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- PDB-4ezd: Crystal Structure of the UT-B Urea Transporter from Bos Taurus Bo... -

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Basic information

Entry
Database: PDB / ID: 4ezd
TitleCrystal Structure of the UT-B Urea Transporter from Bos Taurus Bound to Selenourea
ComponentsUrea transporter 1
KeywordsTRANSPORT PROTEIN / Membrane protein / channel / urea transport / slc14 / Structural Genomics / PSI-Biology / New York Consortium on Membrane Protein Structure / NYCOMPS
Function / homology
Function and homology information


Transport of bile salts and organic acids, metal ions and amine compounds / urea channel activity / urea transmembrane transport / urea transmembrane transporter activity / water transmembrane transporter activity / establishment of localization in cell / basolateral plasma membrane / identical protein binding / plasma membrane
Similarity search - Function
Urea transporter / Urea transporter / Ammonium transporter fold / Ammonium transporter AmtB like domains / Ammonium/urea transporter / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
beta-D-glucopyranose / selenourea / Chem-SPL / Urea transporter 1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsCao, Y. / Levin, E.J. / Zhou, M. / New York Consortium on Membrane Protein Structure (NYCOMPS)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structure and permeation mechanism of a mammalian urea transporter.
Authors: Levin, E.J. / Cao, Y. / Enkavi, G. / Quick, M. / Pan, Y. / Tajkhorshid, E. / Zhou, M.
History
DepositionMay 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2012Group: Database references
Revision 1.2Jul 25, 2012Group: Other
Revision 1.3Jan 9, 2013Group: Database references
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Feb 28, 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: Urea transporter 1
B: Urea transporter 1
C: Urea transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,86930
Polymers124,4893
Non-polymers6,38027
Water3,315184
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14610 Å2
ΔGint-44 kcal/mol
Surface area41520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.002, 106.227, 105.816
Angle α, β, γ (deg.)90.000, 98.180, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is the asymmetric unit.

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Urea transporter 1 / Solute carrier family 14 member 1 / Urea transporter B / UT-B / Urea transporter / erythrocyte


Mass: 41496.449 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: SLC14A1, UT-B / Plasmid: pFastBac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q5QF96

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Sugars , 2 types, 18 molecules

#3: Sugar
ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 193 molecules

#2: Chemical
ChemComp-SEY / selenourea


Mass: 123.016 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH4N2Se
#5: Chemical ChemComp-SPL / OCTANOIC ACID (2-HYDROXY-1-HYDROXYMETHYL-HEPTADEC-3-ENYL)-AMIDE / CERAMIDE


