3ZQ6

ADP-ALF4 COMPLEX OF M. THERM. TRC40

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

A Conserved Archaeal Pathway for Tail-Anchored Membrane Protein Insertion.

Sherrill, J., Mariappan, M., Dominik, P., Hegde, R.S., Keenan, R.J.

(2011) Traffic 12: 1119

  • DOI: 10.1111/j.1600-0854.2011.01229.x
  • Primary Citation of Related Structures:  
    3ZQ6

  • PubMed Abstract: 

    • Eukaryotic tail-anchored (TA) membrane proteins are inserted into the endoplasmic reticulum by a post-translational TRC40 pathway, but no comparable pathway is known in other domains of life. The crystal structure of an archaebacterial TRC40 sequence homolog bound to ADP•AlF(4) (-) reveals characteristic features of eukaryotic TRC40, including a zinc-mediated dimer and a large hydrophobic groove ...

    Eukaryotic tail-anchored (TA) membrane proteins are inserted into the endoplasmic reticulum by a post-translational TRC40 pathway, but no comparable pathway is known in other domains of life. The crystal structure of an archaebacterial TRC40 sequence homolog bound to ADP•AlF(4) (-) reveals characteristic features of eukaryotic TRC40, including a zinc-mediated dimer and a large hydrophobic groove. Moreover, archaeal TRC40 interacts with the transmembrane domain of TA substrates and directs their membrane insertion. Thus, the TRC40 pathway is more broadly conserved than previously recognized.

    Organizational Affiliation: 

    Department of Biochemistry & Molecular Biology, University of Chicago, Gordon Center for Integrative Science, Room W238, Chicago, IL 60637, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PUTATIVE ARSENICAL PUMP-DRIVING ATPASEA, B, C, D324Methanothermobacter thermautotrophicusMutation(s): 0 
EC: 3.6.3.16 (PDB Primary Data), 7.3.2.7 (UniProt)
UniProt
Find proteins for O27555 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H))
Explore O27555 
Go to UniProtKB:  O27555
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO27555
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP
Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
N [auth C],
R [auth D]		ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
ALF
Query on ALF
Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
O [auth C],
S [auth D]		TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
I [auth A],
V [auth D]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
K
Query on K
Download Ideal Coordinates CCD File 
H [auth A],
M [auth B],
Q [auth C],
U [auth D]		POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
P [auth C],
T [auth D]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 206.948α = 90
b = 49.768β = 115.04
c = 147.363γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-22
    Type: Initial release
  • Version 1.1: 2011-08-03
    Changes: Derived calculations, Non-polymer description
  • Version 1.2: 2011-08-24
    Changes: Database references