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- PDB-4pd8: Structure of vcCNT-7C8C bound to pyrrolo-cytidine -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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.

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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


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: 4.08 Å3/Da / Density % sol: 69.88 %
Crystal growTemperature: 290 K / Method: liquid diffusion / pH: 8.5 / Details: 37-42% PEG 400, 100 mM CaCl2

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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: _

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

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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: 2.75→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

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