6KVX | pdb_00006kvx

Crystal structure of the N-terminal domain single mutant (D119A) of the human mitochondrial calcium uniporter fused with T4 lysozyme

• PDB DOI: https://doi.org/10.2210/pdb6KVX/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Tequatrovirus T4, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2019-09-05 Released: 2020-05-27 
• Deposition Author(s): Lee, Y., Park, J., Lee, G., Yoon, S., Min, C.K., Kim, T.G., Yamamoto, T., Kim, D.H., Lee, K.W., Eom, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.262 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Models: experimental

Literature

Crystal structure of the N-terminal domain single mutant (D119A) of the human mitochondrial calcium uniporter fused with T4 lysozyme

Lee, Y., Park, J.S., Kang, J.Y., Eom, S.H.

(2020) Sci Rep 

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 29.97 kDa 
• Atom Count: 2,047 
• Modeled Residue Count: 253 
• Deposited Residue Count: 261 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endolysin,Calcium uniporter protein, mitochondrial	A	261	Tequatrovirus T4, Homo sapiens This entity is chimeric	Mutation(s): 4  Gene Names: e, T4Tp126, MCU, C10orf42, CCDC109A EC: 3.2.1.17
UniProt & NIH Common Fund Data Resources
Find proteins for D9IEF7 (Enterobacteria phage T4) Explore D9IEF7  Go to UniProtKB:  D9IEF7
Find proteins for Q8NE86 (Homo sapiens) Explore Q8NE86  Go to UniProtKB:  Q8NE86
PHAROS:  Q8NE86 GTEx:  ENSG00000156026
UniProt Groups	D9IEF7Q8NE86

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.262 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 97.899	α = 90
b = 97.899	β = 90
c = 61.619	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
Coot	model building
PHASER	phasing
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-27 
Deposition Author(s): Lee, Y., Park, J., Lee, G., Yoon, S., Min, C.K., Kim, T.G., Yamamoto, T., Kim, D.H., Lee, K.W., Eom, S.H.

Revision History  

• Version 1.0: 2020-05-27
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description