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- PDB-22vd: Cryo-EM structure of DOCK11 -

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Basic information

Entry
Database: PDB / ID: 22vd
TitleCryo-EM structure of DOCK11
ComponentsDedicator of cytokinesis protein 11
KeywordsSIGNALING PROTEIN / RhoGEF
Function / homology
Function and homology information


marginal zone B cell differentiation / B cell homeostasis / regulation of Rho protein signal transduction / positive regulation of filopodium assembly / small GTPase-mediated signal transduction / CDC42 GTPase cycle / positive regulation of GTPase activity / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity / small GTPase binding ...marginal zone B cell differentiation / B cell homeostasis / regulation of Rho protein signal transduction / positive regulation of filopodium assembly / small GTPase-mediated signal transduction / CDC42 GTPase cycle / positive regulation of GTPase activity / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity / small GTPase binding / Factors involved in megakaryocyte development and platelet production / cytosol
Similarity search - Function
Dedicator of cytokinesis D, C2 domain / : / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / DOCK6-11, TPR domain / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C ...Dedicator of cytokinesis D, C2 domain / : / Dedicator of cytokinesis C/D, N-terminal / Dedicator of cytokinesis C/D, N terminal / DOCK6-11, TPR domain / Dedicator of cytokinesis / C2 DOCK-type domain / DOCKER domain / Dedicator of cytokinesis, C-terminal, lobe A / Dedicator of cytokinesis, C-terminal, lobe C / DOCKER, Lobe A / DOCKER, Lobe B / DOCKER, Lobe C / DHR-2, Lobe A / C2 domain in Dock180 and Zizimin proteins / DHR-2, Lobe C / DHR-2, Lobe B / C2 DOCK-type domain profile. / DOCKER domain profile. / PH domain / PH domain profile. / C2 domain superfamily / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Armadillo-type fold
Similarity search - Domain/homology
Dedicator of cytokinesis protein 11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsHisano, T. / Kukimoto-Niino, M. / Shinoda, T. / Katsura, K. / Shirouzu, M.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJCR22E3 Japan
Other governmentNational Center for Geriatrics and Gerontology, 24-7 Japan
Other governmentBiology of Intracellular Environments Japan
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Structural basis for membrane-dependent positive feedback regulation of DOCK11 by activated Cdc42.
Authors: Tamao Hisano / Takehiro Shinoda / Mutsuko Kukimoto-Niino / Kazushige Katsura / Ryohei Kondo / Yoshiko Ishizuka-Katsura / Yukako Miyata-Yabuki / Kazuharu Hanada / Reiko Nakagawa / Akihiko ...Authors: Tamao Hisano / Takehiro Shinoda / Mutsuko Kukimoto-Niino / Kazushige Katsura / Ryohei Kondo / Yoshiko Ishizuka-Katsura / Yukako Miyata-Yabuki / Kazuharu Hanada / Reiko Nakagawa / Akihiko Nishikimi / Mikako Shirouzu /
Abstract: The guanine nucleotide exchange factor DOCK11 is widely expressed across tissues and activates Cdc42, a Rho family GTPase that regulates cytoskeletal remodeling and cell polarity. Loss-of-function ...The guanine nucleotide exchange factor DOCK11 is widely expressed across tissues and activates Cdc42, a Rho family GTPase that regulates cytoskeletal remodeling and cell polarity. Loss-of-function mutations in DOCK11 have recently been linked to inborn errors of immunity. DOCK11 has also been implicated in facilitating hepatitis B virus infection in hepatocytes and has emerged as a potential target for therapeutic interventions. A positive feedback mechanism has been proposed for DOCK11-mediated Cdc42 activation; however, the structural basis for this regulation has remained unclear. Here we report the cryoelectron microscopy structures of full-length DOCK11 as an apo dimer, a binary complex with nucleotide-free Cdc42, and a ternary complex containing both nucleotide-free and activated Cdc42. DOCK11 predominantly adopts a U-shaped dimer that binds to nucleotide-free Cdc42 via the catalytic domain, whereas activated Cdc42 engages a distal site within the armadillo-repeat domain. Biochemical and cellular analyses demonstrate that binding of activated Cdc42 is critical for enhancing the membrane-dependent nucleotide exchange activity of DOCK11, promoting its localization to the plasma membrane, and facilitating intracellular activation of Cdc42. We also determined the structure of the membrane-bound ternary complex using membrane-coated grids. Strikingly, the ternary complex adopts an extended conformation that aligns multiple membrane-contact elements, revealing how activated Cdc42 stabilizes DOCK11 membrane binding for efficient exchange activity. Collectively, these findings provide a structural framework for the coordinated mechanism underlying membrane-dependent positive feedback in Rho GTPase signaling.
History
DepositionJan 25, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 21, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dedicator of cytokinesis protein 11
B: Dedicator of cytokinesis protein 11


Theoretical massNumber of molelcules
Total (without water)476,7922
Polymers476,7922
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Dedicator of cytokinesis protein 11 / Activated Cdc42-associated guanine nucleotide exchange factor / ACG / Zizimin-2


Mass: 238396.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DOCK11, ZIZ2 / Cell line (production host): FreeStyle 293-F / Production host: Homo sapiens (human) / References: UniProt: Q5JSL3
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The DOCK11 dimer / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50.3 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
19PHENIX1.21_5207model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 511163 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 22VF

22vf


Pdb chain-ID: A / Accession code: 22VF / Details: DOCK11 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 3.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00328914
ELECTRON MICROSCOPYf_angle_d0.66739068
ELECTRON MICROSCOPYf_dihedral_angle_d12.71910930
ELECTRON MICROSCOPYf_chiral_restr0.0424356
ELECTRON MICROSCOPYf_plane_restr0.0054986

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