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- PDB-9f63: Crystal structure of Saccharomyces cerevisiae pH nine-sensitive p... -

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Basic information

Entry
Database: PDB / ID: 9f63
TitleCrystal structure of Saccharomyces cerevisiae pH nine-sensitive protein 1 (PNS1)
ComponentsProtein PNS1
KeywordsMEMBRANE PROTEIN / Choline transporter-like family / CTL
Function / homologyCholine transporter-like / Plasma-membrane choline transporter / transmembrane transporter activity / cell periphery / transmembrane transport / membrane / plasma membrane / Protein PNS1
Function and homology information
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.73 Å
AuthorsDriller, J.H. / Pedersen, B.P.
Funding support Denmark, European Union, 2items
OrganizationGrant numberCountry
LundbeckfondenR380-2021-1207 Denmark
H2020 Marie Curie Actions of the European Commission890822European Union
CitationJournal: Life Sci Alliance / Year: 2026
Title: Structural and biochemical comparison of the FLVCR and CTL membrane protein families in eukaryotes.
Authors: Lynette Nel / Jan H Driller / Ronja Driller / Kelly M Frain / Bjørn P Pedersen /
Abstract: The organic cation choline is essential for eukaryotic metabolism. Recently, the feline leukemia virus subgroup C receptor-related (FLVCR, SLC49) family was demonstrated as central for basal choline ...The organic cation choline is essential for eukaryotic metabolism. Recently, the feline leukemia virus subgroup C receptor-related (FLVCR, SLC49) family was demonstrated as central for basal choline transport, questioning the role of the choline transporter-like (CTL, SLC44) family in this capacity. Here, we use oocytes to confirm that FLVCR1 (SLC49A1) and FLVCR2 (SLC49A2) proteins are choline transporters. CTL1 (SLC44A1) does not transport choline under the same conditions, supported by other CTL proteins, CherI and PNS1, which also display no choline transport activity. We present the atomic structures of FLVCR2, CTL1, and PNS1. The 3.4 Å cryo-EM structure of FLVCR2 has choline in the binding pocket. The 3.3 Å cryo-EM structure of CTL1 and the 2.7 Å crystal structure of PNS1 reveal an unusual protein fold, weakly related to the mitochondrial carrier family (SLC25). The unusual fold appears incompatible with transmembrane transport and implies a different and, so far, unknown function for CTL proteins. Our results support FLVCR proteins as choline transporters and suggest a nontransport role for CTL proteins.
History
DepositionApr 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1May 27, 2026Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein PNS1


Theoretical massNumber of molelcules
Total (without water)63,4641
Polymers63,4641
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area22520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.449, 91.262, 108.372
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2

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Components

#1: Protein Protein PNS1 / pH nine-sensitive protein 1


Mass: 63463.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PNS1, YOR161C, O3568 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q12412
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.49 Å3/Da / Density % sol: 64.8 %
Crystal growTemperature: 292 K / Method: lipidic cubic phase
Details: 0.1M (NH4)2PO4, 0.1M HEPES 7.0, 32% PEG 400, 6mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9764 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9764 Å / Relative weight: 1
ReflectionResolution: 2.73→48.47 Å / Num. obs: 18374 / % possible obs: 100 % / Redundancy: 6.4 % / Biso Wilson estimate: 81.12 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.057 / Rrim(I) all: 0.145 / Χ2: 1 / Net I/σ(I): 8.8 / Num. measured all: 118497
Reflection shellResolution: 2.73→2.86 Å / % possible obs: 100 % / Redundancy: 6.7 % / Rmerge(I) obs: 2.212 / Num. measured all: 16041 / Num. unique obs: 2397 / CC1/2: 0.413 / Rpim(I) all: 0.922 / Rrim(I) all: 2.399 / Χ2: 1 / Net I/σ(I) obs: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimlessdata scaling
XDSdata reduction
PHASER1.18.2_3874phasing
RefinementMethod to determine structure: SAD / Resolution: 2.73→29.29 Å / SU ML: 0.4165 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.0027
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2846 918 5.01 %
Rwork0.2322 17396 -
obs0.2348 18314 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 88.2 Å2
Refinement stepCycle: LAST / Resolution: 2.73→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3369 0 0 12 3381
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00663467
X-RAY DIFFRACTIONf_angle_d0.85214703
X-RAY DIFFRACTIONf_chiral_restr0.0469528
X-RAY DIFFRACTIONf_plane_restr0.007566
X-RAY DIFFRACTIONf_dihedral_angle_d23.9495458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.73-2.880.36581280.3112429X-RAY DIFFRACTION99.53
2.88-3.060.37111290.30052454X-RAY DIFFRACTION99.92
3.06-3.290.31891290.25692436X-RAY DIFFRACTION100
3.29-3.620.30181300.24992470X-RAY DIFFRACTION99.96
3.62-4.140.28551300.22082479X-RAY DIFFRACTION99.96
4.14-5.220.2851320.22182507X-RAY DIFFRACTION99.92
5.22-29.290.24991400.21612621X-RAY DIFFRACTION99.75
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)
11.842344683640.05285041543490.2199409699272.692396716381.03514014862.61329147235-0.09616414312940.04454759118130.0762544367848-0.009899363600330.0174157663009-0.2156877992830.02781398885570.3453004868150.07374064315530.5148739102920.003841517329680.02870583508990.5445467032780.04239591684380.500927168052-21.345063342527.1608279983-21.4443089556
25.71832428124-4.58903719611-3.096280067351.999985188344.405597517412.000041315960.06017219970290.1281092727250.148626383821-0.8578430080580.4152927828221.52291475961-0.5874465043-1.89055143995-0.4675213469681.16983844760.0528258673073-0.03311465021791.123039872140.0544880131851.203352876575.3471190907620.8104118343-57.1164887124
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11(chain 'A' and resid 128 through 537)128 - 53740 - 422
22(chain 'A' and resid 110 through 115 )110 - 11534 - 39

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