4XZS | pdb_00004xzs

Crystal Structure of TRIAP1-MBP fusion

• PDB DOI: https://doi.org/10.2210/pdb4XZS/pdb

• Classification: APOPTOSIS
• Organism(s): Escherichia coli K-12, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-02-04 Released: 2016-01-20 
• Deposition Author(s): Miliara, X., Garnett, J.A., Abid-Ali, F., Perez-Dorado, I., Matthews, S.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 
  0.242 (Depositor), 0.244 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Structural insight into the TRIAP1/PRELI-like domain family of mitochondrial phospholipid transfer complexes.

Miliara, X., Garnett, J.A., Tatsuta, T., Abid Ali, F., Baldie, H., Perez-Dorado, I., Simpson, P., Yague, E., Langer, T., Matthews, S.

(2015) EMBO Rep 16: 824-835

• PubMed: 26071602 
• DOI: https://doi.org/10.15252/embr.201540229
• Primary Citation Related Structures: 
  4XZS, 4XZV


• PubMed Abstract: 
  

  The composition of the mitochondrial membrane is important for its architecture and proper function. Mitochondria depend on a tightly regulated supply of phospholipid via intra-mitochondrial synthesis and by direct import from the endoplasmic reticulum. The Ups1/PRELI-like family together with its mitochondrial chaperones (TRIAP1/Mdm35) represent a unique heterodimeric lipid transfer system that is evolutionary conserved from yeast to man. Work presented here provides new atomic resolution insight into the function of a human member of this system. Crystal structures of free TRIAP1 and the TRIAP1-SLMO1 complex reveal how the PRELI domain is chaperoned during import into the intermembrane mitochondrial space. The structural resemblance of PRELI-like domain of SLMO1 with that of mammalian phoshatidylinositol transfer proteins (PITPs) suggest that they share similar lipid transfer mechanisms, in which access to a buried phospholipid-binding cavity is regulated by conformationally adaptable loops.

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Organizational Affiliation: 
• Department of Life Sciences, Imperial College London, London, UK.
Department of Life Sciences, Imperial College London, London, UK School of Biological and Chemical Sciences, Joseph Priestley Building Queen Mary University of London, London, UK.
Institute for Genetics, Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany.
Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK.
Department of Life Sciences, Imperial College London, London, UK [e-mail].

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 98.56 kDa 
• Atom Count: 6,794 
• Modeled Residue Count: 841 
• Deposited Residue Count: 892 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltose-binding periplasmic protein,TP53-regulated inhibitor of apoptosis 1	A, B	446	Escherichia coli K-12, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: malE, b4034, JW3994, TRIAP1, 15E1.1, HSPC132
UniProt & NIH Common Fund Data Resources
Find proteins for O43715 (Homo sapiens) Explore O43715  Go to UniProtKB:  O43715
PHAROS:  O43715 GTEx:  ENSG00000170855
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9  Go to UniProtKB:  P0AEX9
UniProt Groups	O43715P0AEX9

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	C, D	2		N/A
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001	C, D	alpha-maltose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free:  0.242 (Depositor), 0.244 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.39	α = 90
b = 56.01	β = 106.35
c = 100.28	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Miliara, X., Garnett, J.A., Abid-Ali, F., Perez-Dorado, I., Matthews, S.J.

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-11-06
  Changes: Structure summary