8R1A | pdb_00008r1a

Model of the membrane-bound GBP1 oligomer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 26.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

wwPDB Validation 3D Report Full Report

Validation slider image for 8R1A

This is version 1.3 of the entry. See complete history

Literature

Structural insights into the activation mechanism of antimicrobial GBP1.

Weismehl, M.Chu, X.Kutsch, M.Lauterjung, P.Herrmann, C.Kudryashev, M.Daumke, O.

(2024) EMBO J 43: 615-636

  • DOI: https://doi.org/10.1038/s44318-023-00023-y
  • Primary Citation Related Structures: 
    8R1A

  • PubMed Abstract: 

    The dynamin-related human guanylate-binding protein 1 (GBP1) mediates host defenses against microbial pathogens. Upon GTP binding and hydrolysis, auto-inhibited GBP1 monomers dimerize and assemble into soluble and membrane-bound oligomers, which are crucial for innate immune responses. How higher-order GBP1 oligomers are built from dimers, and how assembly is coordinated with nucleotide-dependent conformational changes, has remained elusive. Here, we present cryo-electron microscopy-based structural data of soluble and membrane-bound GBP1 oligomers, which show that GBP1 assembles in an outstretched dimeric conformation. We identify a surface-exposed helix in the large GTPase domain that contributes to the oligomerization interface, and we probe its nucleotide- and dimerization-dependent movements that facilitate the formation of an antimicrobial protein coat on a gram-negative bacterial pathogen. Our results reveal a sophisticated activation mechanism for GBP1, in which nucleotide-dependent structural changes coordinate dimerization, oligomerization, and membrane binding to allow encapsulation of pathogens within an antimicrobial protein coat.


  • Organizational Affiliation
    • Structural Biology, Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany.

Macromolecule Content 

  • Total Structure Weight: 418.92 kDa 
  • Atom Count: 28,566 
  • Modeled Residue Count: 3,522 
  • Deposited Residue Count: 3,618 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Guanylate binding protein 1
A, B, C, D, E
A, B, C, D, E, F
603Homo sapiensMutation(s): 1 
EC: 3.6.1 (UniProt), 3.6.5 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P32455 (Homo sapiens)
Explore P32455 
Go to UniProtKB:  P32455
PHAROS:  P32455
GTEx:  ENSG00000117228 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32455
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP

Query on GDP



Download:Ideal Coordinates CCD File
I [auth A]
L [auth B]
O [auth C]
R [auth D]
U [auth E]
I [auth A],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
X [auth F]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
AF3

Query on AF3



Download:Ideal Coordinates CCD File
G [auth A]
J [auth B]
M [auth C]
P [auth D]
S [auth E]
G [auth A],
J [auth B],
M [auth C],
P [auth D],
S [auth E],
V [auth F]
ALUMINUM FLUORIDE
Al F3
KLZUFWVZNOTSEM-UHFFFAOYSA-K
MG

Query on MG



Download:Ideal Coordinates CCD File
H [auth A]
K [auth B]
N [auth C]
Q [auth D]
T [auth E]
H [auth A],
K [auth B],
N [auth C],
Q [auth D],
T [auth E],
W [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 26.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SUBTOMOGRAM AVERAGING 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Helmholtz AssociationGermany--
German Research Foundation (DFG)GermanyINST 335/588-1 FUGG

Revision History  (Full details and data files)

  • Version 1.0: 2024-01-17
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Database references