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- PDB-8oo1: Wide inward-open liganded UraA in complex with a conformation-sel... -

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Basic information

Entry
Database: PDB / ID: 8oo1
TitleWide inward-open liganded UraA in complex with a conformation-selective synthetic nanobody
Components
  • Sy45
  • Uracil permease
KeywordsMEMBRANE PROTEIN / SLC23 / Uracil transporter / UraA / sybody / nanobody
Function / homologyxanthine transmembrane transporter activity / Xanthine/uracil permease / Xanthine/uracil permeases family signature. / Nucleobase cation symporter 2 family / Permease family / symporter activity / plasma membrane / URACIL / Uracil permease
Function and homology information
Biological speciesEscherichia coli O157:H7 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsKuhn, B.T. / Geertsma, E.R.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB807-P23, CEF-MC Germany
CitationJournal: Nat Commun / Year: 2024
Title: Interdomain-linkers control conformational transitions in the SLC23 elevator transporter UraA.
Authors: Kuhn, B.T. / Zoller, J. / Zimmermann, I. / Gemeinhardt, T. / Ozkul, D.H. / Langer, J.D. / Seeger, M.A. / Geertsma, E.R.
History
DepositionApr 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: 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 / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uracil permease
B: Sy45
C: Uracil permease
D: Sy45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,57015
Polymers125,3724
Non-polymers3,19811
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13130 Å2
ΔGint-47 kcal/mol
Surface area40860 Å2
Unit cell
Length a, b, c (Å)86.250, 116.820, 94.300
Angle α, β, γ (deg.)90.000, 100.485, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 5 through 412 or resid 550 through 502))A5 - 411
121(chain 'A' and (resid 5 through 412 or resid 550 through 502))A470
131(chain 'A' and (resid 5 through 412 or resid 550 through 502))A501 - 502
141(chain 'A' and (resid 5 through 412 or resid 550 through 502))A550
251(chain 'C' and (resid 5 through 412 or resid 550 through 502))C5 - 411
261(chain 'C' and (resid 5 through 412 or resid 550 through 502))C470
271(chain 'C' and (resid 5 through 412 or resid 550 through 502))C501 - 502
281(chain 'C' and (resid 5 through 412 or resid 550 through 502))C550
192chain 'B'B1 - 124
2102(chain 'D' and resid 1 through 125)D1 - 124

NCS ensembles :
ID
1
2

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Components

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Protein / Antibody , 2 types, 4 molecules ACBD

#1: Protein Uracil permease / Uracil transporter / Uracil/H(+) symporter UraA


Mass: 46017.875 Da / Num. of mol.: 2 / Mutation: G320P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria) / Gene: uraA, Z3760, ECs3359 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: P0AGM8
#2: Antibody Sy45


Mass: 16668.318 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli MC1061 (bacteria)

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Sugars , 2 types, 7 molecules

#4: Sugar
ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#6: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 2 types, 4 molecules

#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4N2O2 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.73 Å3/Da / Density % sol: 67.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 50 mM Tris, 50 mM magnesium acetate, 0.1% Benzamidine, 40% (v/v) PEG400, 1 mM uracil

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.01→49.42 Å / Num. obs: 23194 / % possible obs: 63.6 % / Redundancy: 6.8 % / Biso Wilson estimate: 50.78 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.159 / Rrim(I) all: 0.172 / Net I/σ(I): 10.14
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
3.01-3.090.322840.9580.351
3.09-3.180.432160.880.4661
3.18-3.270.4753630.8780.5171
3.27-3.370.4555320.9170.4961
3.37-3.480.6177170.8810.671
3.48-3.60.6499630.8880.7041
3.6-3.740.5613860.9380.6061
3.74-3.890.619370.9390.6541
3.89-4.060.51520610.9720.5571
4.06-4.260.37219620.9870.4021
4.26-4.490.27919030.9890.3031
4.49-4.760.22317670.9940.2411
4.76-5.090.22516720.9940.2421
5.09-5.50.24215770.9910.2611
5.5-6.030.23114390.9910.2491
6.03-6.740.17813020.9920.1921
6.74-7.780.09411580.9970.1021
7.78-9.530.0499760.9980.0531
9.53-13.480.0417580.9990.0441

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHENIX1.17.1_3660phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→49.42 Å / SU ML: 0.5047 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 34.0967
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2944 989 5.11 %
Rwork0.2711 18373 -
obs0.2724 19362 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.08 Å2
Refinement stepCycle: LAST / Resolution: 3.7→49.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7935 0 219 0 8154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00168330
X-RAY DIFFRACTIONf_angle_d0.452911334
X-RAY DIFFRACTIONf_chiral_restr0.03691403
X-RAY DIFFRACTIONf_plane_restr0.00341359
X-RAY DIFFRACTIONf_dihedral_angle_d20.14071205
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.90.3391150.32642316X-RAY DIFFRACTION86.6
3.9-4.140.34521420.29472669X-RAY DIFFRACTION99.93
4.14-4.460.2761310.26642659X-RAY DIFFRACTION99.89
4.46-4.910.27241620.24492644X-RAY DIFFRACTION99.72
4.91-5.620.29261330.2562691X-RAY DIFFRACTION99.96
5.62-7.070.27681470.28052673X-RAY DIFFRACTION99.96
7.07-49.420.28371590.25472721X-RAY DIFFRACTION99.41
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)
10.6525142558-0.485326095926-0.1398395763191.00228037414-0.04189696479451.146396586450.233289955043-0.02937827124520.076795993155-0.1283416734720.08945457412450.167793575641-0.545396218789-0.228407035620.258763655910.3743416376790.0258629516920.05935693298760.259847674323-0.07677486211440.2525544224615.8854369284615.153292297118.4489021748
20.398698242235-0.319506960353-0.3519258135960.3522183963810.4311200958891.274053008140.09371948335490.00813174509201-0.183424959811-0.1102328755260.0137269993113-0.107820324286-0.1698200667280.239875325206-0.07906707886060.147197778068-0.0251550012976-0.03631433490960.461988281837-0.04148915622870.38208494667827.6055615349-0.644319311237-4.08971642855
30.6185165028440.186943191155-0.381607272430.7228315001660.06726092844561.163875102030.0003405652891470.189274016068-0.04860093686890.2010595650350.1119018226410.1365053288570.629823928915-0.2543038064680.2907347819880.3940637877270.01412677363320.05236656083590.221008060643-0.06494477604210.1415455458773.94909422755-25.054541747731.2034748089
40.409793363936-0.0559817327614-0.3773387092660.2846706636090.7328293240432.00619068111-0.07114220255670.175237038732-0.05705084430260.0733377169055-0.0129426333072-0.0308859161660.3234468427280.171350358313-0.0344863074870.08409048855090.0370361351324-0.06771548949360.352787022823-0.03341767458480.26388114065415.9378789945-8.947729640659.9757509845
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 4 through 412)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 125)
3X-RAY DIFFRACTION3(chain 'C' and resid 5 through 412)
4X-RAY DIFFRACTION4(chain 'D' and resid 0 through 125)

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