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- PDB-6qv0: Structure of ATP-bound outward-facing TM287/288 in complex with s... -

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Basic information

Entry
Database: PDB / ID: 6qv0
TitleStructure of ATP-bound outward-facing TM287/288 in complex with sybody Sb_TM35
Components
  • ABC transporter, ATP-binding protein
  • Sb_TM35
  • Uncharacterized ABC transporter ATP-binding protein TM_0288
KeywordsMEMBRANE PROTEIN / ABC exporter / ABC transporter / Membrane Transporter / sybody / nanobody
Function / homology
Function and homology information


ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / transmembrane transport / ATP hydrolysis activity / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. ...Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / ABC transporter, ATP-binding protein / Uncharacterized ABC transporter ATP-binding protein TM_0288
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.12 Å
AuthorsHutter, C.A.J. / Huerlimann, L.M. / Zimmermann, I. / Egloff, P. / Seeger, M.A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationPP00P3_144823 Switzerland
CitationJournal: Nat Commun / Year: 2019
Title: The extracellular gate shapes the energy profile of an ABC exporter.
Authors: Hutter, C.A.J. / Timachi, M.H. / Hurlimann, L.M. / Zimmermann, I. / Egloff, P. / Goddeke, H. / Kucher, S. / Stefanic, S. / Karttunen, M. / Schafer, L.V. / Bordignon, E. / Seeger, M.A.
History
DepositionMar 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ABC transporter, ATP-binding protein
B: Uncharacterized ABC transporter ATP-binding protein TM_0288
C: ABC transporter, ATP-binding protein
D: Uncharacterized ABC transporter ATP-binding protein TM_0288
E: Sb_TM35
F: Sb_TM35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)295,36414
Polymers293,2386
Non-polymers2,1268
Water00
1
A: ABC transporter, ATP-binding protein
B: Uncharacterized ABC transporter ATP-binding protein TM_0288
E: Sb_TM35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,6827
Polymers146,6193
Non-polymers1,0634
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18180 Å2
ΔGint-122 kcal/mol
Surface area52620 Å2
MethodPISA
2
C: ABC transporter, ATP-binding protein
D: Uncharacterized ABC transporter ATP-binding protein TM_0288
F: Sb_TM35
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,6827
Polymers146,6193
Non-polymers1,0634
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18310 Å2
ΔGint-128 kcal/mol
Surface area52960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.280, 77.290, 207.180
Angle α, β, γ (deg.)90.000, 112.550, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ABC transporter, ATP-binding protein


Mass: 65016.781 Da / Num. of mol.: 2 / Fragment: ABC transporter / Mutation: D41A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0287 / Plasmid: pBXNH3 / Production host: Escherichia coli (E. coli) / Variant (production host): MC1061 / References: UniProt: Q9WYC3
#2: Protein Uncharacterized ABC transporter ATP-binding protein TM_0288


Mass: 67758.914 Da / Num. of mol.: 2 / Fragment: ABC transporter / Mutation: D65A, E517A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0288 / Plasmid: pBXNH3 / Production host: Escherichia coli (E. coli) / Variant (production host): MC1061 / References: UniProt: Q9WYC4
#3: Antibody Sb_TM35


Mass: 13843.184 Da / Num. of mol.: 2 / Fragment: sybody
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pBXPHM3 / Production host: Escherichia coli (E. coli) / Variant (production host): MC1061
#4: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg

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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: 4.19 Å3/Da / Density % sol: 70.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Sodium acetate, 0.025M NaCl, 12% (w/v) PEG 6000

