6ZG3

the structure of ECF PanT transporter in a complex with a nanobody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

In vitro reconstitution of dynamically interacting integral membrane subunits of energy-coupling factor transporters.

Setyawati, I.Stanek, W.K.Majsnerowska, M.Swier, L.J.Y.M.Pardon, E.Steyaert, J.Guskov, A.Slotboom, D.J.

(2020) Elife 9

  • DOI: https://doi.org/10.7554/eLife.64389
  • Primary Citation of Related Structures:  
    6ZG3

  • PubMed Abstract: 

    Energy-coupling factor (ECF) transporters mediate import of micronutrients in prokaryotes. They consist of an integral membrane S-component (that binds substrate) and ECF module (that powers transport by ATP hydrolysis). It has been proposed that different S-components compete for docking onto the same ECF module, but a minimal liposome-reconstituted system, required to substantiate this idea, is lacking. Here, we co-reconstituted ECF transporters for folate (ECF-FolT2) and pantothenate (ECF-PanT) into proteoliposomes, and assayed for crosstalk during active transport. The kinetics of transport showed that exchange of S-components is part of the transport mechanism. Competition experiments suggest much slower substrate association with FolT2 than with PanT. Comparison of a crystal structure of ECF-PanT with previously determined structures of ECF-FolT2 revealed larger conformational changes upon binding of folate than pantothenate, which could explain the kinetic differences. Our work shows that a minimal in vitro system with two reconstituted transporters recapitulates intricate kinetics behaviour observed in vivo.


  • Organizational Affiliation

    Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Energy-coupling factor transporter ATP-binding protein EcfA1
A, F
300Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002Mutation(s): 0 
Gene Names: ecfA1cbiO1Ldb0424
EC: 7
Membrane Entity: Yes 
UniProt
Find proteins for Q1GBJ0 (Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14))
Explore Q1GBJ0 
Go to UniProtKB:  Q1GBJ0
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1GBJ0
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Energy-coupling factor transporter ATP-binding protein EcfA2
B, G
287Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002Mutation(s): 0 
Gene Names: ecfA2cbiO2Ldb0425
EC: 3.6.3
Membrane Entity: Yes 
UniProt
Find proteins for Q1GBI9 (Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14))
Explore Q1GBI9 
Go to UniProtKB:  Q1GBI9
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UniProt GroupQ1GBI9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Conserved hypothetical membrane protein
C, H
215Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002Mutation(s): 0 
Gene Names: Ldb0463
Membrane Entity: Yes 
UniProt
Find proteins for Q1GBG0 (Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14))
Explore Q1GBG0 
Go to UniProtKB:  Q1GBG0
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UniProt GroupQ1GBG0
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Putative cobalt ABC transporter, permease protein
D, I
265Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 = JCM 1002Mutation(s): 0 
Gene Names: cbiQLdb0426
Membrane Entity: Yes 
UniProt
Find proteins for Q1GBI8 (Lactobacillus delbrueckii subsp. bulgaricus (strain ATCC 11842 / DSM 20081 / BCRC 10696 / JCM 1002 / NBRC 13953 / NCIMB 11778 / NCTC 12712 / WDCM 00102 / Lb 14))
Explore Q1GBI8 
Go to UniProtKB:  Q1GBI8
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UniProt GroupQ1GBI8
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
CA14381 nanobody
E, J
136Lama glamaMutation(s): 0 
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Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LMT
Query on LMT

Download Ideal Coordinates CCD File 
AA [auth I]
M [auth C]
N [auth C]
S [auth D]
W [auth G]
AA [auth I],
M [auth C],
N [auth C],
S [auth D],
W [auth G],
X [auth H],
Z [auth H]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
CIT
Query on CIT

Download Ideal Coordinates CCD File 
O [auth C],
Y [auth H]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
BA [auth I]
CA [auth J]
K [auth A]
L [auth B]
P [auth C]
BA [auth I],
CA [auth J],
K [auth A],
L [auth B],
P [auth C],
Q [auth C],
R [auth C],
T [auth D],
U [auth D],
V [auth E]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 97.29α = 88.997
b = 110.47β = 102.271
c = 110.5γ = 102.244
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific Research (NWO)Netherlands--

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-03
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description