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- PDB-5i6c: The structure of the eukaryotic purine/H+ symporter, UapA, in com... -

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Basic information

Entry
Database: PDB / ID: 5i6c
TitleThe structure of the eukaryotic purine/H+ symporter, UapA, in complex with Xanthine
ComponentsUric acid-xanthine permease
KeywordsTRANSPORT PROTEIN / membrane protein eukaryotic uric acid/xanthine H+ symporter
Function / homology
Function and homology information


xanthine transport / xanthine transmembrane transporter activity / autophagosome lumen / purine nucleobase binding / urate transport / urate transmembrane transporter activity / fungal-type vacuole / endosome membrane / plasma membrane
Similarity search - Function
Xanthine/uracil permease / Xanthine/uracil permeases family signature. / Nucleobase cation symporter 2 family / Permease family
Similarity search - Domain/homology
XANTHINE / Uric acid-xanthine permease
Similarity search - Component
Biological speciesAspergillus nidulans FGSC A4 (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.7 Å
AuthorsAlguel, Y. / Amillis, S. / Leung, J. / Lambrinidis, G. / Capaldi, S. / Scull, N.J. / Craven, G. / Iwata, S. / Armstrong, A. / Mikros, E. ...Alguel, Y. / Amillis, S. / Leung, J. / Lambrinidis, G. / Capaldi, S. / Scull, N.J. / Craven, G. / Iwata, S. / Armstrong, A. / Mikros, E. / Diallinas, G. / Cameron, A.D. / Byrne, B.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: Nat Commun / Year: 2016
Title: Structure of eukaryotic purine/H(+) symporter UapA suggests a role for homodimerization in transport activity.
Authors: Alguel, Y. / Amillis, S. / Leung, J. / Lambrinidis, G. / Capaldi, S. / Scull, N.J. / Craven, G. / Iwata, S. / Armstrong, A. / Mikros, E. / Diallinas, G. / Cameron, A.D. / Byrne, B.
History
DepositionFeb 16, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uric acid-xanthine permease
B: Uric acid-xanthine permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,7568
Polymers122,4092
Non-polymers2,3476
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8590 Å2
ΔGint-37 kcal/mol
Surface area37070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.090, 173.830, 82.390
Angle α, β, γ (deg.)90.00, 111.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Uric acid-xanthine permease / UAPA transporter


Mass: 61204.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus nidulans FGSC A4 (mold) / Gene: uapA, AN6932 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q07307
#2: Chemical ChemComp-XAN / XANTHINE


Mass: 152.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N4O2
#3: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.1 Å3/Da / Density % sol: 69.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion / Details: Peg300, 0.1 MES ph 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.992 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.992 Å / Relative weight: 1
ReflectionResolution: 3.7→76.9 Å / Num. obs: 20599 / % possible obs: 97.8 % / Redundancy: 2.5 % / CC1/2: 0.99 / Rmerge(I) obs: 0.102 / Net I/σ(I): 7.7
Reflection shellResolution: 3.7→3.8 Å / Rmerge(I) obs: 0.965

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
xia2data scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 3.7→76.861 Å / SU ML: 0.71 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 43.01
RfactorNum. reflection% reflection
Rfree0.3267 1065 5.18 %
Rwork0.2963 --
obs0.2978 20574 97.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Refinement stepCycle: LAST / Resolution: 3.7→76.861 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6979 0 148 0 7127
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067292
X-RAY DIFFRACTIONf_angle_d1.1039944
X-RAY DIFFRACTIONf_dihedral_angle_d11.2942509
X-RAY DIFFRACTIONf_chiral_restr0.0411226
X-RAY DIFFRACTIONf_plane_restr0.0091222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.86840.44911100.40292439X-RAY DIFFRACTION98
3.8684-4.07230.41091350.3792456X-RAY DIFFRACTION98
4.0723-4.32750.38711290.32332438X-RAY DIFFRACTION98
4.3275-4.66150.32691320.2822458X-RAY DIFFRACTION98
4.6615-5.13060.33051520.28152427X-RAY DIFFRACTION98
5.1306-5.87270.32621310.32472438X-RAY DIFFRACTION98
5.8727-7.39810.29821510.32522455X-RAY DIFFRACTION98
7.3981-76.87740.2911250.25012398X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.46430.03030.66923.3391-0.42152.9008-0.12820.05940.7718-0.21060.49870.2211-0.3516-0.129-01.5216-0.01570.01191.5620.03331.5078-62.3381-15.63956.3839
24.7815-1.34521.3613.62120.09714.3070.1807-0.6005-1.3184-0.13930.0002-1.09640.10380.36690.00011.49880.00270.11271.58070.17192.3112-36.5038-42.42529.7886
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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