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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: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.11→49.19 Å / Num. obs: 55123 / % possible obs: 62.6 % / Redundancy: 6.726 % / Biso Wilson estimate: 81.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.187 / Rrim(I) all: 0.202 / Χ2: 0.923 / Net I/σ(I): 9.25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.11-3.196.5960.942.282030.7721.0213.2
3.19-3.286.7070.77535390.8090.848.5
3.28-3.386.5210.862.548980.7520.93314.7
3.38-3.486.5010.762.9413360.8480.82522.5
3.48-3.596.5580.7672.9718830.8490.83232.8
3.59-3.725.9841.2121.816750.8531.32529.9
3.72-3.866.3590.8362.7438530.9250.91170.9
3.86-4.026.0240.7752.7736580.8930.84771
4.02-4.26.4850.5684.0149410.9490.61899.6
4.2-4.47.2090.4215.5347640.980.45399.6
4.4-4.647.2580.297.4645340.9910.31399.6
4.64-4.927.190.2558.0542830.9930.27599.6
4.92-5.267.0790.2757.7540510.9890.29799.5
5.26-5.686.9880.2967.3237630.9850.3299.7
5.68-6.236.9120.2967.3734740.9750.31999.7
6.23-6.966.5240.1959.931830.9880.21299.7
6.96-8.045.9750.11114.7827720.9930.12299.6
8.04-9.846.6680.04731.1223970.9980.05199.6
9.84-13.927.0310.03741.6418740.9990.0499.9
13.92-49.196.5240.02946.3310420.9990.03295.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.12→49.19 Å / Cor.coef. Fo:Fc: 0.834 / Cor.coef. Fo:Fc free: 0.829 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.557
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2797 5.07 %RANDOM
Rwork0.244 ---
obs0.245 55122 62.9 %-
Displacement parametersBiso max: 191.43 Å2 / Biso mean: 71.88 Å2 / Biso min: 13.25 Å2
Baniso -1Baniso -2Baniso -3
1-3.8586 Å20 Å2-4.0569 Å2
2---3.6906 Å20 Å2
3----0.168 Å2
Refine analyzeLuzzati coordinate error obs: 0.58 Å
Refinement stepCycle: final / Resolution: 3.12→49.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19958 0 128 0 20086
Biso mean--50.92 --
Num. residues----2529
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d7276SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3444HARMONIC5
X-RAY DIFFRACTIONt_it20451HARMONIC20
X-RAY DIFFRACTIONt_nbd10SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2727SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact23714SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d20451HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg27707HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion1.78
X-RAY DIFFRACTIONt_other_torsion20.54
LS refinement shellResolution: 3.12→3.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.352 49 4.44 %
Rwork0.2969 1054 -
all0.2989 1103 -
obs--7.17 %
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)
10.32290.05430.47220.5966-0.43843.812-0.07750.10850.03210.0573-0.06660.1012-0.55330.00180.14410.03310.0093-0.0902-0.3096-0.03130.046346.26455.261157.3282
20.53480.11930.64770.0957-0.23494.63920.12890.2929-0.1794-0.192-0.101-0.00470.50730.6437-0.0279-0.04320.1338-0.0489-0.2582-0.098-0.042455.6174-10.716848.9269
30.51160.10990.39240.28340.26571.6671-0.2-0.18050.1017-0.0225-0.02940.0052-0.6257-0.49290.22940.00760.0748-0.10330.0501-0.0455-0.1284-23.313644.979578.5427
40.7446-0.02270.83330.1946-0.00442.74150.08660.0328-0.2544-0.1238-0.0230.00420.0955-0.2255-0.0636-0.1786-0.035-0.0305-0.0735-0.0519-0.011-18.990126.60670.9462
5-1.41934.85923.12441.6051-2.09278.437-0.029-0.01780.37180.15790.0706-0.2243-0.25450.0832-0.04160.3102-0.2606-0.04870.12750.1276-0.45156.771334.0797-14.1308
63.944.20691.00511.392-2.0038.4306-0.04530.01650.2650.18920.045-0.2969-0.16480.13040.00030.1891-0.3935-0.07990.11530.155-0.5098-6.903365.84455.4021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 569
2X-RAY DIFFRACTION2{ B|* }B22 - 591
3X-RAY DIFFRACTION3{ C|* }C1 - 569
4X-RAY DIFFRACTION4{ D|* }D18 - 591
5X-RAY DIFFRACTION5{ E|* }E1 - 124
6X-RAY DIFFRACTION6{ F|* }F1 - 124

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