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- PDB-5nv9: Substrate-bound outward-open state of a Na+-coupled sialic acid s... -

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Entry
Database: PDB / ID: 5nv9
TitleSubstrate-bound outward-open state of a Na+-coupled sialic acid symporter reveals a novel Na+-site
ComponentsPutative sodium:solute symporter
KeywordsMEMBRANE PROTEIN / membrane symporter / sialic acid / Outward-open / sodium-coupled
Function / homology
Function and homology information


symporter activity / sodium ion transport / membrane
Similarity search - Function
Sodium/solute symporter / Sodium/glucose symporter superfamily / Sodium:solute symporter family / Sodium:solute symporter family profile.
Similarity search - Domain/homology
PHOSPHATE ION / N-acetyl-beta-neuraminic acid / Putative sodium:solute symporter
Similarity search - Component
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsWahlgren, W.Y. / North, R.A. / Dunevall, E. / Paz, A. / Goyal, P. / Bisignano, P. / Grabe, M. / Dobson, R. / Abramson, J. / Ramaswamy, S. / Friemann, R.
Funding support Sweden, Italy, United States, India, New Zealand, 7items
OrganizationGrant numberCountry
Swedish Research Council2011-5790 Sweden
Swedish Research Council2010-1795, 221-2013-730 Sweden
Swedish Governmental Agency for Innovation Systems (VINNOVA)2013-04655 Sweden
Italian Ministry of Instruction University and ResearchPON01_00937 Italy
National Institutes of HealthR01GM078844, R01GM089740 United States
Indo-Swedish grant awarded by Department of BiotechnologyBT/IN/Sweden/41/SR/2013 India
Royal Society of New ZealandUOC1506 New Zealand
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 2.0May 16, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Non-polymer description / Polymer sequence / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / entity_poly / entity_poly_seq / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _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 / _entity.formula_weight / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_poly_seq_scheme.mon_id / _pdbx_unobs_or_zero_occ_residues.auth_comp_id / _pdbx_unobs_or_zero_occ_residues.label_comp_id
Revision 2.1Oct 16, 2019Group: Data collection / Category: chem_comp / reflns_shell / Item: _chem_comp.type
Revision 2.2Jul 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative sodium:solute symporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8946
Polymers54,9331
Non-polymers9615
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1100 Å2
ΔGint-5 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.590, 98.070, 54.780
Angle α, β, γ (deg.)90.00, 92.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative sodium:solute symporter


Mass: 54932.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (strain HI4320) (bacteria)
Strain: HI4320 / Gene: PMI2976 / Production host: Escherichia coli (E. coli) / References: UniProt: B4EZY7

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Sugars , 2 types, 2 molecules

#3: Sugar ChemComp-SLB / N-acetyl-beta-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: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 3 types, 223 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 3.19 Å3/Da / Density % sol: 61.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M sodium citrate pH 5, 0.2-0.5M potassium chloride, 30-40% pentaerythritol propoxylate (5/4/PO/OH)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.97858 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 30, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97858 Å / Relative weight: 1
ReflectionResolution: 1.95→78.4 Å / Num. obs: 49833 / % possible obs: 99.2 % / Redundancy: 3.24 % / Net I/σ(I): 6.43

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
XSCALEdata scaling
SHELXSphasing
RefinementResolution: 1.95→78.4 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.029 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.141
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. A NA IS MODELLED AT THE NA3 BINDING SITE DUE TO TWO REASONS: THE BOND DISTANCES ARE BETWEEN 2.1-2.5A WHICH IS CONSISTENT WITH NA, AS WELL ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. A NA IS MODELLED AT THE NA3 BINDING SITE DUE TO TWO REASONS: THE BOND DISTANCES ARE BETWEEN 2.1-2.5A WHICH IS CONSISTENT WITH NA, AS WELL AS THE COORDINATION NUMBER 5.
RfactorNum. reflection% reflectionSelection details
Rfree0.24346 2536 5.1 %RANDOM
Rwork0.19882 ---
obs0.20104 47316 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.973 Å2
Baniso -1Baniso -2Baniso -3
1-2.91 Å20 Å20.17 Å2
2---1.27 Å20 Å2
3----1.65 Å2
Refinement stepCycle: 1 / Resolution: 1.95→78.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3707 0 63 220 3990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.023872
X-RAY DIFFRACTIONr_bond_other_d0.0010.023800
X-RAY DIFFRACTIONr_angle_refined_deg1.7351.9835273
X-RAY DIFFRACTIONr_angle_other_deg0.92538710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6265482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.93222.5132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16915572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1481515
X-RAY DIFFRACTIONr_chiral_restr0.1080.2632
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214231
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02907
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1112.7541922
X-RAY DIFFRACTIONr_mcbond_other2.1072.7521921
X-RAY DIFFRACTIONr_mcangle_it2.9344.1122400
X-RAY DIFFRACTIONr_mcangle_other2.9354.1142401
X-RAY DIFFRACTIONr_scbond_it2.9953.1491950
X-RAY DIFFRACTIONr_scbond_other2.9543.1451947
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2684.5992866
X-RAY DIFFRACTIONr_long_range_B_refined6.32224.6864788
X-RAY DIFFRACTIONr_long_range_B_other6.13124.3684707
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.398 196 -
Rwork0.404 3447 -
obs--99.48 %

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