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- PDB-5f5p: Molecular Basis for Shroom2 Recognition by Rock1 -

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Basic information

Entry
Database: PDB / ID: 5f5p
TitleMolecular Basis for Shroom2 Recognition by Rock1
Components
  • Protein Shroom2
  • Rho-associated protein kinase 1
KeywordsPROTEIN BINDING / coiled-coil / complex / cytoskeleton / kinase
Function / homology
Function and homology information


establishment of melanosome localization / eye pigment granule organization / cellular pigment accumulation / apical constriction / podocyte cell migration / regulation of angiotensin-activated signaling pathway / myoblast migration / membrane to membrane docking / regulation of keratinocyte differentiation / Rho-dependent protein serine/threonine kinase activity ...establishment of melanosome localization / eye pigment granule organization / cellular pigment accumulation / apical constriction / podocyte cell migration / regulation of angiotensin-activated signaling pathway / myoblast migration / membrane to membrane docking / regulation of keratinocyte differentiation / Rho-dependent protein serine/threonine kinase activity / negative regulation of membrane protein ectodomain proteolysis / positive regulation of connective tissue replacement / response to transforming growth factor beta / lens morphogenesis in camera-type eye / regulation of cell junction assembly / negative regulation of amyloid precursor protein catabolic process / bleb / ear development / camera-type eye morphogenesis / embryonic morphogenesis / bleb assembly / neuron projection arborization / melanosome organization / regulation of cell motility / positive regulation of amyloid-beta clearance / leukocyte tethering or rolling / negative regulation of biomineral tissue development / regulation of establishment of endothelial barrier / response to angiotensin / regulation of synapse maturation / negative regulation of motor neuron apoptotic process / camera-type eye development / regulation of stress fiber assembly / RHO GTPases Activate ROCKs / actomyosin structure organization / Sema4D induced cell migration and growth-cone collapse / aortic valve morphogenesis / apical protein localization / RHOBTB1 GTPase cycle / cortical actin cytoskeleton organization / regulation of neuron differentiation / RND3 GTPase cycle / motor neuron apoptotic process / regulation of establishment of cell polarity / negative regulation of bicellular tight junction assembly / ligand-gated sodium channel activity / tau-protein kinase activity / regulation of focal adhesion assembly / leukocyte migration / leukocyte cell-cell adhesion / RHOB GTPase cycle / EPHA-mediated growth cone collapse / apical junction complex / Apoptotic cleavage of cellular proteins / positive regulation of cardiac muscle hypertrophy / RHOC GTPase cycle / mRNA destabilization / negative regulation of amyloid-beta formation / mitotic cytokinesis / RHOH GTPase cycle / smooth muscle contraction / epithelial to mesenchymal transition / RHOA GTPase cycle / positive regulation of focal adhesion assembly / regulation of synaptic vesicle endocytosis / bicellular tight junction / regulation of cell adhesion / negative regulation of protein binding / Rho protein signal transduction / ruffle / EPHB-mediated forward signaling / positive regulation of autophagy / centriole / regulation of cell migration / regulation of microtubule cytoskeleton organization / actin filament organization / negative regulation of angiogenesis / blood vessel diameter maintenance / protein localization to plasma membrane / regulation of actin cytoskeleton organization / adherens junction / brain development / beta-catenin binding / peptidyl-serine phosphorylation / small GTPase binding / VEGFA-VEGFR2 Pathway / Schaffer collateral - CA1 synapse / tau protein binding / neuron projection development / cytoplasmic stress granule / actin filament binding / cell migration / G alpha (12/13) signalling events / lamellipodium / actin binding / actin cytoskeleton organization / secretory granule lumen / Potential therapeutics for SARS / microtubule / cytoskeleton
Similarity search - Function
Apx/Shrm Domain 1 / Apx/Shroom domain ASD1 / ASD1 domain profile. / Apx/Shrm Domain 2 / Shroom family / Apx/Shroom domain ASD2 / ASD2 domain profile. / Rho-associated protein kinase 1, HR1 / ROCK, Rho binding domain / Rho-associated protein kinase 1/2 ...Apx/Shrm Domain 1 / Apx/Shroom domain ASD1 / ASD1 domain profile. / Apx/Shrm Domain 2 / Shroom family / Apx/Shroom domain ASD2 / ASD2 domain profile. / Rho-associated protein kinase 1, HR1 / ROCK, Rho binding domain / Rho-associated protein kinase 1/2 / Rho Binding / Rho-binding (RhoBD) domain profile. / MRCK kinase PH domain / : / 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. / PDZ domain / Pleckstrin homology domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / 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 / Protein Shroom2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.568 Å
AuthorsZalewski, J.K. / VanDemark, A.P. / Heroux, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097204 United States
CitationJournal: J. Biol. Chem. / Year: 2016
Title: Structure of the Shroom-Rho Kinase Complex Reveals a Binding Interface with Monomeric Shroom That Regulates Cell Morphology and Stimulates Kinase Activity.
Authors: Zalewski, J.K. / Mo, J.H. / Heber, S. / Heroux, A. / Gardner, R.G. / Hildebrand, J.D. / VanDemark, A.P.
History
DepositionDec 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Derived calculations
Revision 1.2Dec 14, 2016Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Shroom2
B: Protein Shroom2
C: Rho-associated protein kinase 1
D: Rho-associated protein kinase 1
E: Rho-associated protein kinase 1
F: Rho-associated protein kinase 1
G: Protein Shroom2
H: Protein Shroom2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,41010
Polymers138,3398
Non-polymers712
Water00
1
A: Protein Shroom2
B: Protein Shroom2
C: Rho-associated protein kinase 1
D: Rho-associated protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2406
Polymers69,1704
Non-polymers712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Rho-associated protein kinase 1
F: Rho-associated protein kinase 1
G: Protein Shroom2
H: Protein Shroom2


