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 

wwPDB Validation   3D Report Full Report


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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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