[English] 日本語
Yorodumi
- PDB-8tzi: Human equilibrative nucleoside transporter-1, JH-ENT-01 bound -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tzi
TitleHuman equilibrative nucleoside transporter-1, JH-ENT-01 bound
ComponentsEquilibrative nucleoside transporter 1
KeywordsTRANSPORT PROTEIN/INHIBITOR / adenosine transport / adenosine reuptake inhibitor / nucleoside / hENT1 / equilibrative nucleoside transporter / SLC29 / TRANSPORT PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


adenine transmembrane transporter activity / guanine transmembrane transporter activity / purine nucleoside transmembrane transporter activity / cytidine transport / inosine transport / hypoxanthine transport / thymine transport / guanine transmembrane transport / uracil transmembrane transport / pyrimidine nucleobase transmembrane transport ...adenine transmembrane transporter activity / guanine transmembrane transporter activity / purine nucleoside transmembrane transporter activity / cytidine transport / inosine transport / hypoxanthine transport / thymine transport / guanine transmembrane transport / uracil transmembrane transport / pyrimidine nucleobase transmembrane transport / uracil transmembrane transporter activity / pyrimidine-containing compound transmembrane transport / purine nucleobase transmembrane transport / cytidine transmembrane transporter activity / nucleoside transport / uridine transmembrane transport / adenosine transport / Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane / nucleobase transport / nucleoside transmembrane transport / nucleoside transmembrane transporter activity / adenine transport / pyrimidine- and adenosine-specific:sodium symporter activity / purine nucleoside transmembrane transport / uridine transmembrane transporter activity / neurotransmitter uptake / Ribavirin ADME / neurotransmitter transmembrane transporter activity / xenobiotic transmembrane transport / Azathioprine ADME / nucleobase-containing compound metabolic process / neurotransmitter transport / transport across blood-brain barrier / lactation / xenobiotic metabolic process / excitatory postsynaptic potential / cellular response to glucose stimulus / presynapse / basolateral plasma membrane / cellular response to hypoxia / postsynapse / apical plasma membrane / membrane / plasma membrane
Similarity search - Function
Nucleoside transporter ENT1/ENT2 / Nucleoside transporter / Equilibrative nucleoside transporter / MFS transporter superfamily
Similarity search - Domain/homology
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / : / Equilibrative nucleoside transporter 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWright, N.J. / Lee, S.Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM137421 United States
CitationJournal: Nat Commun / Year: 2024
Title: Design of an equilibrative nucleoside transporter subtype 1 inhibitor for pain relief.
Authors: Wright, N.J. / Matsuoka, Y. / Park, H. / He, W. / Webster, C.G. / Furutani, K. / Fedor, J.G. / McGinnis, A. / Zhao, Y. / Chen, O. / Bang, S. / Fan, P. / Spasojevic, I. / Hong, J. / Ji, R.R. / Lee, S.Y.
History
DepositionAug 26, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2025Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Equilibrative nucleoside transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7308
Polymers48,8641
Non-polymers2,8667
Water21612
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.413, 72.413, 173.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

-
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.: 1 / Mutation: L168F, P175A, N288K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC29A1, ENT1 / Cell line (production host): HEK293S GnTI-/- / Production host: Homo sapiens (human) / References: UniProt: Q99808
#2: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H40O4
#3: Chemical ChemComp-U00 / 3-[4-[3-[3,4-dimethoxy-5-[[4-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]phenyl]methoxy]phenyl]carbonyloxypropyl]-1,4-diazepan-1-yl]propyl 3,4,5-trimethoxybenzoate


Mass: 726.790 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H48N3O12 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.34 %
Crystal growTemperature: 298 K / Method: lipidic cubic phase / pH: 9
Details: 35-50% PEG400, 0.1 M glycine, 0.5 M sodium chloride

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→62.71 Å / Num. obs: 15151 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 47.81 Å2 / CC1/2: 0.97 / Net I/σ(I): 3.9
Reflection shellResolution: 2.7→2.83 Å / Num. unique obs: 1945 / CC1/2: 0.328

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487phasing
XDSdata reduction
Aimlessdata scaling
PHENIX1.19.2_4158phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 6OB7

6ob7


Resolution: 2.7→58.99 Å / SU ML: 0.332 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.672
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflection
Rfree0.256 749 4.97 %
Rwork0.229 --
obs0.226 15074 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.09 Å2
Refinement stepCycle: LAST / Resolution: 2.7→58.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2955 0 143 12 3110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033175
X-RAY DIFFRACTIONf_angle_d0.5444296
X-RAY DIFFRACTIONf_dihedral_angle_d14.0321071
X-RAY DIFFRACTIONf_chiral_restr0.037501
X-RAY DIFFRACTIONf_plane_restr0.004509
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.910.33681510.29082815X-RAY DIFFRACTION100
2.91-3.20.31741460.24682815X-RAY DIFFRACTION100
3.2-3.660.24751480.2182833X-RAY DIFFRACTION100
3.67-4.620.2691490.21432869X-RAY DIFFRACTION99
4.62-58.990.21181550.20992993X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more