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- PDB-5nva: Substrate-bound outward-open state of a Na+-coupled sialic acid s... -

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Entry
Database: PDB / ID: 5nva
TitleSubstrate-bound outward-open state of a Na+-coupled sialic acid symporter reveals a novel Na+-site
ComponentsPutative sodium:solute symporter
KeywordsMEMBRANE PROTEIN / membrane transporter / sialic acid / Outward-open / sodium-coupled
Function / homologySodium/solute symporter / Sodium/glucose symporter superfamily / Sodium:solute symporter family / Sodium:solute symporter family profile. / symporter activity / sodium ion transport / membrane / N-acetyl-beta-neuraminic acid / Putative sodium:solute symporter
Function and homology information
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsWahlgren, W.Y. / North, R.A. / Dunevall, E. / Goyal, P. / Grabe, M. / Dobson, R. / Abramson, J. / Ramaswamy, S. / Friemann, R.
Funding support Sweden, Italy, United States, India, New Zealand, United Kingdom, 9items
OrganizationGrant numberCountry
Swedish Research Council2011-5790 Sweden
Swedish Research Council2010-1759 Sweden
Swedish Research Council221-2013-730 Sweden
The Swedish Governmental Agency for Innovation Systems (VINNOVA)2013-04655 Sweden
Italian Ministry of Instruction University and ResearchPON01_00937 Italy
National Institutes of HealthR01GM078844 and R01GM089740 United States
Indo-Swedish grant by the Department of BiotechnologyBT/IN/Sweden/41/SR/2013 India
Royal Society of New ZealandUOC1506 New Zealand
Wellcome TrustWT/099165/Z/12/Z United Kingdom
CitationJournal: Nat Commun / Year: 2018
Title: Substrate-bound outward-open structure of a Na+-coupled sialic acid symporter reveals a new Na+site.
Authors: Wahlgren, W.Y. / Dunevall, E. / North, R.A. / Paz, A. / Scalise, M. / Bisignano, P. / Bengtsson-Palme, J. / Goyal, P. / Claesson, E. / Caing-Carlsson, R. / Andersson, R. / Beis, K. / ...Authors: Wahlgren, W.Y. / Dunevall, E. / North, R.A. / Paz, A. / Scalise, M. / Bisignano, P. / Bengtsson-Palme, J. / Goyal, P. / Claesson, E. / Caing-Carlsson, R. / Andersson, R. / Beis, K. / Nilsson, U.J. / Farewell, A. / Pochini, L. / Indiveri, C. / Grabe, M. / Dobson, R.C.J. / Abramson, J. / Ramaswamy, S. / Friemann, R.
History
DepositionMay 3, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1May 16, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 16, 2019Group: Data collection / Category: chem_comp / reflns_shell / Item: _chem_comp.type
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4May 8, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative sodium:solute symporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6324
Polymers54,2761
Non-polymers3553
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area590 Å2
ΔGint-1 kcal/mol
Surface area18320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.788, 97.764, 151.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Putative sodium:solute symporter


Mass: 54276.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (strain HI4320) (bacteria)
Gene: PMI2976 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EZY7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Sugar ChemComp-SLB / N-acetyl-beta-neuraminic acid / N-acetylneuraminic acid / sialic acid / O-sialic acid / 5-N-ACETYL-BETA-D-NEURAMINIC ACID / BETA-SIALIC ACID / N-Acetylneuraminic acid


Type: D-saccharide, beta linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-neuraminic acidCOMMON NAMEGMML 1.0
b-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 3.33 Å3/Da / Density % sol: 63.09 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1M sodium citrate pH5, 0.2-0.25M potassium chloride, 30-40% (w/v) pentaerythritol propoxylate (5/4/PO/OH)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→82.18 Å / Num. obs: 33923 / % possible obs: 96.64 % / Redundancy: 4.9 % / Net I/σ(I): 8.39

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→82.176 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.09
Details: A NA IS MODELLED AT THE NA3 BINDING SITE BOND DISTANCES ARE BETWEEN 2.1 TO 2.5A WHICH IS CONSISTENT WITH NA, AS WELL AS THE COORDINATION NUMBER 5.
RfactorNum. reflection% reflection
Rfree0.2608 3602 5.88 %
Rwork0.2243 --
obs0.2264 61303 93.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.26→82.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3639 0 23 164 3826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023761
X-RAY DIFFRACTIONf_angle_d0.5065122
X-RAY DIFFRACTIONf_dihedral_angle_d3.8732941
X-RAY DIFFRACTIONf_chiral_restr0.038613
X-RAY DIFFRACTIONf_plane_restr0.004619
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.28980.34021430.33522068X-RAY DIFFRACTION86
2.2898-2.32120.35761390.31542187X-RAY DIFFRACTION91
2.3212-2.35430.32011400.30232178X-RAY DIFFRACTION94
2.3543-2.38950.30061380.29842219X-RAY DIFFRACTION93
2.3895-2.42680.34171400.28182290X-RAY DIFFRACTION95
2.4268-2.46660.32361400.27812205X-RAY DIFFRACTION94
2.4666-2.50910.37691420.29072236X-RAY DIFFRACTION94
2.5091-2.55480.31191370.28332282X-RAY DIFFRACTION95
2.5548-2.60390.32761380.27482249X-RAY DIFFRACTION95
2.6039-2.6570.31351390.25672235X-RAY DIFFRACTION94
2.657-2.71480.22631390.24832249X-RAY DIFFRACTION94
2.7148-2.7780.30681400.24152210X-RAY DIFFRACTION94
2.778-2.84750.32641340.23152259X-RAY DIFFRACTION95
2.8475-2.92440.28641400.22692253X-RAY DIFFRACTION94
2.9244-3.01050.30791400.21592229X-RAY DIFFRACTION94
3.0105-3.10770.28821400.21672231X-RAY DIFFRACTION94
3.1077-3.21880.21561420.21422258X-RAY DIFFRACTION94
3.2188-3.34760.25021310.20412207X-RAY DIFFRACTION94
3.3476-3.50.2331420.19552237X-RAY DIFFRACTION93
3.5-3.68450.23981350.19522216X-RAY DIFFRACTION94
3.6845-3.91540.27181360.20612217X-RAY DIFFRACTION93
3.9154-4.21770.25251330.19872225X-RAY DIFFRACTION93
4.2177-4.64210.20821420.18682207X-RAY DIFFRACTION93
4.6421-5.31370.21561360.20432214X-RAY DIFFRACTION92
5.3137-6.69420.26211350.2352154X-RAY DIFFRACTION91
6.6942-82.22990.18691410.18762186X-RAY DIFFRACTION92

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