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- PDB-4l2w: Crystal structure of the Shroom-Binding domain of human Rock1 -

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Basic information

Entry
Database: PDB / ID: 4l2w
TitleCrystal structure of the Shroom-Binding domain of human Rock1
ComponentsRho-associated protein kinase 1
KeywordsPROTEIN BINDING / coiled-coil / Shroom SD2 / kinase / myosin
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 / epithelial to mesenchymal transition / smooth muscle contraction / RHOA GTPase cycle / regulation of cell adhesion / canonical NF-kappaB signal transduction / regulation of microtubule cytoskeleton organization / positive regulation of autophagy / 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 / 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 / SAD / Resolution: 2.49 Å
AuthorsMohan, S. / VanDemark, A.P.
CitationJournal: Plos One / Year: 2013
Title: Structure of a highly conserved domain of Rock1 required for Shroom-mediated regulation of cell morphology.
Authors: Mohan, S. / Das, D. / Bauer, R.J. / Heroux, A. / Zalewski, J.K. / Heber, S. / Dosunmu-Ogunbi, A.M. / Trakselis, M.A. / Hildebrand, J.D. / Vandemark, A.P.
History
DepositionJun 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,3044
Polymers40,3044
Non-polymers00
Water48627
1
C: Rho-associated protein kinase 1
D: Rho-associated protein kinase 1


Theoretical massNumber of molelcules
Total (without water)20,1522
Polymers20,1522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-22 kcal/mol
Surface area11220 Å2
MethodPISA
2
A: Rho-associated protein kinase 1
B: Rho-associated protein kinase 1


Theoretical massNumber of molelcules
Total (without water)20,1522
Polymers20,1522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-20 kcal/mol
Surface area11170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.500, 56.230, 80.740
Angle α, β, γ (deg.)90.000, 119.140, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Rho-associated protein kinase 1


Mass: 10076.093 Da / Num. of mol.: 4 / Fragment: Shroom binding Domain (UNP residues 834-914) / Mutation: E884A, K885A, E886A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROCK1 / Plasmid: pET151 D-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13464
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.5 Å3/Da / Density % sol: 64.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6
Details: 0.1M Citrate, 1.0M Ammonium Sulfate, pH 6.0, VAPOR DIFFUSION, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2010
RadiationMonochromator: Double silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 6.1 % / Av σ(I) over netI: 30.74 / Number: 130748 / Rmerge(I) obs: 0.087 / Χ2: 2.03 / D res high: 2.4 Å / D res low: 50 Å / Num. obs: 21426 / % possible obs: 98.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.515098.210.0496.6146.5
5.176.5199.310.0612.7736.5
4.525.1799.710.0532.5116.8
4.14.5299.910.0532.0736.8
3.814.199.610.0712.4186.7
3.583.8199.710.0892.3556.7
3.413.5810010.1172.0576.8
3.263.4110010.1521.497
3.133.2610010.2041.7756.9
3.023.1310010.211.1927
2.933.0210010.2451.0476.8
2.852.9399.910.2871.0896.6
2.772.8510010.3721.0496.3
2.72.7799.910.3891.0236
2.642.798.710.5493.4675.4
2.592.6499.110.5431.0685.2
2.532.5998.510.5740.9254.9
2.492.5396.610.6742.5094.6
2.442.4995.610.6351.1784.2
2.42.4493.810.6570.9564.1
ReflectionResolution: 2.49→50 Å / Num. all: 20969 / Num. obs: 17172 / % possible obs: 88.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.076 / Χ2: 1.873 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.49-2.544.90.5475370.89156.1
2.54-2.595.10.5055810.913161.5
2.59-2.645.40.4236470.979167
2.64-2.695.30.4326781.034169.9
2.69-2.755.40.3357371.007176.1
2.75-2.825.70.3177681.069178.9
2.82-2.895.60.2758111.112187.1
2.89-2.965.70.248761.164189.3
2.96-3.055.80.2219191.175194.9
3.05-3.155.80.1749211.372196.5
3.15-3.265.80.1659481.483199.1
3.26-3.395.90.1429561.778199.7
3.39-3.555.90.1099661.971100
3.55-3.7360.0829922.2151100
3.73-3.975.90.079622.5531100
3.97-4.275.90.0599612.818199.9
4.27-4.75.80.0559813.066199.9
4.7-5.385.80.0569652.934199.6
5.38-6.785.70.0569832.489199.1
6.78-505.70.0449833.025195.8

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
157.2584.87712.409S201
258.3071.30713.652S200.971
363.02626.78116.293S200.85
461.35830.74217.247S200.673
564.41622.8716.838S200.334
655.6378.54611.777S200.261
754.19229.45510.381S200.216
860.414-2.67913.512S200.145

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.49→38.315 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.32 / σ(F): 1.35 / Phase error: 30.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2756 801 5.03 %Random
Rwork0.2359 ---
obs0.2379 15930 79.98 %-
all-15930 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.42 Å2 / Biso mean: 66.2001 Å2 / Biso min: 20.23 Å2
Refinement stepCycle: LAST / Resolution: 2.49→38.315 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2204 0 0 27 2231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062212
X-RAY DIFFRACTIONf_angle_d0.8382959
X-RAY DIFFRACTIONf_chiral_restr0.047337
X-RAY DIFFRACTIONf_plane_restr0.002394
X-RAY DIFFRACTIONf_dihedral_angle_d19.112891
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.49-2.64110.2951460.3014960100630
2.6411-2.8450.28831010.30621978207963
2.845-3.13120.3371380.30542756289488
3.1312-3.5840.29211640.260231193283100
3.584-4.51430.24191810.197531403321100
4.5143-38.31910.27161710.21023176334798
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)
10.78780.2144-0.19340.26340.1762-0.0027-0.15480.1628-0.95290.0024-0.0321-0.4301-0.0614-0.0994-0.01760.1474-0.0509-0.07060.1390.09560.32029.1544-34.660432.179
20.37160.05140.23020.4180.05870.16310.18740.483-0.22470.2634-0.0445-0.0489-0.4785-0.28030.00190.30420.0183-0.00010.2511-0.00030.22931.2371-29.831330.226
30.56090.3486-0.04790.3521-0.35870.7070.49720.22480.17320.3052-0.26660.0833-0.7070.0593-0.00360.385-0.0452-0.00090.40720.0690.242846.7008-10.42547.2697
41.43910.5403-0.46540.2157-0.66540.5941-0.27310.1222-0.9765-0.1294-0.2396-0.43250.04430.0847-0.04590.4985-0.0790.04540.5283-0.06830.505148.1073-18.60924.7528
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN C AND (RESID 838:904)C0
2X-RAY DIFFRACTION2CHAIN D AND (RESID 835:902)D0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 837:903)A0
4X-RAY DIFFRACTION4CHAIN B AND (RESID 838:904)B0

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