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- PDB-5d3m: Folate ECF transporter: AMPPNP bound state -

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Basic information

Entry
Database: PDB / ID: 5d3m
TitleFolate ECF transporter: AMPPNP bound state
Components
  • Energy-coupling factor transporter ATP-binding protein EcfA1
  • Energy-coupling factor transporter ATP-binding protein EcfA2
  • Energy-coupling factor transporter transmembrane protein EcfT
  • S-component for folate
KeywordsTRANSPORT PROTEIN / ECF transporter / folate / membrane protein / vitamin transport
Function / homology
Function and homology information


Translocases / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
ECF transporter S component, folate family / ECF transporter, substrate-specific component / ECF transporter transmembrane protein EcfT / ECF transporter, substrate-specific component / Arp2/3 complex 21 kDa subunit ARPC3 - #20 / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter ATP-binding protein EcfA1 / ABC/ECF transporter, transmembrane component / Cobalt transport protein / Cobalt import ATP-binding protein cbiO. ...ECF transporter S component, folate family / ECF transporter, substrate-specific component / ECF transporter transmembrane protein EcfT / ECF transporter, substrate-specific component / Arp2/3 complex 21 kDa subunit ARPC3 - #20 / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter ATP-binding protein EcfA1 / ABC/ECF transporter, transmembrane component / Cobalt transport protein / Cobalt import ATP-binding protein cbiO. / : / ABC transporter, CbiO/EcfA subunit / Arp2/3 complex 21 kDa subunit ARPC3 / 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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Energy-coupling factor transporter transmembrane protein EcfT / Conserved hypothetical membrane protein / Energy-coupling factor transporter transmembrane protein EcfT / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter ATP-binding protein EcfA1
Similarity search - Component
Biological speciesLactobacillus delbrueckii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.303 Å
AuthorsGuskov, A. / Swier, L.J.Y.M. / Slotboom, D.J.
Funding support1items
OrganizationGrant numberCountry
European Research Council282083
CitationJournal: Nat Commun / Year: 2016
Title: Structural insight in the toppling mechanism of an energy-coupling factor transporter.
Authors: Swier, L.J. / Guskov, A. / Slotboom, D.J.
History
DepositionAug 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Energy-coupling factor transporter ATP-binding protein EcfA1
B: Energy-coupling factor transporter ATP-binding protein EcfA2
C: S-component for folate
D: Energy-coupling factor transporter transmembrane protein EcfT
E: Energy-coupling factor transporter ATP-binding protein EcfA1
F: Energy-coupling factor transporter ATP-binding protein EcfA2
G: S-component for folate
H: Energy-coupling factor transporter transmembrane protein EcfT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,72912
Polymers230,7048
Non-polymers2,0254
Water00
1
A: Energy-coupling factor transporter ATP-binding protein EcfA1
B: Energy-coupling factor transporter ATP-binding protein EcfA2
C: S-component for folate
D: Energy-coupling factor transporter transmembrane protein EcfT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3646
Polymers115,3524
Non-polymers1,0122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13720 Å2
ΔGint-105 kcal/mol
Surface area44970 Å2
MethodPISA
2
E: Energy-coupling factor transporter ATP-binding protein EcfA1
F: Energy-coupling factor transporter ATP-binding protein EcfA2
G: S-component for folate
H: Energy-coupling factor transporter transmembrane protein EcfT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3646
Polymers115,3524
Non-polymers1,0122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13770 Å2
ΔGint-104 kcal/mol
Surface area44530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.070, 97.260, 105.450
Angle α, β, γ (deg.)84.67, 64.78, 62.59
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Energy-coupling factor transporter ATP-binding protein EcfA1 / ECF transporter A component EcfA1


Mass: 32906.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: 10His-tag with TEV cleavage site at N-terminus / Source: (gene. exp.) Lactobacillus delbrueckii (bacteria) / Gene: ecfA1, cbiO1, Ldb0424 / Production host: Escherichia coli (E. coli)
References: UniProt: Q1GBJ0, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Protein Energy-coupling factor transporter ATP-binding protein EcfA2 / ECF transporter A component EcfA2


Mass: 31672.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus delbrueckii (bacteria) / Gene: ecfA2, cbiO2, Ldb0425 / Production host: Escherichia coli (E. coli)
References: UniProt: Q1GBI9, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#3: Protein S-component for folate


Mass: 20483.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: STREPII-tag at C-terminus / Source: (gene. exp.) Lactobacillus delbrueckii (bacteria) / Gene: Ldb1625 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1G929
#4: Protein Energy-coupling factor transporter transmembrane protein EcfT / ECF transporter T component EcfT


Mass: 30290.283 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus delbrueckii (bacteria) / Gene: cbiQ, ecfT, LBVIB27_01965, LBVIB44_01960, SB57_06620 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A061BSU4, UniProt: Q1GBI8*PLUS
#5: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.34 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50mM TRIS, 17% PEG 350 MME, 2% NG, 10mM spermidine, 10mM MgCl2, 10mM AMP-PNP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972423 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972423 Å / Relative weight: 1
ReflectionResolution: 3.3→44 Å / Num. obs: 40590 / % possible obs: 94.4 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.026 / Net I/σ(I): 12
Reflection shellResolution: 3.3→3.4 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.867 / Mean I/σ(I) obs: 0.5 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HZU

4hzu


Resolution: 3.303→43.862 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 37.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2892 1708 5.07 %Random selection
Rwork0.2504 ---
obs0.2523 33718 78.83 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.303→43.862 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15430 0 124 0 15554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615888
X-RAY DIFFRACTIONf_angle_d1.40421558
X-RAY DIFFRACTIONf_dihedral_angle_d18.0735792
X-RAY DIFFRACTIONf_chiral_restr0.0522492
X-RAY DIFFRACTIONf_plane_restr0.0052680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3028-3.39990.3837140.4219301X-RAY DIFFRACTION9
3.3999-3.50960.4453460.388923X-RAY DIFFRACTION27
3.5096-3.6350.38441220.35062185X-RAY DIFFRACTION65
3.635-3.78050.35921790.32093153X-RAY DIFFRACTION93
3.7805-3.95240.34591650.30583235X-RAY DIFFRACTION96
3.9524-4.16060.35281750.28743256X-RAY DIFFRACTION96
4.1606-4.42110.26291530.25713258X-RAY DIFFRACTION94
4.4211-4.76210.2751890.23543105X-RAY DIFFRACTION94
4.7621-5.24060.27671700.2393204X-RAY DIFFRACTION94
5.2406-5.99730.3171600.27493179X-RAY DIFFRACTION94
5.9973-7.54970.32491750.2773160X-RAY DIFFRACTION93
7.5497-43.86590.2331600.2023051X-RAY DIFFRACTION91
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)
10.38520.340.01220.2960.04160.4890.30440.38570.544-0.7097-0.9513-0.0225-0.5027-0.7302-0.00081.22130.35-0.35961.67-0.42511.325717.62761.8518-42.1674
23.16012.3251-0.33952.5746-0.94415.34930.3878-0.4203-0.19280.3791-0.0305-0.16381.04030.8171-0.00691.02540.3953-0.04061.2595-0.06321.130123.03149.9958-24.5357
30.15470.341-0.07741.9676-0.88580.4869-0.35530.5871-1.67311.2683-1.1322-0.0160.5364-1.5201-0.11621.4231-0.30080.70521.3499-0.29122.32466.493256.78317.6236
40.93770.61570.4870.80590.1510.3176-0.1096-0.3396-1.44020.4257-0.74110.21770.6089-1.11850.00051.0419-0.19030.07831.450.2091.35881.336862.10533.0535
52.43811.214-1.18522.87451.44862.370.1597-0.1493-0.2684-0.113-0.2867-0.93020.05310.2379-0.00010.6776-0.0714-0.02730.7887-0.12320.94479.303573.8783-9.4527
66.5505-1.0371-2.36832.62063.11486.5321-0.3658-1.1851-1.66281.17190.2542-0.84610.835-0.5201-2.10290.64970.6642-0.1932.65140.7361.711826.978553.33373.4871
72.91070.3367-0.71930.69880.26580.3599-0.0095-1.2363-1.45460.05940.1446-0.23310.36520.0836-0.24291.0632-0.6711-0.72873.23921.143.400441.495165.31962.3508
82.5023-0.61590.25291.04890.00340.02860.7570.3267-0.2994-0.69270.3520.37421.6518-2.04020.54411.627-0.4123-0.33591.2027-0.07170.8966-16.805356.6221-26.4798
