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- PDB-6qd5: X-ray Structure of the Human Urea Channel SLC14A1/UT1 -

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Basic information

Entry
Database: PDB / ID: 6qd5
TitleX-ray Structure of the Human Urea Channel SLC14A1/UT1
ComponentsUrea transporter 1
KeywordsTRANSPORT PROTEIN / urea / SLC / transport / integral membrane protein / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


urea channel activity / urea transport / Transport of bile salts and organic acids, metal ions and amine compounds / urea transmembrane transporter activity / urea transmembrane transport / water transmembrane transporter activity / establishment of localization in cell / transmembrane transport / basolateral plasma membrane / 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
CHOLESTEROL HEMISUCCINATE / Urea transporter 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.398 Å
AuthorsDietz, L. / Chi, G. / Pike, A.C.W. / Moreau, C. / Man, H. / Snee, M. / Scacioc, A. / Shrestha, L. / Mukhopadhyay, S.M.M. / Mckinley, G. ...Dietz, L. / Chi, G. / Pike, A.C.W. / Moreau, C. / Man, H. / Snee, M. / Scacioc, A. / Shrestha, L. / Mukhopadhyay, S.M.M. / Mckinley, G. / Ellis, K. / Kliszcak, M. / Chalk, R. / Borkowska, O. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Durr, K.L. / Structural Genomics Consortium (SGC)
Funding support1items
OrganizationGrant numberCountry
European Commission115766
CitationJournal: To Be Published
Title: X-ray Structure of the Human Urea Channel SLC14A1/UT1
Authors: Dietz, L. / Chi, G. / Pike, A.C.W. / Moreau, C. / Man, H. / Snee, M. / Scacioc, A. / Shrestha, L. / Mukhopadhyay, S.M.M. / Mckinley, G. / Ellis, K. / Kliszcak, M. / Chalk, R. / Borkowska, O. ...Authors: Dietz, L. / Chi, G. / Pike, A.C.W. / Moreau, C. / Man, H. / Snee, M. / Scacioc, A. / Shrestha, L. / Mukhopadhyay, S.M.M. / Mckinley, G. / Ellis, K. / Kliszcak, M. / Chalk, R. / Borkowska, O. / Burgess-Brown, N.A. / von Delft, F. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Durr, K.L. / Structural Genomics Consortium (SGC)
History
DepositionDec 31, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 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 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,09911
Polymers40,1771
Non-polymers2,92210
Water1,27971
1
A: Urea transporter 1
hetero molecules

A: Urea transporter 1
hetero molecules

A: Urea transporter 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,29833
Polymers120,5323
Non-polymers8,76530
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
Buried area16820 Å2
ΔGint-29 kcal/mol
Surface area39630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.331, 112.331, 87.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 40177.410 Da / Num. of mol.: 1 / Mutation: N211Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC14A1, HUT11, JK, RACH1, UT1, UTE / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q13336
#2: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-Y01 / CHOLESTEROL HEMISUCCINATE


Mass: 486.726 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H50O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 4.12 Å3/Da / Density % sol: 70.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 36% PEG400 -- 0.1M tris pH 8.5 -- 0.05M lithium sulfate -- 0.05M sodium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.398→47.335 Å / Num. obs: 24788 / % possible obs: 99.75 % / Redundancy: 2 % / Biso Wilson estimate: 50.76 Å2 / CC1/2: 0.996 / Rpim(I) all: 0.04728 / Net I/av σ(I): 9.15 / Net I/σ(I): 9.02
Reflection shellResolution: 2.398→2.484 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.29 / Num. unique obs: 2434 / CC1/2: 0.475 / Rpim(I) all: 0.6137 / % possible all: 98.66

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EZC

4ezc


Resolution: 2.398→47.335 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.12
RfactorNum. reflection% reflection
Rfree0.2251 1165 4.7 %
Rwork0.1754 --
obs0.1777 24762 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.398→47.335 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2702 0 201 71 2974
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092981
X-RAY DIFFRACTIONf_angle_d1.0464055
X-RAY DIFFRACTIONf_dihedral_angle_d8.3641734
X-RAY DIFFRACTIONf_chiral_restr0.053490
X-RAY DIFFRACTIONf_plane_restr0.007464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3977-2.50690.31731520.26852880X-RAY DIFFRACTION99
2.5069-2.6390.26551350.22282951X-RAY DIFFRACTION100
2.639-2.80430.27761260.18592953X-RAY DIFFRACTION100
2.8043-3.02080.21461550.16232942X-RAY DIFFRACTION100
3.0208-3.32480.20521690.15832907X-RAY DIFFRACTION100
3.3248-3.80570.2041420.152971X-RAY DIFFRACTION100
3.8057-4.7940.21211410.15442967X-RAY DIFFRACTION100
4.794-47.34410.22831450.19393026X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 133.7854 Å / Origin y: 61.1717 Å / Origin z: -1.3724 Å
111213212223313233
T0.2466 Å20.0217 Å2-0.0092 Å2-0.4557 Å2-0.05 Å2--0.3337 Å2
L2.3788 °2-0.1709 °2-0.1208 °2-3.1428 °2-0.1413 °2--1.8226 °2
S0.0266 Å °-0.0122 Å °-0.0571 Å °-0.0104 Å °0.0167 Å °-0.5005 Å °0.0509 Å °0.4758 Å °-0.0499 Å °
Refinement TLS groupSelection details: all

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