6SUR | pdb_00006sur

The Rab33B-Atg16L1 crystal structure

• PDB DOI: https://doi.org/10.2210/pdb6SUR/pdb

• Classification: CELL CYCLE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2019-09-16 Released: 2020-08-05 
• Deposition Author(s): Metje-Sprink, J., Kuehnel, K.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.47 Å
• R-Value Free: 
  0.239 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the Rab33B/Atg16L1 effector complex.

Metje-Sprink, J., Groffmann, J., Neumann, P., Barg-Kues, B., Ficner, R., Kuhnel, K., Schalk, A.M., Binotti, B.

(2020) Sci Rep 10: 12956-12956

• PubMed: 32737358 
• DOI: https://doi.org/10.1038/s41598-020-69637-0
• Primary Citation Related Structures: 
  6SUR


• PubMed Abstract: 
  

  The Atg12-Atg5/Atg16L1 complex is recruited by WIPI2b to the site of autophagosome formation. Atg16L1 is an effector of the Golgi resident GTPase Rab33B. Here we identified a minimal stable complex of murine Rab33B(30-202) Q92L and Atg16L1(153-210). Atg16L1(153-210) comprises the C-terminal part of the Atg16L1 coiled-coil domain. We have determined the crystal structure of the Rab33B Q92L/Atg16L1(153-210) effector complex at 3.47 Å resolution. This structure reveals that two Rab33B molecules bind to the diverging α-helices of the dimeric Atg16L1 coiled-coil domain. We mutated Atg16L1 and Rab33B interface residues and found that they disrupt complex formation in pull-down assays and cellular co-localization studies. The Rab33B binding site of Atg16L1 comprises 20 residues and immediately precedes the WIPI2b binding site. Rab33B mutations that abolish Atg16L binding also abrogate Rab33B association with the Golgi stacks. Atg16L1 mutants that are defective in Rab33B binding still co-localize with WIPI2b in vivo. The close proximity of the Rab33B and WIPI2b binding sites might facilitate the recruitment of Rab33B containing vesicles to provide a source of lipids during autophagosome biogenesis.

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Organizational Affiliation: 
• Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, 37077, Göttingen, Germany. [e-mail].
Institute for Biosafety in Plant Biotechnology, Julius Kuehn-Institute, 06484, Quedlinburg, Germany. [e-mail].
Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, 37077, Göttingen, Germany.
Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077, Göttingen, Germany.
Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, 37077, Göttingen, Germany. [e-mail].
Nature Communications, 4 Crinan Street, London, N1 9XW, UK. [e-mail].
Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, 60607, USA.
Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, 37077, Göttingen, Germany. [e-mail].
Department of Biochemistry, University of Würzburg, 97074, Würzburg, Germany. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: cross-linking, native gel electrophoresis

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 162.81 kDa 
• Atom Count: 10,672 
• Modeled Residue Count: 1,319 
• Deposited Residue Count: 1,380 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Rab-33B	A, B, C, D, E, F	173	Mus musculus	Mutation(s): 1  Gene Names: Rab33b EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for O35963 (Mus musculus) Explore O35963  Go to UniProtKB:  O35963
IMPC:  MGI:1330805

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Autophagy-related protein 16-1	G [auth I], H [auth J], I [auth K], J [auth L], K [auth M], L [auth N]	57	Mus musculus	Mutation(s): 0  Gene Names: Atg16l1, Apg16l
UniProt & NIH Common Fund Data Resources
Find proteins for Q8C0J2 (Mus musculus) Explore Q8C0J2  Go to UniProtKB:  Q8C0J2
IMPC:  MGI:1924290

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	N [auth A], P [auth B], R [auth C], T [auth D], V [auth E], X [auth F]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
MG	M [auth A], O [auth B], Q [auth C], S [auth D], U [auth E], W [auth F]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.47 Å
• R-Value Free:  0.239 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.4	α = 90
b = 204.9	β = 92.6
c = 107.2	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
PHASER	phasing
XSCALE	data scaling
XDS	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-08-05 
Deposition Author(s): Metje-Sprink, J., Kuehnel, K.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	SFB860

Revision History  

• Version 1.0: 2020-08-05
  Type: Initial release
  
• Version 1.1: 2020-08-12
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description