14A1/UT1

Dietz, L., Chi, G., Pike, A.C.W., Moreau, C., Man, H., Snee, M., Scacioc, A., Shrestha, L., Mukhopadhyay, S.M.M., Mckinley, G., Ellis, K., Kliszcak, M., Chalk, R., Borkowska, O., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Durr, K.L., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: mass spectrometry

Macromolecule Content

• Total Structure Weight: 43.1 kDa 
• Atom Count: 2,974 
• Modelled Residue Count: 356 
• Deposited Residue Count: 367 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Urea transporter 1	A	367	Homo sapiens	Mutation(s): 3  Gene Names: SLC14A1, HUT11, JK, RACH1, UT1, UTE Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q13336 (Homo sapiens) Explore Q13336  Go to UniProtKB:  Q13336
PHAROS:  Q13336 GTEx:  ENSG00000141469

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Y01	I [auth A]	CHOLESTEROL HEMISUCCINATE C31 H50 O4 WLNARFZDISHUGS-MIXBDBMTSA-N
BOG	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
PG4	J [auth A], K [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.225 
• R-Value Work: 0.175 
• R-Value Observed: 0.178 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.331	α = 90
b = 112.331	β = 90
c = 87.94	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-09 
Deposition Author(s): Dietz, L., Chi, G., Pike, A.C.W., Moreau, C., Man, H., Snee, M., Scacioc, A., Shrestha, L., Mukhopadhyay, S.M.M., Mckinley, G., Ellis, K., Kliszcak, M., Chalk, R., Borkowska, O., Burgess-Brown, N.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Durr, K.L., Structural Genomics Consortium (SGC)

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Funding Organization	Location	Grant Number
European Commission		115766

Revision History  

• Version 1.0: 2019-01-09
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-01-24
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary