7P41 | pdb_00007p41

Crystal Structure of human mARC1 A165T Variant

• PDB DOI: https://doi.org/10.2210/pdb7P41/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens, Tequatrovirus T4
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-07-09 Released: 2021-08-18 
• Deposition Author(s): Struwe, M.A., Scheidig, A.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.186 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Letter to the editor: The clinically relevant MTARC1 p.Ala165Thr variant impacts neither the fold nor active site architecture of the human mARC1 protein.

Struwe, M.A., Clement, B., Scheidig, A.

(2022) Hepatol Commun 6: 3277-3278

• PubMed: 35560545 
• DOI: https://doi.org/10.1002/hep4.1984
• Primary Citation of Related Structures:  
  7P41


• PubMed Abstract: 
  

  A study recently published in Hepatology Communications provided insights into a variant of MTARC1 protein, which conveys protection against liver disease. Here, we report a crystal structure of the variant protein at near-atomic resolution and compare it to the structure of the wildtype protein.

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Organizational Affiliation: 

Zoologisches Institut/Strukturbiologie, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 51.39 kDa 
• Atom Count: 4,164 
• Modelled Residue Count: 444 
• Deposited Residue Count: 448 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitochondrial amidoxime-reducing component 1,Endolysin,Mitochondrial amidoxime-reducing component 1	A [auth D]	448	Homo sapiens, Tequatrovirus T4	Mutation(s): 0  Gene Names: MTARC1, MARC1, MOSC1, e, T4Tp126 EC: 1.7 (PDB Primary Data), 3.2.1.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q5VT66 (Homo sapiens) Explore Q5VT66  Go to UniProtKB:  Q5VT66
PHAROS:  Q5VT66 GTEx:  ENSG00000186205
Find proteins for D9IEF7 (Enterobacteria phage T4) Explore D9IEF7  Go to UniProtKB:  D9IEF7
UniProt Groups	Q5VT66D9IEF7

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MTE (Subject of Investigation/LOI)	C [auth D]	PHOSPHONIC ACIDMONO-(2-AMINO-5,6-DIMERCAPTO-4-OXO-3,7,8A,9,10,10A-HEXAHYDRO-4H-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-7-YLMETHYL)ESTER C10 H14 N5 O6 P S2 HPEUEJRPDGMIMY-IFQPEPLCSA-N
B3P	D	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C11 H26 N2 O6 HHKZCCWKTZRCCL-UHFFFAOYSA-N
EFK (Subject of Investigation/LOI)	B [auth D]	oxidanyl(oxidanylidene)molybdenum H Mo O2 VEWPYRVWJVBLDN-UHFFFAOYSA-M
CL	E [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.186 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.063	α = 90
b = 74.887	β = 90
c = 111.164	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
RESOLVE	model building
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-08-18 
Deposition Author(s): Struwe, M.A., Scheidig, A.J.

Revision History  

• Version 1.0: 2021-08-18
  Type: Initial release
  
• Version 1.1: 2022-05-25
  Changes: Database references
• Version 1.2: 2022-11-02
  Changes: Database references
• Version 1.3: 2024-01-31
  Changes: Data collection, Refinement description