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- PDB-6qv2: Structure of ATPgS-bound outward-facing TM287/288 in complex with... -

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Basic information

Entry
Database: PDB / ID: 6qv2
TitleStructure of ATPgS-bound outward-facing TM287/288 in complex with nanobody Nb_TM#2
Components
  • ABC transporter, ATP-binding proteinATP-binding cassette transporter
  • Nb_TM No.2
  • 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 / 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. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
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: 4.23 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

Downloads & links

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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_TM No.2
F: Nb_TM No.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,00514
Polymers293,8156
Non-polymers2,1908
Water0
1
A: ABC transporter, ATP-binding protein
B: Uncharacterized ABC transporter ATP-binding protein TM_0288
E: Nb_TM No.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,0037
Polymers146,9073
Non-polymers1,0954
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: ABC transporter, ATP-binding protein
D: Uncharacterized ABC transporter ATP-binding protein TM_0288
F: Nb_TM No.2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,0037
Polymers146,9073
Non-polymers1,0954
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.600, 113.070, 126.890
Angle α, β, γ (deg.)83.180, 73.000, 67.370
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ABC transporter, ATP-binding protein / ATP-binding cassette transporter


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) / Strain (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) / Strain (production host): MC1061 / References: UniProt: Q9WYC4
#3: Antibody Nb_TM No.2


Mass: 14131.722 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) / Strain (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: 3.82 Å3/Da / Density % sol: 67.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M TRIS, 0.1M NaCl, 30% (v/v) PEG 400

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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: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.22→32.59 Å / Num. obs: 18010 / % possible obs: 57.4 % / Redundancy: 3.533 % / Biso Wilson estimate: 111.97 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.052 / Rrim(I) all: 0.061 / Χ2: 0.934 / Net I/σ(I): 16.12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
4.22-4.323.5830.3513.25480.8380.412.1
4.32-4.443.3260.2624.761380.8310.3136.1
4.44-4.572.940.283.872340.8770.34710.7
4.57-4.712.7810.2923.643420.880.36915.6
4.71-4.873.2270.293.994620.9130.3522.4
4.87-5.043.0720.2813.815970.930.34530.4
5.04-5.233.6760.313.978210.9480.36441.8
5.23-5.443.7870.3923.3811200.9350.45659.6
5.44-5.683.7140.612.1615700.8780.71288.5
5.68-5.963.6730.6342.0617180.8750.74199.4
5.96-6.283.6430.4812.7116000.8810.56599.1
6.28-6.673.6060.2924.3315170.9520.34299.5
6.67-7.133.6070.2255.4614210.9670.26399.1
7.13-7.73.5180.1368.5413290.9860.1699.2
7.7-8.433.3060.06915.512300.9950.08399
8.43-9.433.0490.03528.0311130.9970.04398.8
9.43-10.883.340.02345.079510.9990.02898.4
10.88-13.333.8870.01865.878250.9990.0299.2
13.33-18.853.8150.01582.7765410.01899.7
18.85-32.593.7340.01117.7732010.01292.8

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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: 4.23→32.59 Å / Cor.coef. Fo:Fc: 0.722 / Cor.coef. Fo:Fc free: 0.644 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 1.673
RfactorNum. reflection% reflectionSelection details
Rfree0.33 919 5.12 %RANDOM
Rwork0.306 ---
obs0.307 17961 57.9 %-
Displacement parametersBiso max: 300 Å2 / Biso mean: 167.72 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--26.0363 Å2-1.7135 Å23.211 Å2
2--34.4756 Å2-26.9889 Å2
3----8.4393 Å2
Refine analyzeLuzzati coordinate error obs: 1.1 Å
Refinement stepCycle: final / Resolution: 4.23→32.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19958 0 128 0 20086
Biso mean--146.73 --
Num. residues----2534
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d7300SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes3442HARMONIC5
X-RAY DIFFRACTIONt_it20310HARMONIC20
X-RAY DIFFRACTIONt_nbd10SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2728SEMIHARMONIC5
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_contact22938SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d20442HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg27674HARMONIC20.9
X-RAY DIFFRACTIONt_omega_torsion1.39
X-RAY DIFFRACTIONt_other_torsion21.64
LS refinement shellResolution: 4.23→4.56 Å / Rfactor Rfree error: 0 / Total num. of bins used: 45
RfactorNum. reflection% reflection
Rfree0.3916 20 5 %
Rwork0.3529 380 -
all0.3545 400 -
obs--6.31 %
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)
10.7295-1.05730.74971.511-2.54860.20030.2781-0.1159-0.08420.0064-0.0027-0.0020.9097-0.3792-0.2754-0.1807-0.02460.25290.4865-0.02670.281754.406836.813659.2721
2-2.7131-1.9188-1.9342.3471-0.97821.8130.7265-0.29490.48460.0564-0.03660.68370.6655-0.461-0.6899-0.6126-0.1299-0.2782-0.148-0.0657-0.127570.626541.70170.4102
3-0.25480.09890.19432.37423.55420.3769-0.21320.3329-0.04320.33320.5381-0.1071-0.0408-0.108-0.3249-0.15250.0692-0.26880.10240.09520.061210.079740.735123.6457
40.22861.0543-0.07743.9688-0.35050.0261-0.10230.1409-0.01140.13350.2165-0.0433-0.0716-0.0204-0.1142-0.2207-0.0522-0.3268-0.0023-0.16150.22326.551936.169912.5626
517.4030.7931.13916.66722.561815.82250.0434-0.31920.4125-0.3069-0.2652-0.36530.47420.33950.22180.5453-0.0833-0.09230.6041-0.26970.6744108.385658.56263.1019
614.07250.2108-3.750515.97551.71418.2026-0.3163-0.1893-0.1972-0.29150.3257-0.0851-0.05110.1038-0.00930.5391-0.0966-0.09030.5678-0.26540.673864.69120.123819.9976
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|* }C2 - 569
4X-RAY DIFFRACTION4{ D|* }D22 - 591
5X-RAY DIFFRACTION5{ E|* }E1 - 129
6X-RAY DIFFRACTION6{ F|* }F1 - 129

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