91.85831.45580.79261.75251.66882.13040.76690.1646-1.15240.4666-0.1308-0.18061.2357-0.12482.9711.4914-0.7327-0.93661.7125-0.50121.7594-26.624650.3304-34.0943
101.36650.1189-1.68661.301-0.29822.10110.3256-0.05950.02560.0250.31690.2135-0.45970.10740.41452.2103-0.2895-0.27632.69480.56070.751-33.234465.4885-46.5774
110.44070.13430.17460.05250.12420.4690.3396-0.0373-0.55210.2050.22690.0622-0.18150.4520.15282.0833-0.0081-0.78841.9425-0.15810.5582-27.545554.7838-48.2225
121.71681.03610.78690.62850.66222.54650.8435-0.2079-0.60431.3372-0.7966-0.65560.837-0.0086-0.45073.62920.5329-1.05651.1615-0.27120.7083-14.3142.8371-29.1411
130.4861-0.3309-0.03390.26560.30360.7-1.04030.7516-0.0627-0.56030.14551.2979-1.03140.7442-0.00131.69370.0831-0.53771.2221-0.01911.6021-18.459277.2499-45.0003
140.07360.02370.05310.1250.04320.0463-0.11070.06550.93240.03740.03110.619-0.4512-0.5445-0.00041.6689-0.074-0.65683.40950.47832.3478-38.537865.2256-64.9049
151.5688-0.2001-0.45740.87291.03382.4127-1.6623-0.7663-0.9373-0.2131-0.45020.8165-0.763-3.289-0.50481.1920.2551-0.02781.9902-0.07561.1017-21.149375.0905-36.4646
160.9268-0.1148-0.63411.02840.43970.5757-0.0969-1.12981.03070.3433-0.51230.2472-0.44-1.015-1.00091.3120.34270.98110.9901-1.01771.394-2.418359.6834-25.2449
172.9328-0.2595-0.81060.0127-0.11341.17240.05990.4460.0388-0.7386-0.50520.00390.0409-0.9344-0.0391.59450.0726-0.21871.05920.03750.6852-11.520168.3239-25.9956
180.459-0.1260.0761.4503-1.11270.8611-0.2406-0.277-0.46980.4024-0.8912-0.68511.81530.1734-0.15991.7896-0.5050.15471.0966-0.06691.414317.819934.9547-58.0937
193.1021-1.9467-1.15692.496-0.52515.4950.2191-0.14420.3234-0.53880.1424-0.3379-0.69820.7285-0.00060.9395-0.34740.10711.14770.03481.188223.106346.9397-75.6147
204.375-1.5432-0.54371.7986-0.1310.2457-0.5242-1.31442.2976-0.3311-1.56680.3111-0.9614-0.5926-0.9191.26050.5287-0.53241.5009-0.66743.44362.748240.6563-108.7051
210.535-0.6046-0.49910.70460.62630.6394-0.02980.83021.1461-1.8415-0.69650.0485-1.3147-0.7342-0.04912.0869-0.0485-0.21860.8142-0.04542.0849.943139.3998-106.9605
221.16650.0991-0.66161.14410.70690.9375-0.25970.45622.5136-0.941-0.93410.6087-0.1657-1.4017-0.04471.34940.0995-0.21311.59250.21241.49281.514834.6715-103.2697
232.31-1.6121.23651.9284-0.19752.593-0.1276-0.00280.27540.3044-0.2872-0.6517-0.16640.37460.00010.83740.1079-0.04150.808-0.06171.02789.551622.9468-90.6805
243.01041.5672-0.96153.24031.88613.56430.14931.10181.3556-0.8571-0.1636-0.3596-0.6031-0.1226-1.3880.6347-0.82090.11772.36560.59870.947422.118443.6344-106.8807
252.57912.13731.89584.3936-0.58263.17220.2571-0.40362.0815-0.0524-0.34720.219-1.22341.3481-1.8240.8705-0.46340.8082.16710.31612.845535.093443.4253-98.5796
260.6849-0.16370.20720.2358-0.3290.4779-0.8718-0.020.79340.50860.7172-0.2049-0.0605-0.4343-0.03421.29420.43280.72462.88290.38232.016141.694931.6598-102.4605
273.1042-0.5236-0.07071.21280.1390.01540.5809-0.1557-0.32210.59120.12270.6317-1.4552-2.48890.37981.68950.26340.20461.2671-0.08970.7882-16.67340.1174-73.7233
280.4881-0.3433-0.12680.46050.44950.63910.6561-0.17081.1318-0.4593-0.4003-0.1241-0.5279-0.4519-0.42261.79240.76691.29672.32420.10952.1184-26.744345.1739-65.4538
292.16081.4291-0.05673.6358-1.34670.6374-0.59560.01160.01610.2831-0.1751-0.1392-0.9362-0.3549-0.42165.46810.4941.29922.80420.67182.4245-33.841232.3892-52.6532
300.64240.29890.44860.28120.42150.63690.1554-0.09010.3423-0.13490.0958-0.01750.11530.03220.81871.6524-0.05410.94661.99720.28211.128-27.390642.2061-51.8027
