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- PDB-6oh3: X-ray crystal structure of the mouse CMP-sialic acid transporter ... -

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Basic information

Entry
Database: PDB / ID: 6oh3
TitleX-ray crystal structure of the mouse CMP-sialic acid transporter in complex with CMP-sialic acid, by lipidic cubic phase
ComponentsCMP-sialic acid transporter
KeywordsTRANSPORT PROTEIN / drug/metabolite transporter / nucleotide-sugar / sialic acid / glycosylation
Function / homology
Function and homology information


CMP-N-acetylneuraminate transmembrane transporter activity / CMP-N-acetylneuraminate transmembrane transport / Transport of nucleotide sugars / Sialic acid metabolism / N-acetylneuraminate metabolic process / CMP-N-acetylneuraminate biosynthetic process / antiporter activity / Golgi membrane / membrane
Similarity search - Function
Nucleotide-sugar transporter / Nucleotide-sugar transporter
Similarity search - Domain/homology
Chem-NCC / CMP-sialic acid transporter
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsAhuja, S. / Whorton, M.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM130909 United States
CitationJournal: Elife / Year: 2019
Title: Structural basis for mammalian nucleotide sugar transport.
Authors: Ahuja, S. / Whorton, M.R.
History
DepositionApr 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CMP-sialic acid transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4672
Polymers35,8521
Non-polymers6141
Water543
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)140.096, 50.123, 50.419
Angle α, β, γ (deg.)90.00, 109.25, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CMP-sialic acid transporter / CMP-Sia-Tr / Solute carrier family 35 member A1


Mass: 35852.055 Da / Num. of mol.: 1 / Fragment: residues 1-322
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Slc35a1 / Production host: Komagataella pastoris (fungus) / Strain (production host): SMD1168H / References: UniProt: Q61420
#2: Chemical ChemComp-NCC / CYTIDINE-5'-MONOPHOSPHATE-5-N-ACETYLNEURAMINIC ACID


Mass: 614.451 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H31N4O16P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 293.15 K / Method: lipidic cubic phase
Details: 28.05% PEG 350 MME, 40 mM Tris pH 8.0, and 40 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.75→48 Å / Num. obs: 8305 / % possible obs: 99.8 % / Redundancy: 4.1 % / Net I/σ(I): 6
Reflection shellResolution: 2.75→2.85 Å / Num. unique obs: 561

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→48 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.924 / SU B: 27.572 / SU ML: 0.47 / Cross valid method: THROUGHOUT / ESU R Free: 0.41 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27923 403 4.6 %RANDOM
Rwork0.25627 ---
obs0.25718 8305 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 77.613 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0 Å2-1.83 Å2
2--0.03 Å2-0 Å2
3---1.17 Å2
Refinement stepCycle: 1 / Resolution: 2.75→48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 41 3 2288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022329
X-RAY DIFFRACTIONr_bond_other_d0.0010.022226
X-RAY DIFFRACTIONr_angle_refined_deg1.031.9943189
X-RAY DIFFRACTIONr_angle_other_deg0.8135103
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8135302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45423.28164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.35815352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.412154
X-RAY DIFFRACTIONr_chiral_restr0.0430.2410
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022535
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02483
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4428.0491214
X-RAY DIFFRACTIONr_mcbond_other1.4438.0481213
X-RAY DIFFRACTIONr_mcangle_it2.44812.0711514
X-RAY DIFFRACTIONr_mcangle_other2.44712.0731515
X-RAY DIFFRACTIONr_scbond_it1.5028.181115
X-RAY DIFFRACTIONr_scbond_other1.5028.1791116
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.5712.2281676
X-RAY DIFFRACTIONr_long_range_B_refined4.45598.6122738
X-RAY DIFFRACTIONr_long_range_B_other4.45598.5942739
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.753→2.825 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 29 -
Rwork0.379 598 -
obs--99.05 %

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