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- PDB-2etr: Crystal Structure of ROCK I bound to Y-27632 -

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Basic information

Entry
Database: PDB / ID: 2etr
TitleCrystal Structure of ROCK I bound to Y-27632
ComponentsRho-associated protein kinase 1
KeywordsTRANSFERASE / dimerization / dimer / phosphorylation / kinase / Yoshitomi
Function / homology
Function and homology information


regulation of amyloid-beta formation / regulation of angiotensin-activated signaling pathway / apical constriction / Rho-dependent protein serine/threonine kinase activity / podocyte cell migration / regulation of keratinocyte differentiation / positive regulation of phosphatase activity / myoblast migration / positive regulation of connective tissue replacement / membrane to membrane docking ...regulation of amyloid-beta formation / regulation of angiotensin-activated signaling pathway / apical constriction / Rho-dependent protein serine/threonine kinase activity / podocyte cell migration / regulation of keratinocyte differentiation / positive regulation of phosphatase activity / myoblast migration / positive regulation of connective tissue replacement / membrane to membrane docking / negative regulation of membrane protein ectodomain proteolysis / response to transforming growth factor beta / negative regulation of myosin-light-chain-phosphatase activity / regulation of cell junction assembly / positive regulation of dephosphorylation / negative regulation of bicellular tight junction assembly / regulation of synapse maturation / bleb / positive regulation of amyloid-beta clearance / negative regulation of amyloid precursor protein catabolic process / neuron projection arborization / bleb assembly / embryonic morphogenesis / leukocyte tethering or rolling / negative regulation of biomineral tissue development / negative regulation of phosphorylation / actomyosin structure organization / aspartic-type endopeptidase inhibitor activity / regulation of establishment of endothelial barrier / RHO GTPases Activate ROCKs / negative regulation of motor neuron apoptotic process / regulation of stress fiber assembly / regulation of cell motility / Sema4D induced cell migration and growth-cone collapse / aortic valve morphogenesis / response to angiotensin / regulation of establishment of cell polarity / motor neuron apoptotic process / RHOBTB1 GTPase cycle / RND3 GTPase cycle / regulation of synaptic vesicle endocytosis / cortical actin cytoskeleton organization / regulation of neuron differentiation / regulation of focal adhesion assembly / leukocyte cell-cell adhesion / RHOB GTPase cycle / tau-protein kinase activity / leukocyte migration / negative regulation of amyloid-beta formation / EPHA-mediated growth cone collapse / mRNA destabilization / positive regulation of cardiac muscle hypertrophy / RHOC GTPase cycle / Apoptotic cleavage of cellular proteins / positive regulation of focal adhesion assembly / RHOH GTPase cycle / mitotic cytokinesis / Rho protein signal transduction / smooth muscle contraction / RHOA GTPase cycle / epithelial to mesenchymal transition / canonical NF-kappaB signal transduction / regulation of microtubule cytoskeleton organization / positive regulation of autophagy / regulation of cell adhesion / regulation of cell migration / ruffle / EPHB-mediated forward signaling / centriole / blood vessel diameter maintenance / negative regulation of angiogenesis / negative regulation of protein binding / regulation of autophagy / protein localization to plasma membrane / regulation of actin cytoskeleton organization / tau protein binding / Schaffer collateral - CA1 synapse / small GTPase binding / VEGFA-VEGFR2 Pathway / cytoplasmic stress granule / neuron projection development / G alpha (12/13) signalling events / lamellipodium / actin cytoskeleton organization / peptidyl-serine phosphorylation / secretory granule lumen / Potential therapeutics for SARS / positive regulation of MAPK cascade / cytoskeleton / non-specific serine/threonine protein kinase / protein kinase activity / Golgi membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / Neutrophil degranulation / positive regulation of gene expression / signal transduction / extracellular region / ATP binding
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) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain ...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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-Y27 / Rho-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsJacobs, M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: The Structure of Dimeric ROCK I Reveals the Mechanism for Ligand Selectivity.
Authors: Jacobs, M. / Hayakawa, K. / Swenson, L. / Bellon, S. / Fleming, M. / Taslimi, P. / Doran, J.
History
DepositionOct 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)96,5194
Polymers96,0252
Non-polymers4952
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-41 kcal/mol
Surface area36450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.865, 180.865, 91.456
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is the same as the asymmetric unit - 2 kinase catalytic domains connected via a dimerization domain

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Components

#1: Protein Rho-associated protein kinase 1 / Rho-associated / coiled-coil containing protein kinase 1 / p160 ROCK-1 / p160ROCK


Mass: 48012.285 Da / Num. of mol.: 2 / Fragment: N-terminal and kinase domain, residues 6-415
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROCK1 / Plasmid: pBEV10 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13464, EC: 2.7.1.37
#2: Chemical ChemComp-Y27 / (R)-TRANS-4-(1-AMINOETHYL)-N-(4-PYRIDYL) CYCLOHEXANECARBOXAMIDE / Y-27632


Mass: 247.336 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H21N3O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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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: 4.5 Å3/Da / Density % sol: 72.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 4.5% PEG3350, 100mM MES, pH 5.5, 50mM CaCl2, 10mM DTT, 0.45 mM protein, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 10, 2001
RadiationMonochromator: APS-ID32 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 52928 / Num. obs: 48059 / % possible obs: 90.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Rmerge(I) obs: 0.086 / Χ2: 1.724 / Net I/σ(I): 10.6
Reflection shellResolution: 2.6→2.68 Å / % possible obs: 46.3 % / Rmerge(I) obs: 0.41 / Num. measured obs: 2025 / Χ2: 1.021 / % possible all: 46.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.7data extraction
AMoREphasing
CNX2002refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ATP

1atp


Resolution: 2.6→19.83 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 323018.188 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2283 4.8 %RANDOM
Rwork0.251 ---
all0.252 49467 --
obs0.252 47184 89 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 23.778 Å2 / ksol: 0.304 e/Å3
Displacement parametersBiso mean: 66.4 Å2
Baniso -1Baniso -2Baniso -3
1-2.97 Å210.8 Å20 Å2
2--2.97 Å20 Å2
3----5.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.63 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6473 0 36 108 6617
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d1.21
X-RAY DIFFRACTIONc_mcbond_it1.871.5
X-RAY DIFFRACTIONc_mcangle_it3.22
X-RAY DIFFRACTIONc_scbond_it2.732
X-RAY DIFFRACTIONc_scangle_it4.142.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.38 127 3.2 %
Rwork0.38 3832 -
all-3959 -
obs--45.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.topprotein_rep.param
X-RAY DIFFRACTION2inhib.rtfwater_rep.param
X-RAY DIFFRACTION3mass1.datmissing.dat
X-RAY DIFFRACTION4water.topparmxray.xpl

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