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- PDB-5euu: Rat prestin STAS domain in complex with chloride -

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Basic information

Entry
Database: PDB / ID: 5euu
TitleRat prestin STAS domain in complex with chloride
ComponentsPrestin,Prestin
KeywordsTRANSPORT PROTEIN / Anion-binding site / protein-anion complex
Function / homology
Function and homology information


oxalate transport / lateral wall of outer hair cell / fructose transmembrane transport / response to salicylic acid / sulfate transmembrane transporter activity / negative regulation of monoatomic ion transmembrane transport / secondary active sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / response to potassium ion / response to auditory stimulus ...oxalate transport / lateral wall of outer hair cell / fructose transmembrane transport / response to salicylic acid / sulfate transmembrane transporter activity / negative regulation of monoatomic ion transmembrane transport / secondary active sulfate transmembrane transporter activity / oxalate transmembrane transporter activity / response to potassium ion / response to auditory stimulus / monoatomic anion transmembrane transport / response to salt / chloride:bicarbonate antiporter activity / response to thyroid hormone / bicarbonate transport / bicarbonate transmembrane transporter activity / positive regulation of cell motility / chloride transport / chloride transmembrane transporter activity / spectrin binding / cochlea development / cytoskeletal motor activity / positive regulation of cell size / lateral plasma membrane / monoatomic ion transmembrane transport / chloride transmembrane transport / regulation of membrane potential / response to ischemia / sensory perception of sound / regulation of cell shape / basolateral plasma membrane / response to xenobiotic stimulus / protein homodimerization activity / identical protein binding / plasma membrane
Similarity search - Function
STAS domain / Sulphate anion transporter, conserved site / SLC26A transporters signature. / SLC26A/SulP transporter / SLC26A/SulP transporter domain / Sulfate permease family / Transcription Regulator spoIIAA / STAS domain / STAS domain profile. / STAS domain ...STAS domain / Sulphate anion transporter, conserved site / SLC26A transporters signature. / SLC26A/SulP transporter / SLC26A/SulP transporter domain / Sulfate permease family / Transcription Regulator spoIIAA / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Prestin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsLolli, G. / Pasqualetto, E. / Costanzi, E. / Bonetto, G. / Battistutta, R.
Funding support Italy, 2items
OrganizationGrant numberCountry
European Community's Seventh Framework Programme (FP7/2007-2013) under BioStruct-Xgrant agreement Number 283570
Fondazione Cassa di Risparmio di Padova e RovigoProgetto di Eccellenza Italy
Citation
Journal: Biochem.J. / Year: 2016
Title: The STAS domain of mammalian SLC26A5 prestin harbours an anion-binding site.
Authors: Lolli, G. / Pasqualetto, E. / Costanzi, E. / Bonetto, G. / Battistutta, R.
#1: Journal: J.Mol.Biol. / Year: 2010
Title: Structure of the Cytosolic Portion of the Motor Protein Prestin and Functional Role of the STAS Domain in SLC26/SulP Anion Transporters
Authors: Pasqualetto, E. / Aiello, R. / Gesiot, L. / Bonetto, G. / Bellanda, M. / Battistutta, R.
History
DepositionNov 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prestin,Prestin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3688
Polymers15,7671
Non-polymers6027
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-6 kcal/mol
Surface area7830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.133, 62.133, 66.587
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Prestin,Prestin / Solute carrier family 26 member 5


Mass: 15766.707 Da / Num. of mol.: 1 / Fragment: STAS domain,STAS domain,STAS domain,STAS domain
Mutation: Residues 564-636 (variable loop) are deleted, GlySer are inserted between position 563 and 637,Residues 564-636 (variable loop) are deleted, GlySer are inserted between position 563 and ...Mutation: Residues 564-636 (variable loop) are deleted, GlySer are inserted between position 563 and 637,Residues 564-636 (variable loop) are deleted, GlySer are inserted between position 563 and 637,Residues 564-636 (variable loop) are deleted, GlySer are inserted between position 563 and 637,Residues 564-636 (variable loop) are deleted, GlySer are inserted between position 563 and 637
Source method: isolated from a genetically manipulated source
Details: Residues 564-636 (variable loop) are deleted, GlySer are inserted between position 563 and 637
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Slc26a5, Pres / Plasmid: pET SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9EPH0

