5KC1 | pdb_00005kc1

Structure of the C-terminal dimerization domain of Atg38

• PDB DOI: https://doi.org/10.2210/pdb5KC1/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-06-04 Released: 2016-10-05 
• Deposition Author(s): Ohashi, Y., Soler, N., Garcia-Ortegon, M., Zhang, L., Perisic, O., Masson, G.R., Johnson, C.M., Williams, R.J.
• Funding Organization(s): Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.241 (Depositor), 0.247 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Characterization of Atg38 and NRBF2, a fifth subunit of the autophagic Vps34/PIK3C3 complex.

Ohashi, Y., Soler, N., Garcia Ortegon, M., Zhang, L., Kirsten, M.L., Perisic, O., Masson, G.R., Burke, J.E., Jakobi, A.J., Apostolakis, A.A., Johnson, C.M., Ohashi, M., Ktistakis, N.T., Sachse, C., Williams, R.L.

(2016) Autophagy 12: 2129-2144

• PubMed: 27630019 
• DOI: https://doi.org/10.1080/15548627.2016.1226736
• Primary Citation Related Structures: 
  5KC1, 5KC2


• PubMed Abstract: 
  

  The phosphatidylinositol 3-kinase Vps34 is part of several protein complexes. The structural organization of heterotetrameric complexes is starting to emerge, but little is known about organization of additional accessory subunits that interact with these assemblies. Combining hydrogen-deuterium exchange mass spectrometry (HDX-MS), X-ray crystallography and electron microscopy (EM), we have characterized Atg38 and its human ortholog NRBF2, accessory components of complex I consisting of Vps15-Vps34-Vps30/Atg6-Atg14 (yeast) and PIK3R4/VPS15-PIK3C3/VPS34-BECN1/Beclin 1-ATG14 (human). HDX-MS shows that Atg38 binds the Vps30-Atg14 subcomplex of complex I, using mainly its N-terminal MIT domain and bridges the coiled-coil I regions of Atg14 and Vps30 in the base of complex I. The Atg38 C-terminal domain is important for localization to the phagophore assembly site (PAS) and homodimerization. Our 2.2 Å resolution crystal structure of the Atg38 C-terminal homodimerization domain shows 2 segments of α-helices assembling into a mushroom-like asymmetric homodimer with a 4-helix cap and a parallel coiled-coil stalk. One Atg38 homodimer engages a single complex I. This is in sharp contrast to human NRBF2, which also forms a homodimer, but this homodimer can bridge 2 complex I assemblies.

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Organizational Affiliation: 
• a MRC Laboratory of Molecular Biology , Cambridge , United Kingdom.
b European Molecular Biology Laboratory , Structural and Computational Biology Unit , Heidelberg , Germany.
c European Molecular Biology Laboratory, Hamburg Unit , Hamburg , Germany.
d The Babraham Institute , Cambridge , UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - B2 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 314.57 kDa 
• Atom Count: 4,559 
• Modeled Residue Count: 518 
• Deposited Residue Count: 2,712 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Autophagy-related protein 38	A [auth C], B [auth D], C [auth A], D [auth B], E [auth G], F [auth H], G [auth K], H [auth L], I [auth E], J [auth F], K [auth I], L [auth J]	226	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: ATG38, YLR211C, L8167.20
UniProt
Find proteins for Q05789 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q05789  Go to UniProtKB:  Q05789

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IOD	UA [auth E]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
SO4	PA [auth K]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	GB [auth I], JB [auth J], KB [auth J], O [auth C], OA [auth K], P [auth C], QA [auth L], Y [auth A], Z [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3	BA [auth B], CA [auth G], DA [auth G], EA [auth G], EB [auth I], FA [auth G], FB [auth I], GA [auth H], HB [auth J], KA [auth K], LA [auth K], MA [auth K], N [auth C], S [auth D], T [auth D], W [auth A], X [auth A], ZA [auth F]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
CL	AB [auth F], BB [auth F], SA [auth E], TA [auth E], U [auth D], V [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	AA [auth B], CB [auth I], DB [auth I], HA [auth K], IA [auth K], JA [auth K], M [auth C], Q [auth D], R [auth D], RA [auth E], VA [auth F], WA [auth F], XA [auth F], YA [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
NH4	IB [auth J], NA [auth K]	AMMONIUM ION H4 N QGZKDVFQNNGYKY-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.241 (Depositor), 0.247 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.383	α = 90
b = 249.385	β = 90
c = 50.197	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
autoSHARP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-10-05 
Deposition Author(s): Ohashi, Y., Soler, N., Garcia-Ortegon, M., Zhang, L., Perisic, O., Masson, G.R., Johnson, C.M., Williams, R.J.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MC_U105184308

Revision History  

• Version 1.0: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2016-10-19
  Changes: Database references
• Version 1.2: 2016-11-09
  Changes: Database references
• Version 2.0: 2017-09-13
  Changes: Atomic model, Author supporting evidence, Derived calculations
• Version 2.1: 2024-05-08
  Changes: Data collection, Database references, Derived calculations