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- PDB-3tv7: Human Rho-associated protein kinase 1 (ROCK 1) in COMPLEX WITH RKI1342 -

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Basic information

Entry
Database: PDB / ID: 3tv7
TitleHuman Rho-associated protein kinase 1 (ROCK 1) in COMPLEX WITH RKI1342
ComponentsRho-associated protein kinase 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / dimer / dimerization / myosin / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


regulation of angiotensin-activated signaling pathway / apical constriction / podocyte cell migration / Rho-dependent protein serine/threonine kinase activity / positive regulation of phosphatase activity / regulation of keratinocyte differentiation / myoblast migration / positive regulation of connective tissue replacement / membrane to membrane docking / negative regulation of membrane protein ectodomain proteolysis ...regulation of angiotensin-activated signaling pathway / apical constriction / podocyte cell migration / Rho-dependent protein serine/threonine kinase activity / positive regulation of phosphatase activity / regulation of keratinocyte differentiation / 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 / : / regulation of cell junction assembly / positive regulation of dephosphorylation / negative regulation of bicellular tight junction assembly / bleb / negative regulation of phosphorylation / negative regulation of amyloid precursor protein catabolic process / neuron projection arborization / embryonic morphogenesis / bleb assembly / negative regulation of biomineral tissue development / leukocyte tethering or rolling / regulation of synapse maturation / positive regulation of amyloid-beta clearance / actomyosin structure organization / 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 / response to angiotensin / aortic valve morphogenesis / regulation of establishment of cell polarity / RHOBTB1 GTPase cycle / motor neuron apoptotic process / RND3 GTPase cycle / regulation of synaptic vesicle endocytosis / regulation of neuron differentiation / cortical actin cytoskeleton organization / regulation of focal adhesion assembly / leukocyte cell-cell adhesion / leukocyte migration / RHOB GTPase cycle / tau-protein kinase activity / EPHA-mediated growth cone collapse / mRNA destabilization / positive regulation of cardiac muscle hypertrophy / Apoptotic cleavage of cellular proteins / RHOC GTPase cycle / negative regulation of amyloid-beta formation / positive regulation of focal adhesion assembly / mitotic cytokinesis / Rho protein signal transduction / RHOH GTPase cycle / smooth muscle contraction / epithelial to mesenchymal transition / RHOA GTPase cycle / regulation of cell adhesion / canonical NF-kappaB signal transduction / positive regulation of autophagy / regulation of microtubule cytoskeleton organization / ruffle / EPHB-mediated forward signaling / regulation of cell migration / centriole / negative regulation of angiogenesis / blood vessel diameter maintenance / negative regulation of protein binding / protein localization to plasma membrane / regulation of actin cytoskeleton organization / tau protein binding / Schaffer collateral - CA1 synapse / VEGFA-VEGFR2 Pathway / small GTPase binding / 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 / protein phosphorylation / Golgi membrane / protein serine kinase activity / protein serine/threonine kinase activity / Neutrophil degranulation / positive regulation of gene expression / signal transduction / extracellular region / ATP binding / metal ion binding / plasma membrane / cytosol
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 / 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-07Q / Rho-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsMartin, M.P. / Zhu, J.-Y. / Schonbrunn, E.
CitationJournal: Medchemcomm / Year: 2012
Title: Pyridylthiazole-based ureas as inhibitors of Rho associated protein kinases (ROCK1 and 2).
Authors: Pireddu, R. / Forinash, K.D. / Sun, N.N. / Martin, M.P. / Sung, S.S. / Alexander, B. / Zhu, J.Y. / Guida, W.C. / Schonbrunn, E. / Sebti, S.M. / Lawrence, N.J.
History
DepositionSep 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Sep 13, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)191,54711
Polymers189,9434
Non-polymers1,6047
Water2,342130
1
A: Rho-associated protein kinase 1
B: Rho-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,7425
Polymers94,9712
Non-polymers7713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-25 kcal/mol
Surface area36560 Å2
MethodPISA
2
C: Rho-associated protein kinase 1
D: Rho-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,8046
Polymers94,9712
Non-polymers8334
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-18 kcal/mol
Surface area36160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.010, 150.920, 185.570
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 / p160 ...Renal carcinoma antigen NY-REN-35 / Rho-associated / coiled-coil-containing protein kinase 1 / p160 ROCK-1 / p160ROCK


Mass: 47485.660 Da / Num. of mol.: 4 / Fragment: N-terminal kinase domain, residue 6-415
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROCK1 / Plasmid: pFB-Dual-PBL / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q13464, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-07Q / 1-[(1R)-1-(3-methoxyphenyl)ethyl]-3-(4-pyridin-4-yl-1,3-thiazol-2-yl)urea


Mass: 354.426 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H18N4O2S
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 2.78 Å3/Da / Density % sol: 55.81 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 10 mg/ml ROCK1, 75 mm hepes pH 7.4, 2.5 % tacsimate ph 7.4, 5 % PEG 5000 MME, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 26, 2011 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.75→20 Å / Num. obs: 55039 / % possible obs: 99.91 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 48.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 20
Reflection shellResolution: 2.75→2.8 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 5.8 / Num. unique all: 2851 / % possible all: 100

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Processing

Software
NameVersionClassification
StructureStudiodata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CHAIN A OF 2ETR

2etr


Resolution: 2.75→19.828 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 26.16 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2533 1101 2 %RANDOM
Rwork0.2055 ---
obs-55039 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 22.059 Å2 / ksol: 0.325 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.9879 Å2-0 Å2-0 Å2
2--4.3336 Å20 Å2
3----9.3214 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.75→19.828 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12860 0 112 130 13102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01113283
X-RAY DIFFRACTIONf_angle_d1.32917938
X-RAY DIFFRACTIONf_dihedral_angle_d18.5424937
X-RAY DIFFRACTIONf_chiral_restr0.0951882
X-RAY DIFFRACTIONf_plane_restr0.0052326
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.75-2.87480.3951350.2926646X-RAY DIFFRACTION100
2.8748-3.02590.2981370.26686693X-RAY DIFFRACTION100
3.0259-3.21470.33881370.25476694X-RAY DIFFRACTION100
3.2147-3.46170.27871360.23476702X-RAY DIFFRACTION100
3.4617-3.80790.25741370.20496712X-RAY DIFFRACTION100
3.8079-4.35380.24811380.17536731X-RAY DIFFRACTION100
4.3538-5.46620.20761380.17096786X-RAY DIFFRACTION100
5.4662-19.82860.19881430.17836974X-RAY DIFFRACTION100

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