310.3709-0.0751-0.25310.2769-0.10220.67650.2232-0.1390.3342-0.7647-0.0915-0.2977-0.0226-0.04380.96652.5816-0.79211.09311.031-1.12891.4645-17.422653.8088-63.4094
320.12360.1586-0.09620.2534-0.22910.30980.1703-0.10870.05680.0773-0.2944-0.174-0.12760.3397-1.68373.35280.21581.00262.56471.58522.0538-9.285353.9312-82.5582
330.41880.2127-0.1630.54880.53061.1968-1.2701-0.4119-0.13680.1395-0.12680.89890.45430.1051-0.09391.3787-0.24630.44891.04630.01991.4167-18.25219.4092-55.2001
340.0462-0.00770.03520.1294-0.06950.056-0.167-0.3598-0.13290.4466-0.0029-0.01140.3301-1.0298-0.00072.0541-0.37640.67563.1789-0.03812.4216-38.283531.5384-35.1884
350.23680.401-0.28951.4119-0.18350.7577-2.2296-0.33730.6654-0.49270.15130.71250.3348-3.1061-0.50591.1681-0.1834-0.13312.40480.05711.3178-20.932121.643-63.7089
360.45970.61140.13230.98430.47720.3897-0.26521.0636-1.0034-0.25790.056-0.4250.8282-0.46040.50551.7123-0.1976-0.84140.8951-0.64011.4719-2.296537.0927-74.927
372.2338-0.529-0.15260.1302-0.23772.34130.156-0.0304-0.03570.5008-0.550.0826-0.1368-0.1675-0.00031.3705-0.06880.19840.8128-0.13490.8101-11.344728.4325-74.1658
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 21 )
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 280 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 39 )
4X-RAY DIFFRACTION4chain 'B' and (resid 40 through 96 )
5X-RAY DIFFRACTION5chain 'B' and (resid 97 through 211 )
6X-RAY DIFFRACTION6chain 'B' and (resid 212 through 257 )
7X-RAY DIFFRACTION7chain 'B' and (resid 258 through 280 )
8X-RAY DIFFRACTION8chain 'C' and (resid 8 through 106 )
9X-RAY DIFFRACTION9chain 'C' and (resid 107 through 130 )
10X-RAY DIFFRACTION10chain 'C' and (resid 131 through 138 )
11X-RAY DIFFRACTION11chain 'C' and (resid 139 through 146 )
12X-RAY DIFFRACTION12chain 'C' and (resid 147 through 175 )
13X-RAY DIFFRACTION13chain 'D' and (resid 6 through 84 )
14X-RAY DIFFRACTION14chain 'D' and (resid 85 through 102 )
15X-RAY DIFFRACTION15chain 'D' and (resid 103 through 152 )
16X-RAY DIFFRACTION16chain 'D' and (resid 153 through 184 )
17X-RAY DIFFRACTION17chain 'D' and (resid 185 through 264 )
18X-RAY DIFFRACTION18chain 'E' and (resid 2 through 21 )
19X-RAY DIFFRACTION19chain 'E' and (resid 22 through 280 )
20X-RAY DIFFRACTION20chain 'F' and (resid 2 through 16 )
21X-RAY DIFFRACTION21chain 'F' and (resid 17 through 39 )
22X-RAY DIFFRACTION22chain 'F' and (resid 40 through 96 )
23X-RAY DIFFRACTION23chain 'F' and (resid 97 through 211 )
24X-RAY DIFFRACTION24chain 'F' and (resid 212 through 240 )
25X-RAY DIFFRACTION25chain 'F' and (resid 241 through 257 )
26X-RAY DIFFRACTION26chain 'F' and (resid 258 through 280 )
27X-RAY DIFFRACTION27chain 'G' and (resid 8 through 106 )
28X-RAY DIFFRACTION28chain 'G' and (resid 107 through 132 )
29X-RAY DIFFRACTION29chain 'G' and (resid 133 through 138 )
30X-RAY DIFFRACTION30chain 'G' and (resid 139 through 146 )
31X-RAY DIFFRACTION31chain 'G' and (resid 147 through 163 )
32X-RAY DIFFRACTION32chain 'G' and (resid 164 through 175 )
33X-RAY DIFFRACTION33chain 'H' and (resid 6 through 84 )
34X-RAY DIFFRACTION34chain 'H' and (resid 85 through 102 )
35X-RAY DIFFRACTION35chain 'H' and (resid 103 through 152 )
36X-RAY DIFFRACTION36chain 'H' and (resid 153 through 184 )
37X-RAY DIFFRACTION37chain 'H' and (resid 185 through 264 )

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