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- PDB-8omz: Wide inward-open unliganded UraA in complex with a conformation-s... -

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Basic information

Entry
Database: PDB / ID: 8omz
TitleWide inward-open unliganded UraA in complex with a conformation-selective synthetic nanobody
Components
  • Sy45
  • Uracil permease
KeywordsMEMBRANE PROTEIN / SLC23 / Uracil transporter / UraA / sybody / nanobody
Function / homology
Function and homology information


uracil:monoatomic cation symporter activity / uracil transport / uracil import across plasma membrane / uracil transmembrane transporter activity / protein homodimerization activity / membrane / plasma membrane
Similarity search - Function
Xanthine/uracil permease / Xanthine/uracil permeases family signature. / Nucleobase cation symporter 2 family / Permease family
Similarity search - Domain/homology
Biological speciesEscherichia coli O157:H7 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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
DepositionMar 31, 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)130,91122
Polymers125,3724
Non-polymers5,53918
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17160 Å2
ΔGint-9 kcal/mol
Surface area41480 Å2
Unit cell
Length a, b, c (Å)87.140, 118.110, 94.930
Angle α, β, γ (deg.)90.000, 100.424, 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

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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, b2497, JW2482 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: P0AGM7
#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, 14 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.: 11 / 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.: 3 / Source method: obtained synthetically / Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 2 types, 4 molecules

#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM

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Details

Has ligand of interestN
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: 3.83 Å3/Da / Density % sol: 67.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 50 mM Tris, 50 mM magnesium acetate, 34% PEG400, 0.1% benzamidine hydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.5→29.53 Å / Num. obs: 23921 / % possible obs: 99.7 % / Redundancy: 13.583 % / Biso Wilson estimate: 109.101 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.072 / Χ2: 0.917 / Net I/σ(I): 20.67
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.5-3.5913.3220.6544.6417550.9840.68199.9
3.59-3.6914.3140.5235.7717140.9940.54299.8
3.69-3.814.1830.3737.5616920.9950.38799.9
3.8-3.9114.1210.3018.5215930.9970.31399.9
3.91-4.0413.9460.22511.1115840.9980.23499.9
4.04-4.1813.910.16213.4715270.9990.16899.9
4.18-4.3413.6020.12716.3514820.9990.13299.7
4.34-4.5212.8150.10618.6713970.9990.1199.9
4.52-4.7212.6110.08621.4713630.9990.0999.9
4.72-4.9514.0730.08923.4412960.9990.09299.7
4.95-5.2214.2220.07925.5212430.9990.082100
5.22-5.5313.9840.09225.511760.9990.09599.7
5.53-5.9213.8080.08627.2310970.9980.09100
5.92-6.3913.0280.07629.7710390.9990.07999.8
6.39-711.9630.06332.859450.9990.065100
7-7.8313.4880.04742.978600.9990.049100
7.83-9.0413.8020.03550.7176310.03799.6
9.04-11.0713.1010.03352.046420.9990.034100
11.07-15.6511.6060.03149.9250210.032100

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3660-000refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHENIX1.17.1-3660-000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XLS, 1ZVH

5xls

1zvh


Resolution: 3.5→29.53 Å / SU ML: 0.4931 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.5171
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2599 1201 5.1 %
Rwork0.2408 22329 -
obs0.2417 23530 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.45 Å2
Refinement stepCycle: LAST / Resolution: 3.5→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7969 0 378 0 8347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00138522
X-RAY DIFFRACTIONf_angle_d0.386611577
X-RAY DIFFRACTIONf_chiral_restr0.03541447
X-RAY DIFFRACTIONf_plane_restr0.00341363
X-RAY DIFFRACTIONf_dihedral_angle_d19.52831276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.640.3306950.34172198X-RAY DIFFRACTION86.86
3.64-3.810.33981510.31532468X-RAY DIFFRACTION98.53
3.81-4.010.311380.2682489X-RAY DIFFRACTION99.96
4.01-4.260.24031210.2352515X-RAY DIFFRACTION99.66
4.26-4.580.24771470.20662520X-RAY DIFFRACTION99.93
4.58-5.040.27621210.20532531X-RAY DIFFRACTION99.96
5.04-5.770.22791430.23462505X-RAY DIFFRACTION100
5.77-7.250.27591350.23552552X-RAY DIFFRACTION100
7.25-29.530.21491500.2222551X-RAY DIFFRACTION99.59
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)
10.581355389862-0.43431153523-0.3509789551331.35053590218-0.02355576239841.780203895930.0970164183327-0.02675841612750.187130650655-0.1848987896380.08581198368060.0374469731475-0.635828083127-0.06884508879080.04351617084420.635562100732-0.002884772151360.04767505601410.545671315851-0.039132857310.4429452276475.9626456401315.409694493718.4972985541
20.1604789271920.138571757865-0.203784375770.392374760468-0.4465708716550.5270074371720.170278049380.2535016561050.059832022925-0.519414058062-0.262496776231-0.2772105767640.1247945085050.404280572178-0.004233475151320.785490602056-0.05463324742730.07805828402810.799860582819-0.06030475145360.48664111454627.5626269634-0.330931046954-4.16058255965
30.3546243007620.254691756894-0.3306095355561.316230272790.3502724240692.14501454807-0.1220633956230.041363744004-0.1648901734030.329628837730.1224541192090.1035494463960.944761136256-0.10759388539-0.008482072705920.7966568786520.04796148488710.07388173337410.576130310058-0.02185041510690.4615458424613.68975252511-24.954494221331.4678795491
41.135592329570.2339172187470.06006261100920.762454384534-0.1731168790420.1266632869980.136732421061-0.04753394717890.4104391437550.235529610633-0.31585130789-0.05177717760980.2300275288130.39750666153-0.05753625966710.8122250105340.1125810395260.00884352047750.7574363377730.01518119601190.43079541844515.7053578468-8.9352807280660.3162661059
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 3 through 412)
2X-RAY DIFFRACTION2(chain 'B' and resid -1 through 125)
3X-RAY DIFFRACTION3(chain 'C' and resid 4 through 412)
4X-RAY DIFFRACTION4(chain 'D' and resid 0 through 125)

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