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- PDB-6qv1: Structure of ATPgS-bound outward-facing TM287/288 in complex with... -

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Basic information

Entry
Database: PDB / ID: 6qv1
TitleStructure of ATPgS-bound outward-facing TM287/288 in complex with nanobody Nb_TM1
Components
  • ABC transporter, ATP-binding protein
  • Nb_TM1
  • Uncharacterized ABC transporter ATP-binding protein TM_0288
KeywordsMEMBRANE PROTEIN / ABC exporter / ABC transporter / Membrane Transporter / 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ABC transporter, ATP-binding protein / Uncharacterized ABC transporter ATP-binding protein TM_0288
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.48 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: Nb_TM1
F: Nb_TM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,87414
Polymers290,6846
Non-polymers2,1908
Water00
1
A: ABC transporter, ATP-binding protein
B: Uncharacterized ABC transporter ATP-binding protein TM_0288
E: Nb_TM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,4377
Polymers145,3423
Non-polymers1,0954
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18860 Å2
ΔGint-139 kcal/mol
Surface area53980 Å2
MethodPISA
2
C: ABC transporter, ATP-binding protein
D: Uncharacterized ABC transporter ATP-binding protein TM_0288
F: Nb_TM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,4377
Polymers145,3423
Non-polymers1,0954
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18990 Å2
ΔGint-140 kcal/mol
Surface area53980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.750, 199.260, 113.160
Angle α, β, γ (deg.)90.000, 91.260, 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 Nb_TM1


Mass: 12566.146 Da / Num. of mol.: 2 / Fragment: nanobody
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: pBXPHM3 / Production host: Escherichia coli (E. coli) / Variant (production host): MC1061
#4: Chemical
ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*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: 3.52 Å3/Da / Density % sol: 65.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5 / Details: 0.05M Glycine, 0.225M NaCl, 21% (w/v) PEG 550MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.48→34.64 Å / Num. obs: 29868 / % possible obs: 58.2 % / Redundancy: 7.109 % / Biso Wilson estimate: 113 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.058 / Χ2: 0.989 / Net I/σ(I): 16.31
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
3.48-3.577.7410.7973.261080.7390.8542.9
3.57-3.677.6380.7253.443120.750.7788.4
3.67-3.787.5230.6393.815600.8820.68715.4
3.78-3.897.40.5963.849040.8990.64126.2
3.89-4.027.1810.5883.8412310.9170.63436.3
4.02-4.167.0580.534.2514760.9320.57245.2
4.16-4.327.0330.3955.4617030.970.42753.4
4.32-4.56.9120.3016.5318320.9850.32660.9
4.5-4.76.6780.2517.5119450.9880.27367.4
4.7-4.936.8410.2228.3121530.9920.24176.9
4.93-5.197.4740.1989.4122890.9950.21386.8
5.19-5.517.4530.1879.7124240.9960.20196.2
5.51-5.897.3710.2129.6823690.9930.22899.8
5.89-6.367.3720.16112.5421910.9940.17399.9
6.36-6.977.2390.10516.9320220.9980.11399.5
6.97-7.797.0110.06223.9318040.9990.06799.3
7.79-8.996.4470.03937.816120.9990.04298.4
8.99-11.026.7430.02752.5612820.9990.0394.2
11.02-15.587.060.02567.72107510.026100
15.58-34.646.7380.02271.8457610.02496

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.48→34.64 Å / Cor.coef. Fo:Fc: 0.857 / Cor.coef. Fo:Fc free: 0.794 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.979
RfactorNum. reflection% reflectionSelection details
Rfree0.303 1513 5.07 %RANDOM
Rwork0.267 ---
obs0.269 29833 58.2 %-
Displacement parametersBiso max: 299.94 Å2 / Biso mean: 189.73 Å2 / Biso min: 36.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.3093 Å20 Å24.1349 Å2
2--17.2756 Å20 Å2
3----14.9663 Å2
Refine analyzeLuzzati coordinate error obs: 0.7 Å
Refinement stepCycle: final / Resolution: 3.48→34.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19788 0 128 0 19916
Biso mean--134.92 --
Num. residues----2514
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d7244SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3412HARMONIC5
X-RAY DIFFRACTIONt_it20262HARMONIC20
X-RAY DIFFRACTIONt_nbd7SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2714SEMIHARMONIC5
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_contact23188SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d20262HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg27436HARMONIC20.95
X-RAY DIFFRACTIONt_omega_torsion1.68
X-RAY DIFFRACTIONt_other_torsion21.38
LS refinement shellResolution: 3.48→3.71 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.275 40 6.7 %
Rwork0.2985 557 -
all0.297 597 -
obs--6.83 %
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)
12.89450.64770.49298.22571.68811.3972-0.1417-0.52660.57070.3681-0.01970.5683-0.5723-0.1310.1614-0.3135-0.1570.12470.1943-0.1922-0.30080.618664.992738.0277
23.7199-1.65160.46116.8419-2.14162.09830.18580.13580.5635-0.5715-0.16490.5126-0.5714-0.198-0.0209-0.2437-0.1108-0.0638-0.0463-0.0928-0.31474.25362.504318.2411
313.0068-5.9075-3.652711.26123.87811.84130.0950.6826-0.5538-0.5626-0.3058-0.5770.5585-0.49710.2108-0.30870.1746-0.052-0.21040.0304-0.06744.494489.798874.9223
413.5007-4.53992.02149.6509-3.94712.4681-0.2157-0.58140.28420.60450.1854-0.52770.5771-0.35080.0303-0.29480.1795-0.1546-0.3502-0.1759-0.217747.040591.686894.9618
56.74890.5171-2.53648.6656-3.16575.0915-0.01120.0426-0.1722-0.0667-0.05650.08580.56270.02170.0678-0.07-0.1678-0.03950.15580.15080.3147-7.9833-5.056634.1653
68.17793.02920.3798.5529-3.01573.728-0.0053-0.05490.05780.0296-0.0474-0.0102-0.308-0.0510.0527-0.02430.16620.06980.04610.08980.317835.9092159.81680.3098
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A2 - 570
2X-RAY DIFFRACTION2{ B|* }B22 - 594
3X-RAY DIFFRACTION3{ C|* }C2 - 570
4X-RAY DIFFRACTION4{ D|* }D22 - 594
5X-RAY DIFFRACTION5{ E|* }E1 - 115
6X-RAY DIFFRACTION6{ F|* }F1 - 115

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