[English] 日本語
Yorodumi
- PDB-3tij: Crystal structure of a concentrative nucleoside transporter from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tij
TitleCrystal structure of a concentrative nucleoside transporter from Vibrio cholerae
ComponentsNupC family protein
KeywordsMEMBRANE PROTEIN / membrane transporter / nucleoside transporter / drug transporter / uridine / nucleosides
Function / homology
Function and homology information


nucleoside transmembrane transport / nucleoside transmembrane transporter activity / pyrimidine- and adenosine-specific:sodium symporter activity / purine-specific nucleoside:sodium symporter activity / pyrimidine nucleoside transport / purine nucleoside transmembrane transport / symporter activity / identical protein binding / 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
URIDINE / Nucleoside permease
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.436 Å
AuthorsJohnson, Z.L. / Cheong, C.-G. / Lee, S.-Y.
CitationJournal: Nature / Year: 2012
Title: Crystal structure of a concentrative nucleoside transporter from Vibrio cholerae at 2.4A
Authors: Johnson, Z.L. / Cheong, C.G. / Lee, S.Y.
History
DepositionAug 20, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NupC family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8528
Polymers44,1721
Non-polymers2,6807
Water77543
1
A: NupC family protein
hetero molecules

A: NupC family protein
hetero molecules

A: NupC family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,55624
Polymers132,5163
Non-polymers8,04021
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area16310 Å2
ΔGint-87 kcal/mol
Surface area44530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.717, 119.717, 83.136
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

#1: Protein NupC family protein


Mass: 44171.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: VC_2352 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: Q9KPL5
#2: Chemical ChemComp-URI / URIDINE


Mass: 244.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O6
#3: Sugar
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.89 Å3/Da / Density % sol: 68.41 %
Crystal growTemperature: 290 K / Method: microbatch-under-oil / pH: 9
Details: 100 mM CaCl2, 40% PEG400, 100 mM Tris pH 9.0, microbatch-under-oil, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1.06223 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 14, 2011
RadiationMonochromator: Rosenbaum-Rock monochromator high-resolution double-crystal Si (111) sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.06223 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. all: 49041 / Num. obs: 49037 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -1 / Redundancy: 7.9 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 28.256
Reflection shellResolution: 2.42→2.46 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.588 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1213 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
SERGUIdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.436→28.755 Å / SU ML: 0.64 / σ(F): 1.38 / Phase error: 21.83 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2278 2472 5.04 %RANDOM
Rwork0.196 ---
obs0.1975 49037 98.47 %-
all-49041 --
Solvent computationShrinkage radii: 0.49 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.23 Å2 / ksol: 0.337 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.5719 Å2-0 Å20 Å2
2---2.5719 Å2-0 Å2
3---5.1437 Å2
Refinement stepCycle: LAST / Resolution: 2.436→28.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2951 0 76 43 3070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073091
X-RAY DIFFRACTIONf_angle_d0.9374182
X-RAY DIFFRACTIONf_dihedral_angle_d13.3741067
X-RAY DIFFRACTIONf_chiral_restr0.061492
X-RAY DIFFRACTIONf_plane_restr0.003511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4363-2.48310.31381310.27552400X-RAY DIFFRACTION93
2.4831-2.53380.30571260.26072597X-RAY DIFFRACTION97
2.5338-2.58890.26381300.2422535X-RAY DIFFRACTION97
2.5889-2.6490.28071420.23872587X-RAY DIFFRACTION98
2.649-2.71520.2721370.21092551X-RAY DIFFRACTION98
2.7152-2.78860.1961350.21172597X-RAY DIFFRACTION98
2.7886-2.87060.24561400.19882584X-RAY DIFFRACTION99
2.8706-2.96310.23761420.20412589X-RAY DIFFRACTION99
2.9631-3.06890.2431390.21132596X-RAY DIFFRACTION99
3.0689-3.19170.25061320.19612621X-RAY DIFFRACTION99
3.1917-3.33670.1891410.19242608X-RAY DIFFRACTION99
3.3367-3.51230.22051420.1792610X-RAY DIFFRACTION99
3.5123-3.7320.23071400.17562643X-RAY DIFFRACTION100
3.732-4.01940.19951310.18062601X-RAY DIFFRACTION99
4.0194-4.42260.23861440.17262618X-RAY DIFFRACTION100
4.4226-5.05950.23891390.17762603X-RAY DIFFRACTION100
5.0595-6.36310.21921400.22022642X-RAY DIFFRACTION100
6.3631-28.75710.20351410.19932583X-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