[English] 日本語
Yorodumi
- PDB-5l26: Structure of CNTnw in an inward-facing substrate-bound state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5l26
TitleStructure of CNTnw in an inward-facing substrate-bound state
ComponentsNucleoside permease
KeywordsTRANSPORT PROTEIN / transporter / nucleoside / elevator-type alternate access
Function / homology
Function and homology information


nucleoside transmembrane transporter activity / symporter activity / 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 / URIDINE / Nucleoside permease
Similarity search - Component
Biological speciesNeisseria wadsworthii 9715 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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
DepositionJul 31, 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 10, 2017Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
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)143,36718
Polymers134,0243
Non-polymers9,34315
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10180 Å2
ΔGint-117 kcal/mol
Surface area46400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.220, 115.220, 264.028
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: 44674.547 Da / Num. of mol.: 3
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) / 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.: 9 / Source method: obtained synthetically / Formula: C43H80O22
#3: Chemical ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H12N2O6
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Na
#5: Water ChemComp-HOH / water


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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.73 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 1 M NaCl, 35% PEG400, pH 9.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.4→55.052 Å / Num. obs: 53753 / % possible obs: 99.66 % / Redundancy: 7 % / CC1/2: 1 / Rpim(I) all: 0.08 / Net I/σ(I): 4.7
Reflection shellResolution: 3.4→3.61 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.48 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLM7.2.1data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TIJ

3tij


Resolution: 3.4→55.052 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 0.05 / Phase error: 29.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2662 3822 7.11 %
Rwork0.2419 --
obs0.2437 53753 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→55.052 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8651 0 331 3 8985
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029132
X-RAY DIFFRACTIONf_angle_d0.71912450
X-RAY DIFFRACTIONf_dihedral_angle_d9.2712979
X-RAY DIFFRACTIONf_chiral_restr0.0251613
X-RAY DIFFRACTIONf_plane_restr0.0031496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4001-3.44310.31811600.33751896X-RAY DIFFRACTION100
3.4431-3.48840.40881440.31181848X-RAY DIFFRACTION100
3.4884-3.53620.37031280.3251818X-RAY DIFFRACTION100
3.5362-3.58670.33651460.31871894X-RAY DIFFRACTION100
3.5867-3.64020.35641480.29491829X-RAY DIFFRACTION100
3.6402-3.69710.38131460.28781831X-RAY DIFFRACTION100
3.6971-3.75770.27091280.27841884X-RAY DIFFRACTION100
3.7577-3.82240.24821620.26131806X-RAY DIFFRACTION100
3.8224-3.89190.26551370.24821865X-RAY DIFFRACTION100
3.8919-3.96680.281380.26591902X-RAY DIFFRACTION99
3.9668-4.04770.2931280.26811771X-RAY DIFFRACTION100
4.0477-4.13570.29671380.26991907X-RAY DIFFRACTION100
4.1357-4.23190.29531500.24621864X-RAY DIFFRACTION100
4.2319-4.33770.27871340.23911793X-RAY DIFFRACTION100
4.3377-4.45490.24451480.22071825X-RAY DIFFRACTION100
4.4549-4.58590.26081420.22381887X-RAY DIFFRACTION100
4.5859-4.73390.25091420.21081855X-RAY DIFFRACTION99
4.7339-4.9030.25581320.21411833X-RAY DIFFRACTION99
4.903-5.09910.27161420.23321856X-RAY DIFFRACTION100
5.0991-5.3310.29521460.23331810X-RAY DIFFRACTION99
5.331-5.61180.2811340.24231849X-RAY DIFFRACTION100
5.6118-5.9630.30231420.24781859X-RAY DIFFRACTION100
5.963-6.42280.2721420.24651885X-RAY DIFFRACTION100
6.4228-7.0680.25481360.21561849X-RAY DIFFRACTION100
7.068-8.08790.17981460.18771822X-RAY DIFFRACTION99
8.0879-10.17940.16591420.16251852X-RAY DIFFRACTION100
10.1794-55.05920.27431410.27971841X-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