[English] 日本語
Yorodumi
- PDB-5u9w: Structure of CNTnw N149L in the intermediate 3 state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5u9w
TitleStructure of CNTnw N149L in the intermediate 3 state
ComponentsNucleoside permease
KeywordsTRANSPORT PROTEIN / transporter / nucleoside / elevator-type alternate access
Function / homology
Function and homology information


pyrimidine- and adenosine-specific:sodium symporter activity / purine-specific nucleoside:sodium symporter activity / pyrimidine nucleoside transport / purine nucleoside transmembrane transport / plasma membrane
Similarity search - Function
Concentrative nucleoside transporter N-terminal domain / Concentrative nucleoside transporter / Concentrative nucleoside transporter C-terminal domain / Concentrative nucleoside transporter, metazoan/bacterial / Na+ dependent nucleoside transporter N-terminus / Na+ dependent nucleoside transporter C-terminus / Nucleoside transporter/FeoB GTPase, Gate domain / Nucleoside recognition
Similarity search - Domain/homology
Chem-6ZL / Nucleoside permease
Similarity search - Component
Biological speciesNeisseria wadsworthii 9715 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.555 Å
AuthorsHirschi, M. / Johnson, Z.L. / Lee, S.-Y.
CitationJournal: Nature / Year: 2017
Title: Visualizing multistep elevator-like transitions of a nucleoside transporter.
Authors: Hirschi, M. / Johnson, Z.L. / Lee, S.Y.
History
DepositionDec 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1May 3, 2017Group: Database references
Revision 1.2May 17, 2017Group: Database references
Revision 1.3Oct 4, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nucleoside permease
B: Nucleoside permease
C: Nucleoside permease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,9195
Polymers134,0213
Non-polymers1,8982
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7890 Å2
ΔGint-101 kcal/mol
Surface area47840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.588, 115.588, 272.394
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

-
Components

#1: Protein Nucleoside permease


Mass: 44673.602 Da / Num. of mol.: 3 / Mutation: N149L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria wadsworthii 9715 (bacteria) / Gene: nupC, HMPREF9370_1765 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: G4CRQ5
#2: Chemical ChemComp-6ZL / 2-{[(4-O-alpha-D-glucopyranosyl-beta-D-glucopyranosyl)oxy]methyl}-2-octyldecyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside


Mass: 949.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C43H80O22

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.66 Å3/Da / Density % sol: 66.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 10mM Mg(OAc)2, 25% PEG400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97779 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97779 Å / Relative weight: 1
ReflectionResolution: 3.55→30 Å / Num. obs: 24655 / % possible obs: 99.9 % / Redundancy: 8.4 % / CC1/2: 0.93 / Rpim(I) all: 0.05 / Net I/σ(I): 16.4
Reflection shellResolution: 3.55→3.61 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 1.7 / CC1/2: 0.56 / Rpim(I) all: 0.69 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000v705adata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L26

5l26


Resolution: 3.555→29.964 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.8
RfactorNum. reflection% reflection
Rfree0.2756 3463 7.1 %
Rwork0.2531 --
obs0.2547 24655 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.555→29.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8616 0 53 0 8669
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018818
X-RAY DIFFRACTIONf_angle_d0.97412023
X-RAY DIFFRACTIONf_dihedral_angle_d7.6152885
X-RAY DIFFRACTIONf_chiral_restr0.0461515
X-RAY DIFFRACTIONf_plane_restr0.0041495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5546-3.60320.40221450.39191760X-RAY DIFFRACTION97
3.6032-3.65460.38051280.341812X-RAY DIFFRACTION100
3.6546-3.70910.35131520.32771779X-RAY DIFFRACTION100
3.7091-3.76690.33281500.31431821X-RAY DIFFRACTION100
3.7669-3.82860.28321500.28731810X-RAY DIFFRACTION100
3.8286-3.89450.29631090.30281839X-RAY DIFFRACTION100
3.8945-3.96510.27021440.28111824X-RAY DIFFRACTION100
3.9651-4.04120.31681280.27951797X-RAY DIFFRACTION100
4.0412-4.12350.3141400.27821868X-RAY DIFFRACTION100
4.1235-4.21290.23521380.27791786X-RAY DIFFRACTION100
4.2129-4.31060.26291440.25761822X-RAY DIFFRACTION100
4.3106-4.41810.25251340.25031811X-RAY DIFFRACTION100
4.4181-4.53720.25271460.23981815X-RAY DIFFRACTION100
4.5372-4.67020.25131420.25571801X-RAY DIFFRACTION100
4.6702-4.82040.24491300.24531858X-RAY DIFFRACTION100
4.8204-4.99190.2441420.25331824X-RAY DIFFRACTION100
4.9919-5.19080.25741240.26551833X-RAY DIFFRACTION100
5.1908-5.42570.32521400.26981784X-RAY DIFFRACTION100
5.4257-5.70990.33851330.2851827X-RAY DIFFRACTION100
5.7099-6.06490.36411540.2741830X-RAY DIFFRACTION100
6.0649-6.52870.31171320.27711786X-RAY DIFFRACTION100
6.5287-7.17750.28711480.24631834X-RAY DIFFRACTION100
7.1775-8.19740.23491320.20621823X-RAY DIFFRACTION100
8.1974-10.25860.18331340.16481813X-RAY DIFFRACTION100
10.2586-29.96480.28691440.26841774X-RAY DIFFRACTION98

+
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://pdbjlvh1.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