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- PDB-3o0z: Crystal structure of a coiled-coil domain from human ROCK I -

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Basic information

Entry
Database: PDB / ID: 3o0z
TitleCrystal structure of a coiled-coil domain from human ROCK I
ComponentsRho-associated protein kinase 1
KeywordsTRANSFERASE / coiled-coil
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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / 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. ...Rho-associated protein kinase 1, HR1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Rho-associated protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.33 Å
AuthorsTu, D. / Eck, M.J.
CitationJournal: Plos One / Year: 2011
Title: Crystal Structure of a Coiled-Coil Domain from Human ROCK I.
Authors: Tu, D. / Li, Y. / Song, H.K. / Toms, A.V. / Gould, C.J. / Ficarro, S.B. / Marto, J.A. / Goode, B.L. / Eck, M.J.
History
DepositionJul 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)79,5754
Polymers79,5754
Non-polymers00
Water48627
1
A: Rho-associated protein kinase 1
B: Rho-associated protein kinase 1


Theoretical massNumber of molelcules
Total (without water)39,7872
Polymers39,7872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-47 kcal/mol
Surface area24910 Å2
MethodPISA
2
C: Rho-associated protein kinase 1
D: Rho-associated protein kinase 1


Theoretical massNumber of molelcules
Total (without water)39,7872
Polymers39,7872
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-47 kcal/mol
Surface area25670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.588, 84.588, 340.129
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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


Mass: 19893.670 Da / Num. of mol.: 4 / Fragment: coiled-coil domain (unp residues 535-700)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROCK1 / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: Q13464, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
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: 3.82 Å3/Da / Density % sol: 67.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.9
Details: 13% MPD, 100 mM NaCl, 100 mM sodium acetate, 10 mM DTT, 5% glycerol, 10 mM spermidine, pH 4.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2009
RadiationMonochromator: MD2 microdiffractometers / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.33→50 Å / Num. all: 69169 / Num. obs: 69169 / % possible obs: 67.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 30.4 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 30.7
Reflection shellResolution: 2.33→2.41 Å / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 13.2 / Num. unique all: 1487 / % possible all: 14.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.33→42.133 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.89 / Phase error: 36.23 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2861 3641 5.3 %random
Rwork0.2393 ---
obs0.2418 68742 67.94 %-
all-68742 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.125 Å2 / ksol: 0.304 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-16.0982 Å20 Å2-0 Å2
2--16.0982 Å2-0 Å2
3----37.8442 Å2
Refinement stepCycle: LAST / Resolution: 2.33→42.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5162 0 0 27 5189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095296
X-RAY DIFFRACTIONf_angle_d1.0887083
X-RAY DIFFRACTIONf_dihedral_angle_d21.7822198
X-RAY DIFFRACTIONf_chiral_restr0.069776
X-RAY DIFFRACTIONf_plane_restr0.003950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3268-2.35740.6448250.4087504X-RAY DIFFRACTION13
2.3574-2.38970.4906370.3175597X-RAY DIFFRACTION16
2.3897-2.42390.4105360.258673X-RAY DIFFRACTION18
2.4239-2.46010.3774460.2608787X-RAY DIFFRACTION22
2.4601-2.49850.374500.2494880X-RAY DIFFRACTION24
2.4985-2.53940.4255580.24111023X-RAY DIFFRACTION28
2.5394-2.58320.3697650.21741121X-RAY DIFFRACTION31
2.5832-2.63020.3537730.21671299X-RAY DIFFRACTION35
2.6302-2.68080.4031800.25771486X-RAY DIFFRACTION41
2.6808-2.73550.2738980.28951710X-RAY DIFFRACTION46
2.7355-2.7950.35241150.27751990X-RAY DIFFRACTION54
2.795-2.860.27781280.27662369X-RAY DIFFRACTION64
2.86-2.93150.31721720.29133049X-RAY DIFFRACTION82
2.9315-3.01070.35192060.30063674X-RAY DIFFRACTION100
3.0107-3.09930.32192030.29193637X-RAY DIFFRACTION99
3.0993-3.19930.32032040.28253646X-RAY DIFFRACTION99
3.1993-3.31360.3532070.28673690X-RAY DIFFRACTION100
3.3136-3.44620.32582070.25573663X-RAY DIFFRACTION100
3.4462-3.60290.29172090.24533676X-RAY DIFFRACTION100
3.6029-3.79280.26222030.20363692X-RAY DIFFRACTION100
3.7928-4.03020.22782070.19653703X-RAY DIFFRACTION100
4.0302-4.34110.24622070.19473642X-RAY DIFFRACTION100
4.3411-4.77750.19042020.18723697X-RAY DIFFRACTION100
4.7775-5.46750.26082000.21153610X-RAY DIFFRACTION98
5.4675-6.88360.28872040.26423682X-RAY DIFFRACTION100
6.8836-42.14010.25321990.19143601X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.08240.02210.00290.1708-0.04540.0111-0.0039-0.1057-0.0207-0.0637-0.0034-0.0203-0.00420.0574-0.0039-0.01950.01850.02120.2101-0.05350.168370.204260.951199.2365
20.23490.03270.08830.1039-0.00730.0310.0995-0.1733-0.0356-0.04420.028-0.0519-0.04290.0064-0.10680.20320.0285-0.03850.2781-0.04490.234966.681563.5996199.8291
30.1741-0.11320.2517-0.0863-0.23911.02390.1688-0.0082-0.0693-0.24730.01970.03060.6012-0.0193-0.16960.19930.016-0.1168-0.03780.02690.033767.051657.7666106.7352
40.16380.02420.09660.07860.01450.44920.05810.0181-0.0449-0.13980.0382-0.01850.02070.0361-0.07850.45610.0394-0.06110.1721-0.00080.248564.37960.7314108.4198
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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