[English] 日本語
Yorodumi
- PDB-4pd8: Structure of vcCNT-7C8C bound to pyrrolo-cytidine -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4pd8
TitleStructure of vcCNT-7C8C bound to pyrrolo-cytidine
ComponentsNupC family protein
KeywordsTRANSPORT PROTEIN / membrane protein / sodium-coupled transporter / pyrrolo-cytidine / drug transporter
Function / homology
Function and homology information


nucleoside transmembrane transport / nucleoside transmembrane transporter activity / 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
Chem-P0C / Nucleoside permease
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsJohnson, Z.L. / Lee, S.-Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM100984 United States
CitationJournal: Elife / Year: 2014
Title: Structural basis of nucleoside and nucleoside drug selectivity by concentrative nucleoside transporters.
Authors: Johnson, Z.L. / Lee, J.H. / Lee, K. / Lee, M. / Kwon, D.Y. / Hong, J. / Lee, S.Y.
History
DepositionApr 17, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / software
Item: _entity.pdbx_description / _entity.src_method ..._entity.pdbx_description / _entity.src_method / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NupC family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9394
Polymers44,1521
Non-polymers7873
Water543
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)134,81612
Polymers132,4563
Non-polymers2,3609
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
Buried area10360 Å2
ΔGint-148 kcal/mol
Surface area44420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.636, 119.636, 83.064
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Detailsbiological unit is the same as asym.

-
Components

#1: Protein NupC family protein


Mass: 44151.848 Da / Num. of mol.: 1 / Mutation: L7C, I8C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_2352 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 (DE3) / References: UniProt: Q9KPL5
#2: Chemical ChemComp-P0C / 6-methyl-3-(beta-D-ribofuranosyl)-3,7-dihydro-2H-pyrrolo[2,3-d]pyrimidin-2-one / 6-Methyl-3-(beta-D-2-ribofuranosyl)pyrrolo[2,3-d] pyrimidin-2-one


Mass: 281.265 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15N3O5
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM
#5: Water ChemComp-HOH / water / 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: 4.08 Å3/Da / Density % sol: 69.88 %
Crystal growTemperature: 290 K / Method: liquid diffusion / pH: 8.5 / Details: 37-42% PEG 400, 100 mM CaCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.75→50 Å / Num. obs: 17711 / % possible obs: 99.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 64.07 Å2 / Rmerge(I) obs: 0.083 / Χ2: 1.965 / Net I/av σ(I): 22.625 / Net I/σ(I): 9.7 / Num. measured all: 103351
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.75-2.85.50.6568840.559100
2.8-2.855.50.6058740.558100
2.85-2.95.50.5418690.61699.9
2.9-2.965.50.488850.615100
2.96-3.035.60.4158770.667100
3.03-3.15.60.3528860.66199.9
3.1-3.175.70.2958750.693100
3.17-3.265.80.2498740.742100
3.26-3.365.80.1998820.80499.9
3.36-3.465.90.1718920.872100
3.46-3.595.90.1328730.947100
3.59-3.7360.1059011.035100
3.73-3.96.10.0828641.09199.9
3.9-4.116.10.078961.183100
4.11-4.366.10.0618902.02100
4.36-4.76.10.0558901.52299.9
4.7-5.176.10.0638872.45999.9
5.17-5.9260.0698912.595100
5.92-7.465.90.0469013.08499.8
7.46-5060.04692015.04199.1

-
Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TIJ

3tij


Resolution: 2.75→39.16 Å / FOM work R set: 0.8168 / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2472 896 5.06 %
Rwork0.2019 16802 -
obs0.2041 17698 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 184.28 Å2 / Biso mean: 60.97 Å2 / Biso min: 33.71 Å2
Refinement stepCycle: final / Resolution: 2.75→39.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2921 0 54 3 2978
Biso mean--63.35 47.9 -
Num. residues----404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033042
X-RAY DIFFRACTIONf_angle_d0.6464130
X-RAY DIFFRACTIONf_chiral_restr0.021488
X-RAY DIFFRACTIONf_plane_restr0.003509
X-RAY DIFFRACTIONf_dihedral_angle_d10.5751028
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7499-2.92210.28771480.258327842932
2.9221-3.14760.27951480.23127772925
3.1476-3.46420.22211490.207127922941
3.4642-3.96510.21261490.18927942943
3.9651-4.9940.23441470.194128092956
4.994-39.1640.26611550.195928463001

+
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