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Non-polymers , 5 types, 94 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Mes pH 6.5, 1.8 M Ammonium Sulphate, 5% (w/v) PEG400, 0.1% (w/v) octyl-beta-D-glucopyranoside. Crystals were soaked with precipitant solution supplemented with 1 M Ammonium Chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 2 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 23, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 2 Å / Relative weight: 1
ReflectionResolution: 1.87→41.85 Å / Num. all: 196474 / Num. obs: 12555 / % possible obs: 98.8 % / Redundancy: 15.6 % / Rmerge(I) obs: 0.071 / Rsym value: 0.075 / Net I/σ(I): 26.2
Reflection shellResolution: 1.87→1.91 Å / Redundancy: 7 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 2.2 / % possible all: 84.2

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LLO

3llo


Resolution: 1.87→31.067 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 1288 5.49 %
Rwork0.1572 22176 -
obs0.1593 23464 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 152.81 Å2 / Biso mean: 38.2233 Å2 / Biso min: 14.77 Å2
Refinement stepCycle: final / Resolution: 1.87→31.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1014 0 87 87 1188
Biso mean--59.55 42.06 -
Num. residues----129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031065
X-RAY DIFFRACTIONf_angle_d0.7641436
X-RAY DIFFRACTIONf_chiral_restr0.031164
X-RAY DIFFRACTIONf_plane_restr0.003182
X-RAY DIFFRACTIONf_dihedral_angle_d14.107384
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8701-1.9450.33731390.27892210234988
1.945-2.03350.19421120.182224962608100
2.0335-2.14070.1981440.167725352679100
2.1407-2.27470.20461640.143724692633100
2.2747-2.45030.18661530.141924712624100
2.4503-2.69680.18591220.155225272649100
2.6968-3.08670.18311300.159524992629100
3.0867-3.88770.19841830.143224662649100
3.8877-31.07080.18641410.155525032644100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.13690.04850.05550.4025-0.15240.2688-0.0492-0.1718-0.30160.08840.08970.04190.34120.0706-0.00180.2021-0.0002-0.05870.21480.01810.2826-4.833814.0232-12.9306
20.1045-0.1658-0.22380.17540.3131.18890.4048-0.3765-0.22110.3733-0.07180.0653-0.3238-0.43350.10910.237-0.13910.02530.34020.03960.2312-14.128322.76230.6108
30.21690.26510.02360.31420.0499-0.01590.1365-0.2848-0.17360.2531-0.14510.05550.0176-0.1444-0.00060.1643-0.0258-0.00960.26930.00660.2066-10.016527.3197-6.8376
40.20010.2819-0.05130.4258-0.0328-0.00260.2752-0.6224-0.2070.6422-0.3412-0.1368-0.1562-0.033-0.03710.2795-0.1101-0.04950.37570.0220.1728-3.44830.66952.1346
50.16510.0940.09340.12010.02810.07850.0843-0.16170.21290.1042-0.1184-0.0048-0.1530.03180.00050.2165-0.0271-0.02040.2331-0.03170.2476-8.340536.6665-7.5454
60.0984-0.02-0.14010.1544-0.00590.22290.03790.11640.0822-0.08510.1248-0.109-0.16710.27070.00040.1855-0.0268-0.02110.2872-0.00430.22331.740529.792-13.6513
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 505 through 539 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 540 through 552)A0
3X-RAY DIFFRACTION3chain 'A' and (resid 638 through 657 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 658 through 671 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 672 through 698 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 699 through 718 )A0

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