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- EMDB-52224: ROCK2 bound with TDI01 -

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Basic information

Entry
Database: EMDB / ID: EMD-52224
TitleROCK2 bound with TDI01
Map data
Sample
  • Complex: Rho-associated protein kinase 2 bound with inhibitor TDI01
    • Protein or peptide: Rho-associated protein kinase 2
  • Ligand: [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
Keywordsinhibitor / kinase / TRANSFERASE / CYTOSOLIC PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsAijia W / Shenghai C / Qinghua L / Yan H / Haohao D / Bisen D
Funding support China, 1 items
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, 2024-
Header (metadata) releaseJun 17, 2026-
Map releaseJun 17, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52224.png

Downloads & links

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Map

FileDownload / File: emd_52224.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 200 pix.
= 219. Å		1.1 Å/pix.
x 200 pix.
= 219. Å		1.1 Å/pix.
x 200 pix.
= 219. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.095 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.044590227 - 0.0710033
Average (Standard dev.)0.00010484048 (±0.0017307635)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 219.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52224_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52224_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Rho-associated protein kinase 2 bound with inhibitor TDI01

EntireName: Rho-associated protein kinase 2 bound with inhibitor TDI01
Components
  • Complex: Rho-associated protein kinase 2 bound with inhibitor TDI01
    • Protein or peptide: Rho-associated protein kinase 2
  • Ligand: [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

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Supramolecule #1: Rho-associated protein kinase 2 bound with inhibitor TDI01

SupramoleculeName: Rho-associated protein kinase 2 bound with inhibitor TDI01
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Rho-associated protein kinase 2

MacromoleculeName: Rho-associated protein kinase 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.929227 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPGDGAGASR QRKLEALIRD PRSPINVESL LDGLNSLVLD LDFPALRKNK NIDNFLNRYE KIVKKIRGLQ MKAEDYDVVK VIGRGAFGE VQLVRHKASQ KVYAMKLLSK FEMIKRSDSA FFWEERDIMA FANSPWVVQL FYAFQDDRYL YMVMEYMPGG D LVNLMSNY ...String:
MPGDGAGASR QRKLEALIRD PRSPINVESL LDGLNSLVLD LDFPALRKNK NIDNFLNRYE KIVKKIRGLQ MKAEDYDVVK VIGRGAFGE VQLVRHKASQ KVYAMKLLSK FEMIKRSDSA FFWEERDIMA FANSPWVVQL FYAFQDDRYL YMVMEYMPGG D LVNLMSNY DVPEKWAKFY TAEVVLALDA IHSMGLIHRD VKPDNMLLDK HGHLKLADFG TCMKMDETGM VHCDTAVGTP DY ISPEVLK SQGGDGFYGR ECDWWSVGVF LYEMLVGDTP FYADSLVGTY SKIMDHKNSL CFPEDAEISK HAKNLICAFL TDR EVRLGR NGVEEIRQHP FFKNDQWHWD NIRETAAPVV PELSSDIDSS NFDDIEDDKG DVETFPIPKA FVGNQLPFIG FTYY R

UniProtKB: Rho-associated protein kinase 2

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Macromolecule #2: [3,3-bis(fluoranyl)azetidin-1-yl]-[1-methyl-6-[4-[[4-(1~{H}-pyraz...

MacromoleculeName: [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
type: ligand / ID: 2 / Number of copies: 2 / Formula: A1IVI
Molecular weightTheoretical: 485.488 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81591
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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