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- PDB-6ob6: Human equilibrative nucleoside transporter-1, S-(4-nitrobenzyl)-6... -

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Basic information

Entry
Database: PDB / ID: 6ob6
TitleHuman equilibrative nucleoside transporter-1, S-(4-nitrobenzyl)-6-thioinosine bound, merohedrally twinned
ComponentsEquilibrative nucleoside transporter 1
KeywordsTRANSPORT PROTEIN / nucleoside transport / adenosine transport / nucleoside-drug transport / adenosine reuptake inhibitor / SLC29 / hENT1 / ENT / NBMPR / NBTI
Function / homology
Function and homology information


purine nucleoside transmembrane transporter activity / pyrimidine-containing compound transmembrane transport / nucleoside transport / uridine transmembrane transport / adenosine transport / Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / nucleoside transmembrane transport / nucleoside transmembrane transporter activity / neurotransmitter uptake / uridine transmembrane transporter activity ...purine nucleoside transmembrane transporter activity / pyrimidine-containing compound transmembrane transport / nucleoside transport / uridine transmembrane transport / adenosine transport / Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / nucleoside transmembrane transport / nucleoside transmembrane transporter activity / neurotransmitter uptake / uridine transmembrane transporter activity / purine nucleoside transmembrane transport / neurotransmitter transmembrane transporter activity / xenobiotic transmembrane transport / sleep / neurotransmitter transport / Azathioprine ADME / nucleobase-containing compound metabolic process / transport across blood-brain barrier / lactation / excitatory postsynaptic potential / cellular response to glucose stimulus / presynapse / cellular response to hypoxia / postsynapse / basolateral plasma membrane / apical plasma membrane / membrane / plasma membrane
Similarity search - Function
Equilibrative nucleoside transporter 1 / Nucleoside transporter ENT1/ENT2 / Nucleoside transporter / Equilibrative nucleoside transporter / MFS transporter superfamily
Similarity search - Domain/homology
Chem-NBM / Equilibrative nucleoside transporter 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsWright, N.J. / Lee, S.-Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R35NS097241 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2019
Title: Structures of human ENT1 in complex with adenosine reuptake inhibitors.
Authors: Wright, N.J. / Lee, S.Y.
History
DepositionMar 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Sep 18, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_database_related / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / refine / struct_conf / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_site_gen
Item: _atom_site.label_seq_id / _entity.formula_weight ..._atom_site.label_seq_id / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _refine.ls_number_reflns_R_free / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_site_gen.label_seq_id
Revision 2.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 2.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Equilibrative nucleoside transporter 1
B: Equilibrative nucleoside transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,5664
Polymers97,7272
Non-polymers8392
Water00
1
A: Equilibrative nucleoside transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2832
Polymers48,8641
Non-polymers4191
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Equilibrative nucleoside transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2832
Polymers48,8641
Non-polymers4191
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.532, 72.532, 335.458
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Equilibrative nucleoside transporter 1 / Equilibrative nitrobenzylmercaptopurine riboside-sensitive nucleoside transporter / Equilibrative ...Equilibrative nitrobenzylmercaptopurine riboside-sensitive nucleoside transporter / Equilibrative NBMPR-sensitive nucleoside transporter / Nucleoside transporter / es-type / Solute carrier family 29 member 1


Mass: 48863.707 Da / Num. of mol.: 2 / Mutation: L168F, P175A, N288K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC29A1, ENT1 / Plasmid: pEG-BacMam / Cell line (production host): HEK293S GnTI -/- / Production host: Homo sapiens (human) / References: UniProt: Q99808
#2: Chemical ChemComp-NBM / 6-{[(4-nitrophenyl)methyl]sulfanyl}-9-beta-D-ribofuranosyl-9H-purine


Mass: 419.412 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H17N5O6S

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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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 8
Details: 30% PEG 500 MME, 0.1M magnesium chloride hexahydrate, 0.1M Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→62.82 Å / Num. obs: 21282 / % possible obs: 74.9 % / Redundancy: 7.8 %
Details: This X-ray data was anisotropically corrected using the Staraniso webserver
CC1/2: 0.93 / Net I/σ(I): 4
Reflection shellResolution: 2.9→3.08 Å / Mean I/σ(I) obs: 0.8 / Num. unique obs: 815 / CC1/2: 0.33 / % possible all: 21

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
Aimlessdata scaling
STARANISOdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OB7

6ob7


Resolution: 2.9→62.815 Å / Cross valid method: FREE R-VALUE / Phase error: 22.12
RfactorNum. reflection% reflection
Rfree0.2515 812 5.15 %
Rwork0.2053 --
obs0.2137 16467 74.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→62.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5454 0 58 0 5512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025664
X-RAY DIFFRACTIONf_angle_d0.5267723
X-RAY DIFFRACTIONf_dihedral_angle_d9.5063195
X-RAY DIFFRACTIONf_chiral_restr0.035935
X-RAY DIFFRACTIONf_plane_restr0.003918
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9035-3.08520.3093420.2625773X-RAY DIFFRACTION21
3.0852-3.32310.27861030.23731774X-RAY DIFFRACTION48
3.3231-3.65680.25951800.21583415X-RAY DIFFRACTION94
3.6568-4.18440.2531820.20243461X-RAY DIFFRACTION95
4.1844-5.26620.22341400.19472686X-RAY DIFFRACTION73
5.2662-27.95610.27671830.21543485X-RAY DIFFRACTION95

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