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- PDB-8zh5: The Crystal Structure of the ROCK1 from Biortus. -

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Basic information

Entry
Database: PDB / ID: 8zh5
TitleThe Crystal Structure of the ROCK1 from Biortus.
ComponentsRho-associated protein kinase 1
KeywordsTRANSFERASE / Serine/threonine-protein kinase
Function / homology
Function and homology information


regulation of angiotensin-activated signaling pathway / apical constriction / Rho-dependent protein serine/threonine kinase activity / podocyte cell migration / positive regulation of phosphatase activity / myoblast migration / positive regulation of connective tissue replacement / membrane to membrane docking / negative regulation of membrane protein ectodomain proteolysis / regulation of keratinocyte differentiation ...regulation of angiotensin-activated signaling pathway / apical constriction / Rho-dependent protein serine/threonine kinase activity / podocyte cell migration / positive regulation of phosphatase activity / myoblast migration / positive regulation of connective tissue replacement / membrane to membrane docking / negative regulation of membrane protein ectodomain proteolysis / regulation of keratinocyte differentiation / 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 / bleb / regulation of synapse maturation / 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 / positive regulation of amyloid-beta clearance / 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 / actomyosin structure organization / Sema4D induced cell migration and growth-cone collapse / aortic valve morphogenesis / response to angiotensin / regulation of establishment of cell polarity / RHOBTB1 GTPase cycle / regulation of synaptic vesicle endocytosis / motor neuron apoptotic process / RND3 GTPase cycle / 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 / 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 / RHOH GTPase cycle / Rho protein signal transduction / mitotic cytokinesis / smooth muscle contraction / RHOA GTPase cycle / epithelial to mesenchymal transition / canonical NF-kappaB signal transduction / regulation of cell adhesion / positive regulation of autophagy / regulation of microtubule cytoskeleton organization / regulation of cell migration / ruffle / EPHB-mediated forward signaling / centriole / blood vessel diameter maintenance / negative regulation of angiogenesis / negative regulation of protein binding / protein localization to plasma membrane / regulation of actin cytoskeleton organization / Schaffer collateral - CA1 synapse / tau protein binding / 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 / metal ion binding / plasma membrane / cytoplasm
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 / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsWang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Wang, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: The Crystal Structure of the ROCK1 from Biortus.
Authors: Wang, F. / Cheng, W. / Yuan, Z. / Lin, D. / Wang, J.
History
DepositionMay 10, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rho-associated protein kinase 1


Theoretical massNumber of molelcules
Total (without water)47,9551
Polymers47,9551
Non-polymers00
Water1629
1
A: Rho-associated protein kinase 1

A: Rho-associated protein kinase 1


Theoretical massNumber of molelcules
Total (without water)95,9102
Polymers95,9102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area4090 Å2
ΔGint-34 kcal/mol
Surface area36850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.283, 166.283, 64.503
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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: 47955.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROCK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q13464, non-specific serine/threonine protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 4.65 Å3/Da / Density % sol: 73.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M MgAC2, 0.1M NaAC pH4.5, 8% PEG 8000, 1.0M NDSB-256

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 7, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 3.7→48.73 Å / Num. obs: 9205 / % possible obs: 91.4 % / Redundancy: 15.2 % / Rmerge(I) obs: 0.235 / Net I/σ(I): 11.9
Reflection shellResolution: 3.7→4.05 Å / Rmerge(I) obs: 0.917 / Num. unique obs: 2184

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→46.161 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.909 / SU B: 34.703 / SU ML: 0.465 / Cross valid method: FREE R-VALUE / ESU R Free: 0.606
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2595 444 4.837 %
Rwork0.2082 8736 -
all0.211 --
obs-9180 90.64 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 127.764 Å2
Baniso -1Baniso -2Baniso -3
1--5.134 Å20 Å20 Å2
2---5.134 Å20 Å2
3---10.268 Å2
Refinement stepCycle: LAST / Resolution: 3.7→46.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3142 0 0 9 3151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0123216
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162994
X-RAY DIFFRACTIONr_angle_refined_deg0.791.844337
X-RAY DIFFRACTIONr_angle_other_deg0.2931.7846903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5345379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.826521
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.0410571
X-RAY DIFFRACTIONr_dihedral_angle_6_deg9.02910166
X-RAY DIFFRACTIONr_chiral_restr0.0360.2457
X-RAY DIFFRACTIONr_chiral_restr_other0.0020.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023769
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02769
X-RAY DIFFRACTIONr_nbd_refined0.1920.2653
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.22634
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21553
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.21586
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.254
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1090.221
X-RAY DIFFRACTIONr_nbd_other0.1540.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1280.23
X-RAY DIFFRACTIONr_mcbond_it3.71312.761528
X-RAY DIFFRACTIONr_mcbond_other3.71312.761528
X-RAY DIFFRACTIONr_mcangle_it6.52222.9311903
X-RAY DIFFRACTIONr_mcangle_other6.5222.9311904
X-RAY DIFFRACTIONr_scbond_it3.44513.0791688
X-RAY DIFFRACTIONr_scbond_other3.44413.081689
X-RAY DIFFRACTIONr_scangle_it6.22523.9372434
X-RAY DIFFRACTIONr_scangle_other6.22423.9362435
X-RAY DIFFRACTIONr_lrange_it10.544118.8853553
X-RAY DIFFRACTIONr_lrange_other10.543118.8853554
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.7-3.7960.347390.3036370.3057410.9010.91791.22810.263
3.796-3.8990.315260.2776170.2796880.9120.93593.45930.242
3.899-4.0110.325260.2736040.2756910.9110.93691.17220.232
4.011-4.1340.285430.2385710.2416670.920.95892.0540.199
4.134-4.2680.255340.2375510.2386590.9630.95888.77090.198
4.268-4.4160.29210.1955440.1986190.9540.97291.27630.166
4.416-4.5820.283280.1945400.1996220.9490.97391.31830.159
4.582-4.7670.282220.1725080.1765770.9390.97991.85440.147
4.767-4.9760.219260.1824970.1845790.9710.97690.32810.156
4.976-5.2160.263230.1964680.1995340.9520.97591.94760.163
5.216-5.4940.314180.1834460.1885170.950.97889.74860.163
5.494-5.8220.303250.2214330.2255070.9050.96890.33530.185
5.822-6.2170.355180.2394050.2444650.9450.96290.96770.208
6.217-6.7050.216230.2233710.2224370.9510.97190.16020.204
6.705-7.330.207140.1953530.1964080.9780.97589.9510.18
7.33-8.1690.17120.1673260.1673800.9760.98288.94740.162
8.169-9.3840.168160.1822860.1813370.9820.97789.61420.181
9.384-11.3770.234120.1482450.1522860.9890.98889.86010.152
11.377-15.6210.15390.152020.152400.9830.98887.91670.154
15.621-46.1610.36190.371320.3691650.950.91985.45450.427

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