3ZQ6

ADP-ALF4 COMPLEX OF M. THERM. TRC40

• PDB DOI: https://doi.org/10.2210/pdb3ZQ6/pdb

• Classification: HYDROLASE
• Organism(s): Methanothermobacter thermautotrophicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-06-08 Released: 2011-06-22 
• Deposition Author(s): Sherrill, J., Mariappan, M., Dominik, P., Hegde, R.S., Keenan, R.J.

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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 

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

• PubMed: 21658170 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 148.86 kDa 
• Atom Count: 9,917 
• Modelled Residue Count: 1,179 
• Deposited Residue Count: 1,296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUTATIVE ARSENICAL PUMP-DRIVING ATPASE	A, B, C, D	324	Methanothermobacter thermautotrophicus	Mutation(s): 0  EC: 3.6.3.16
UniProt
Find proteins for O27555 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)) Explore O27555  Go to UniProtKB:  O27555

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth A], J [auth B], N [auth C], R [auth D]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N
ALF	F [auth A], K [auth B], O [auth C], S [auth D]	TETRAFLUOROALUMINATE ION Al F4 UYOMQIYKOOHAMK-UHFFFAOYSA-J
ZN	I [auth A], V [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
K	H [auth A], M [auth B], Q [auth C], U [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	G [auth A], L [auth B], P [auth C], T [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 206.948	α = 90
b = 49.768	β = 115.04
c = 147.363	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-22 
Deposition Author(s): Sherrill, J., Mariappan, M., Dominik, P., Hegde, R.S., Keenan, R.J.

Revision History  

• 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
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description