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- PDB-8p0s: Crystal structure HR1 domain of Rho-associated coiled-coil protei... -

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Basic information

Entry
Database: PDB / ID: 8p0s
TitleCrystal structure HR1 domain of Rho-associated coiled-coil protein kinases (ROCK-HR1)
ComponentsRho-associated protein kinase 1
KeywordsSIGNALING PROTEIN / Coiled coil / HR1 / Rho kinase / ROCK / PRK / PKN / Rhotekin
Function / homology
Function and homology information


apical constriction / podocyte cell migration / regulation of angiotensin-activated signaling pathway / positive regulation of phosphatase activity / myoblast migration / membrane to membrane docking / regulation of keratinocyte differentiation / negative regulation of membrane protein ectodomain proteolysis / positive regulation of connective tissue replacement / response to transforming growth factor beta ...apical constriction / podocyte cell migration / regulation of angiotensin-activated signaling pathway / positive regulation of phosphatase activity / myoblast migration / membrane to membrane docking / regulation of keratinocyte differentiation / negative regulation of membrane protein ectodomain proteolysis / positive regulation of connective tissue replacement / response to transforming growth factor beta / regulation of cell junction assembly / negative regulation of bicellular tight junction assembly / positive regulation of dephosphorylation / bleb / negative regulation of amyloid precursor protein catabolic process / embryonic morphogenesis / neuron projection arborization / bleb assembly / leukocyte tethering or rolling / negative regulation of biomineral tissue development / regulation of cell motility / positive regulation of amyloid-beta clearance / regulation of establishment of endothelial barrier / regulation of synapse maturation / negative regulation of motor neuron apoptotic process / RHO GTPases Activate ROCKs / regulation of stress fiber assembly / actomyosin structure organization / Sema4D induced cell migration and growth-cone collapse / response to angiotensin / aortic valve morphogenesis / cortical actin cytoskeleton organization / motor neuron apoptotic process / RHOBTB1 GTPase cycle / regulation of neuron differentiation / RND3 GTPase cycle / regulation of establishment of cell polarity / tau-protein kinase activity / regulation of focal adhesion assembly / leukocyte migration / leukocyte cell-cell adhesion / RHOB GTPase cycle / EPHA-mediated growth cone collapse / Apoptotic cleavage of cellular proteins / RHOC GTPase cycle / positive regulation of cardiac muscle hypertrophy / mRNA destabilization / negative regulation of amyloid-beta formation / regulation of synaptic vesicle endocytosis / mitotic cytokinesis / RHOH GTPase cycle / smooth muscle contraction / positive regulation of focal adhesion assembly / RHOA GTPase cycle / epithelial to mesenchymal transition / Rho protein signal transduction / regulation of cell adhesion / ruffle / positive regulation of autophagy / EPHB-mediated forward signaling / negative regulation of protein binding / centriole / regulation of microtubule cytoskeleton organization / negative regulation of angiogenesis / regulation of cell migration / blood vessel diameter maintenance / protein localization to plasma membrane / regulation of actin cytoskeleton organization / Schaffer collateral - CA1 synapse / small GTPase binding / tau protein binding / VEGFA-VEGFR2 Pathway / cytoplasmic stress granule / neuron projection development / G alpha (12/13) signalling events / lamellipodium / peptidyl-serine phosphorylation / actin cytoskeleton organization / secretory granule lumen / Potential therapeutics for SARS / eukaryotic translation initiation factor 2alpha kinase activity / cytoskeleton / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity
Similarity search - Function
Rho-associated protein kinase 1, HR1 / ROCK, Rho binding domain / Rho-associated protein kinase 1/2 / Rho Binding / Rho-binding (RhoBD) domain profile. / : / 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) ...Rho-associated protein kinase 1, HR1 / ROCK, Rho binding domain / Rho-associated protein kinase 1/2 / Rho Binding / Rho-binding (RhoBD) domain profile. / : / 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Rho-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsDubey, B.N. / Dvorsky, R. / Gremer, L. / Vetter, I.R. / Schmitt, L. / Groth, G. / Ahmadian, M.R.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
German Federal Ministry for Education and Research01GS08100 Germany
CitationJournal: To Be Published
Title: Structural and functional insights into the p160 Rho-associated coiled-coil-containing protein kinase
Authors: Dubey, B.N. / Amin, E. / Dvorsky, R. / Gremer, L. / Moll, J.M. / Wolff, M. / Graewert, M. / Tschapek, B. / Vetter, I.R. / Schmitt, L. / Svergun, D. / Raunser, R. / Groth, G. / Nagel-Steger, L. / Ahmadian, M.R.
History
DepositionMay 10, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho-associated protein kinase 1
B: Rho-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1833
Polymers32,0292
Non-polymers1541
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6670 Å2
ΔGint-61 kcal/mol
Surface area19650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.260, 87.070, 148.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Rho-associated protein kinase 1 / Renal carcinoma antigen NY-REN-35 / Rho-associated / coiled-coil-containing protein kinase 1 / ...Renal carcinoma antigen NY-REN-35 / Rho-associated / coiled-coil-containing protein kinase 1 / coiled-coil-containing protein kinase I / ROCK-I / p160 ROCK-1 / p160ROCK


Mass: 16014.300 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GS is due to the cloning site / Source: (gene. exp.) Homo sapiens (human) / Gene: ROCK1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q13464, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 23% PEG 3350, 150 mM Tri-potassium citrate and 4% MPD (2-methyl-2,4-pentanediol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97924 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 13, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. obs: 116242 / % possible obs: 99.4 % / Redundancy: 3.82 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.57
Reflection shellResolution: 2.2→2.3 Å / Rmerge(I) obs: 0.55 / Num. unique obs: 30449

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158:)refinement
SCALAdata scaling
XDSdata reduction
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→37.05 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 27.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2935 809 5 %
Rwork0.2186 --
obs0.2224 16169 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→37.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2199 0 8 25 2232
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012250
X-RAY DIFFRACTIONf_angle_d1.1392996
X-RAY DIFFRACTIONf_dihedral_angle_d5.718297
X-RAY DIFFRACTIONf_chiral_restr0.055330
X-RAY DIFFRACTIONf_plane_restr0.008401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.340.28381310.22812496X-RAY DIFFRACTION99
2.34-2.520.30831330.23352529X-RAY DIFFRACTION99
2.52-2.770.32931340.24922532X-RAY DIFFRACTION99
2.77-3.170.31391340.25862543X-RAY DIFFRACTION100
3.17-40.28821360.19912593X-RAY DIFFRACTION100
4-37.050.27321410.19932667X-RAY DIFFRACTION99

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