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- PDB-4pd7: Structure of vcCNT bound to zebularine -

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Basic information

Entry
Database: PDB / ID: 4pd7
TitleStructure of vcCNT bound to zebularine
ComponentsNupC family protein
KeywordsTRANSPORT PROTEIN / membrane protein / drug transporter / sodium-coupled transporter / zebularine
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
Zebularine / Nucleoside permease
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.909 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NupC family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,9064
Polymers44,1721
Non-polymers7343
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)134,71712
Polymers132,5163
Non-polymers2,2019
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 area11660 Å2
ΔGint-146 kcal/mol
Surface area43630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.811, 119.811, 82.658
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.

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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 serotype O1 (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: VC_2352 / Plasmid: pET26 / Cell line (production host): C41 (DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KPL5
#2: Chemical ChemComp-ZE8 / Zebularine


Mass: 228.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O5 / Comment: inhibitor*YM
#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


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

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.07 Å3/Da / Density % sol: 69.81 %
Crystal growTemperature: 290 K / Method: liquid diffusion / pH: 9.5 / Details: 37-42% PEG 400, 100 mM CaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 14952 / % possible obs: 99.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 53.69 Å2 / Rmerge(I) obs: 0.141 / Χ2: 1.975 / Net I/av σ(I): 13.524 / Net I/σ(I): 6.5 / Num. measured all: 86190
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.9-2.955.10.7667330.666100
2.95-35.30.6997250.67199.9
3-3.065.40.6677450.815100
3.06-3.125.40.5937440.715100
3.12-3.195.50.4927380.719100
3.19-3.275.50.4397580.752100
3.27-3.355.70.3717300.778100
3.35-3.445.70.3377590.868100
3.44-3.545.80.2697390.821100
3.54-3.655.80.2177400.886100
3.65-3.785.90.1827410.955100
3.78-3.945.90.1477531.041100
3.94-4.1160.1217511.138100
4.11-4.3360.1017401.267100
4.33-4.66.10.0837581.206100
4.6-4.966.20.0827501.75399.9
4.96-5.4660.0957531.699100
5.46-6.2460.0977542.128100
6.24-7.866.10.0557571.63299.9
7.86-5060.05478417.01799.4

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Processing

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

3tij


Resolution: 2.909→39.217 Å / FOM work R set: 0.8159 / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.247 756 5.06 %
Rwork0.2113 14176 -
obs0.213 14932 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.41 Å2 / Biso mean: 45.59 Å2 / Biso min: 19.48 Å2
Refinement stepCycle: final / Resolution: 2.909→39.217 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2868 0 50 3 2921
Biso mean--46.36 29.29 -
Num. residues----404
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032976
X-RAY DIFFRACTIONf_angle_d0.6764039
X-RAY DIFFRACTIONf_chiral_restr0.021490
X-RAY DIFFRACTIONf_plane_restr0.003500
X-RAY DIFFRACTIONf_dihedral_angle_d11.041006
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9088-3.13330.27871460.251927982944
3.1333-3.44850.24951530.217528332986
3.4485-3.94710.20721490.193828202969
3.9471-4.97130.25051510.199728482999
4.9713-39.22090.25581570.217128773034

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