Mass: 425.688 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H51NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 3.35 Å3/Da / Density % sol: 63.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 25% PEG 400, 50 mM sodium sulfate, 50 mM lithium sulfate, 0.2 mM DDAO, 100 mM Tris pH 8.0-8.5, 20 mM selenourea, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9788 Å
DetectorType: ADSC Q315R / Detector: CCD / Date: Jan 29, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 56923 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.168 / Χ2: 1.025 / Net I/σ(I): 6.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.546.70.92127880.941100
2.54-2.596.80.8728840.9431100
2.59-2.646.90.85428061.0161100
2.64-2.6970.72628160.9641100
2.69-2.757.10.6328550.981100
2.75-2.827.10.53828381.0211100
2.82-2.897.10.46328621.0811100
2.89-2.967.20.43828271.0621100
2.96-3.057.20.40628111.0261100
3.05-3.157.20.34528501.1231100
3.15-3.267.10.28328661.0651100
3.26-3.397.10.22928221.0611100
3.39-3.557.10.18128431.0721100
3.55-3.737.10.15828510.9661100
3.73-3.977.10.13228630.9961100
3.97-4.277.10.11828300.9971100
4.27-4.770.10328771.0051100
4.7-5.386.80.09228601.0311100
5.38-6.786.90.09228791.1141100
6.78-5070.10228951.018198.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→47.37 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.2311 / WRfactor Rwork: 0.2008 / Occupancy max: 1 / Occupancy min: 0.62 / FOM work R set: 0.8609 / SU B: 14.915 / SU ML: 0.167 / SU R Cruickshank DPI: 0.3263 / SU Rfree: 0.2304 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.326 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2285 2828 5 %RANDOM
Rwork0.1973 ---
obs0.1988 56835 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.42 Å2 / Biso mean: 51.4817 Å2 / Biso min: 23.55 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20 Å2-0.33 Å2
2---1.77 Å20 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7891 0 410 184 8485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.028520
X-RAY DIFFRACTIONr_angle_refined_deg1.192.0111622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7751034
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78223.962260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.529151239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7721511
X-RAY DIFFRACTIONr_chiral_restr0.0770.21415
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216015
LS refinement shellResolution: 2.499→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 184 -
Rwork0.244 3864 -
all-4048 -
obs--99.7 %
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)
13.4585.24791.45068.44122.85394.0637-0.25720.5111-0.5939-0.76590.5581-0.86020.18170.9515-0.30090.64240.3284-0.06560.8201-0.20691.110749.634-37.014524.139
22.1178-0.10980.1672.3131-0.02661.72770.1014-0.0165-0.44940.1003-0.0484-0.07440.42090.1637-0.0530.16830.0299-0.00780.0932-0.02530.167432.9364-23.107529.3356
30.97330.01030.65441.76540.03561.58030.0899-0.0872-0.22970.3627-0.0738-0.23630.08010.1268-0.01610.1687-0.0169-0.03120.12220.06380.134340.7392-11.221142.8079
46.0607-0.64462.20325.7322-0.92365.97270.42520.2812-0.9005-0.4352-0.1233-0.88930.64711.1139-0.3020.11750.10530.0650.5588-0.07260.522458.5295-15.034925.733
55.3278-0.5631-0.349512.65610.80376.84490.03541.3899-0.0182-1.5202-0.3233-0.6348-0.30740.22110.28780.89860.0124-0.20010.8011-0.0010.26614.86285.405-11.4327
61.9920.3730.76521.98490.24072.3876-0.03350.30380.1687-0.3455-0.0380.4606-0.2329-0.31430.07150.24490.0585-0.06730.244-0.0050.168714.16339.48088.8547
70.8472-0.13210.37161.7097-0.09971.20620.04450.0835-0.2204-0.2089-0.07530.3604-0.0024-0.20180.03070.0590.0109-0.01690.181-0.07330.180614.9284-7.810817.1443
86.4114-1.09182.39243.19410.13394.74730.09140.939-0.2069-1.0446-0.20790.0473-0.08470.06790.11650.70360.00190.05720.5117-0.13130.208625.9676-13.5729-4.4122
98.7588-4.27873.36092.127-1.60037.81821.01931.13370.3447-0.5449-0.5756-0.38230.03231.0175-0.44370.7181-0.4202-0.00930.88970.23451.407662.141527.648626.8933
101.05060.09150.10241.67170.23281.8132-0.03530.00090.21520.2594-0.0493-0.3559-0.28490.27810.08460.1942-0.0545-0.05580.13490.03340.161443.618514.129237.7558
111.5938-0.1346-0.09061.34950.16980.6984-0.03820.05920.1831-0.02-0.1037-0.0858-0.4081-0.02510.14190.3554-0.0016-0.04260.08390.01210.094530.494623.629426.8957
127.0451.2401-0.65535.7849-0.46742.80610.04480.18170.432-0.1436-0.1781-0.7063-0.30270.51920.13330.3153-0.07540.060.30840.12410.289946.54823.022310.8193
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A31 - 51
2X-RAY DIFFRACTION2A52 - 188
3X-RAY DIFFRACTION3A189 - 351
4X-RAY DIFFRACTION4A352 - 375
5X-RAY DIFFRACTION5B31 - 51
6X-RAY DIFFRACTION6B52 - 163
7X-RAY DIFFRACTION7B164 - 360
8X-RAY DIFFRACTION8B361 - 377
9X-RAY DIFFRACTION9C31 - 49
10X-RAY DIFFRACTION10C50 - 207
11X-RAY DIFFRACTION11C208 - 352
12X-RAY DIFFRACTION12C353 - 376

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