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- PDB-9hjq: ROCK2 bound with TDI01 -

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Basic information

Entry
Database: PDB / ID: 9hjq
TitleROCK2 bound with TDI01
ComponentsRho-associated protein kinase 2
KeywordsCYTOSOLIC PROTEIN / inhibitor / kinase / TRANSFERASE
Function / homology
Function and homology information


positive regulation of connective tissue growth factor production / cellular response to acetylcholine / positive regulation of centrosome duplication / regulation of angiotensin-activated signaling pathway / ROCK-subfamily protein kinase / negative regulation of protein localization to lysosome / Rho-dependent protein serine/threonine kinase activity / regulation of keratinocyte differentiation / positive regulation of fibroblast growth factor production / positive regulation of connective tissue replacement ...positive regulation of connective tissue growth factor production / cellular response to acetylcholine / positive regulation of centrosome duplication / regulation of angiotensin-activated signaling pathway / ROCK-subfamily protein kinase / negative regulation of protein localization to lysosome / Rho-dependent protein serine/threonine kinase activity / regulation of keratinocyte differentiation / positive regulation of fibroblast growth factor production / positive regulation of connective tissue replacement / response to transforming growth factor beta / regulation of cell junction assembly / positive regulation of amyloid precursor protein catabolic process / regulation of nervous system process / positive regulation of protein localization to early endosome / host-mediated perturbation of viral process / embryonic morphogenesis / regulation of cellular response to hypoxia / regulation of cell motility / negative regulation of biomineral tissue development / response to angiotensin / negative regulation of nitric oxide biosynthetic process / regulation of establishment of endothelial barrier / RHO GTPases Activate ROCKs / actomyosin structure organization / regulation of stress fiber assembly / Sema4D induced cell migration and growth-cone collapse / cortical actin cytoskeleton organization / aortic valve morphogenesis / RHOBTB1 GTPase cycle / regulation of focal adhesion assembly / positive regulation of amyloid-beta formation / RHOB GTPase cycle / EPHA-mediated growth cone collapse / tau-protein kinase activity / negative regulation of bicellular tight junction assembly / regulation of establishment of cell polarity / mRNA destabilization / positive regulation of cardiac muscle hypertrophy / RHOC GTPase cycle / centrosome duplication / mitotic cytokinesis / smooth muscle contraction / RHOH GTPase cycle / epithelial to mesenchymal transition / RHOA GTPase cycle / regulation of cell adhesion / endopeptidase activator activity / Rho protein signal transduction / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / negative regulation of angiogenesis / blood vessel diameter maintenance / response to ischemia / protein localization to plasma membrane / regulation of actin cytoskeleton organization / regulation of circadian rhythm / VEGFA-VEGFR2 Pathway / tau protein binding / small GTPase binding / cytoplasmic ribonucleoprotein granule / rhythmic process / G alpha (12/13) signalling events / actin cytoskeleton organization / protease binding / Potential therapeutics for SARS / cytoskeleton / protein phosphorylation / positive regulation of MAPK cascade / positive regulation of cell migration / negative regulation of gene expression / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of gene expression / centrosome / structural molecule activity / RNA binding / zinc ion binding / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / Rho-associated protein kinase 2, HR1 domain / ROCK, Rho binding domain / Rho-associated protein kinase 1/2 / Rho Binding / Rho-binding (RhoBD) domain profile. / : / MRCK kinase PH domain / : / HR1 rho-binding domain ...: / Rho-associated protein kinase 2, HR1 domain / ROCK, Rho binding domain / Rho-associated protein kinase 1/2 / Rho Binding / Rho-binding (RhoBD) domain profile. / : / MRCK kinase PH domain / : / HR1 rho-binding domain / REM-1 domain profile. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
: / Rho-associated protein kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsAijia, W. / Shenghai, C. / Qinghua, L. / Yan, H. / Haohao, D. / Bisen, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: ROCK2 bound with TDI01
Authors: Aijia, W. / Shenghai, C. / Qinghua, L. / Yan, H. / Haohao, D. / Bisen, D.
History
DepositionNov 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 17, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho-associated protein kinase 2
B: Rho-associated protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,8294
Polymers91,8582
Non-polymers9712
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Rho-associated protein kinase 2 / Rho kinase 2 / Rho-associated / coiled-coil-containing protein kinase 2 / coiled-coil-containing ...Rho kinase 2 / Rho-associated / coiled-coil-containing protein kinase 2 / coiled-coil-containing protein kinase II / ROCK-II / p164 ROCK-2


Mass: 45929.227 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROCK2, KIAA0619 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O75116, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-A1IVI / [3,3-bis(fluoranyl)azetidin-1-yl]-[1-methyl-6-[4-[[4-(1~{H}-pyrazol-4-yl)phenyl]amino]pyrimidin-2-yl]indol-2-yl]methanone


Mass: 485.488 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H21F2N7O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: Rho-associated protein kinase 2 bound with inhibitor TDI01
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen 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: 1500 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 81591 / Symmetry type: POINT

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