Theoretical massNumber of molelcules
Total (without water)69,1704
Polymers69,1704
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.587, 133.795, 135.871
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Protein Shroom2 / Apical-like protein / Protein APXL


Mass: 24481.703 Da / Num. of mol.: 4 / Fragment: residues 1427-1610
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SHROOM2, APXL / Plasmid: pET151 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIPL / References: UniProt: Q13796
#2: 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: 10103.093 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROCK1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIPL
References: UniProt: Q13464, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
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: 3.64 Å3/Da / Density % sol: 66.17 % / Description: Thin, square plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 3350, 200 mM Magnesium Chloride, 100 mM Tris pH 8.5
PH range: 8.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.57→50 Å / Num. obs: 21121 / % possible obs: 97.8 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.5
Reflection shellResolution: 3.57→3.63 Å / Mean I/σ(I) obs: 1.72 / % possible all: 97.9

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Processing

Software
NameVersionClassification
PHENIX(dev_2219)refinement
Cootmodel building
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3THF

3thf


Resolution: 3.568→19.91 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 41.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2869 953 4.6 %
Rwork0.2709 --
obs0.2732 19901 96.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.568→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7633 0 2 0 7635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027684
X-RAY DIFFRACTIONf_angle_d0.53810281
X-RAY DIFFRACTIONf_dihedral_angle_d11.7344888
X-RAY DIFFRACTIONf_chiral_restr0.0281186
X-RAY DIFFRACTIONf_plane_restr0.0021344
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5681-3.7550.4791230.51082506X-RAY DIFFRACTION86
3.755-3.98850.41061350.38952821X-RAY DIFFRACTION98
3.9885-4.29360.37431210.31952866X-RAY DIFFRACTION97
4.2936-4.72050.31451410.26252793X-RAY DIFFRACTION96
4.7205-5.39160.27421470.26262882X-RAY DIFFRACTION98
5.3916-6.74870.35051430.35782931X-RAY DIFFRACTION99
6.7487-19.910.20471410.19753010X-RAY DIFFRACTION97

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