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- PDB-2v55: Mechanism of multi-site phosphorylation from a ROCK-I:RhoE comple... -

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Basic information

Entry
Database: PDB / ID: 2v55
TitleMechanism of multi-site phosphorylation from a ROCK-I:RhoE complex structure
Components
  • RHO-ASSOCIATED PROTEIN KINASE 1
  • RHO-RELATED GTP-BINDING PROTEIN RHOE
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / RHOE / ZINC / KINASE / ROCK-I / MEMBRANE / APOPTOSIS / CYTOPLASM / G-PROTEINS / METHYLATION / ZINC-FINGER / NUCLEOTIDE-BINDING / PHORBOL-ESTER BINDING / ATP-BINDING / PRENYLATION / LIPOPROTEIN / MULTI-SITE PHOSPHORYLATION / COILED COIL / GTP-BINDING / POLYMORPHISM / STRESS FIBRES / METAL-BINDING / PHOSPHOPROTEIN / GOLGI APPARATUS
Function / homology
Function and homology information


apical constriction / podocyte cell migration / regulation of angiotensin-activated signaling pathway / positive regulation of phosphatase activity / myoblast migration / membrane to membrane docking / regulation of keratinocyte differentiation / negative regulation of membrane protein ectodomain proteolysis / positive regulation of connective tissue replacement / response to transforming growth factor beta ...apical constriction / podocyte cell migration / regulation of angiotensin-activated signaling pathway / positive regulation of phosphatase activity / myoblast migration / membrane to membrane docking / regulation of keratinocyte differentiation / negative regulation of membrane protein ectodomain proteolysis / positive regulation of connective tissue replacement / response to transforming growth factor beta / regulation of cell junction assembly / negative regulation of bicellular tight junction assembly / positive regulation of dephosphorylation / bleb / negative regulation of amyloid precursor protein catabolic process / embryonic morphogenesis / neuron projection arborization / bleb assembly / leukocyte tethering or rolling / negative regulation of biomineral tissue development / regulation of cell motility / positive regulation of amyloid-beta clearance / regulation of establishment of endothelial barrier / regulation of synapse maturation / negative regulation of motor neuron apoptotic process / RHO GTPases Activate ROCKs / regulation of stress fiber assembly / actomyosin structure organization / Sema4D induced cell migration and growth-cone collapse / response to angiotensin / aortic valve morphogenesis / cortical actin cytoskeleton organization / motor neuron apoptotic process / RHOBTB1 GTPase cycle / regulation of neuron differentiation / RND3 GTPase cycle / regulation of establishment of cell polarity / tau-protein kinase activity / regulation of focal adhesion assembly / leukocyte migration / leukocyte cell-cell adhesion / RHOB GTPase cycle / small GTPase-mediated signal transduction / EPHA-mediated growth cone collapse / Apoptotic cleavage of cellular proteins / RHOC GTPase cycle / positive regulation of cardiac muscle hypertrophy / mRNA destabilization / negative regulation of amyloid-beta formation / regulation of synaptic vesicle endocytosis / mitotic cytokinesis / RHOH GTPase cycle / smooth muscle contraction / positive regulation of focal adhesion assembly / RHOA GTPase cycle / epithelial to mesenchymal transition / Rho protein signal transduction / regulation of cell adhesion / ruffle / positive regulation of autophagy / EPHB-mediated forward signaling / negative regulation of protein binding / centriole / regulation of microtubule cytoskeleton organization / negative regulation of angiogenesis / regulation of cell migration / blood vessel diameter maintenance / actin filament organization / protein localization to plasma membrane / regulation of actin cytoskeleton organization / Schaffer collateral - CA1 synapse / small GTPase binding / tau protein binding / VEGFA-VEGFR2 Pathway / cytoplasmic stress granule / neuron projection development / G alpha (12/13) signalling events / lamellipodium / peptidyl-serine phosphorylation / actin cytoskeleton organization / secretory granule lumen / Potential therapeutics for SARS / eukaryotic translation initiation factor 2alpha kinase activity / cytoskeleton / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity
Similarity search - Function
Rho-related GTP-binding protein RhoE / 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. / Small GTPase Rho ...Rho-related GTP-binding protein RhoE / 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. / Small GTPase Rho / small GTPase Rho family 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 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / GUANOSINE-5'-TRIPHOSPHATE / Rho-related GTP-binding protein RhoE / Rho-associated protein kinase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.705 Å
AuthorsKomander, D. / Garg, R. / Wan, P.T.C. / Ridley, A.J. / Barford, D.
CitationJournal: Embo J. / Year: 2008
Title: Mechanism of Multi-Site Phosphorylation from a Rock-I:Rhoe Complex Structure.
Authors: Komander, D. / Garg, R. / Wan, P.T.C. / Ridley, A.J. / Barford, D.
History
DepositionOct 1, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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-RELATED GTP-BINDING PROTEIN RHOE
C: RHO-ASSOCIATED PROTEIN KINASE 1
D: RHO-RELATED GTP-BINDING PROTEIN RHOE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,14713
Polymers138,8954
Non-polymers2,2529
Water00
1
A: RHO-ASSOCIATED PROTEIN KINASE 1
B: RHO-RELATED GTP-BINDING PROTEIN RHOE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,5266
Polymers69,4482
Non-polymers1,0784
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-6.1 kcal/mol
Surface area33100 Å2
MethodPQS
2
C: RHO-ASSOCIATED PROTEIN KINASE 1
D: RHO-RELATED GTP-BINDING PROTEIN RHOE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6227
Polymers69,4482
Non-polymers1,1745
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-6.5 kcal/mol
Surface area33820 Å2
MethodPQS
Unit cell
Length a, b, c (Å)152.477, 152.477, 531.274
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 6:371 OR RESSEQ 378:404 OR RESSEQ 1480:1481 )
211CHAIN C AND (RESSEQ 6:371 OR RESSEQ 375:404 OR RESSEQ 1480:1481 )
112CHAIN B AND (RESSEQ 20:200 OR RESSEQ 1201:1202 )
212CHAIN D AND (RESSEQ 20:200 OR RESSEQ 1201:1202 )

NCS ensembles :
ID
1
2

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein RHO-ASSOCIATED PROTEIN KINASE 1 / ROCK1 / RHO-ASSOCIATED / COILED-COIL-CONTAINING PROTEIN KINASE 1 / P160 ROCK-1 / P160ROCK / RENAL ...ROCK1 / RHO-ASSOCIATED / COILED-COIL-CONTAINING PROTEIN KINASE 1 / P160 ROCK-1 / P160ROCK / RENAL CARCINOMA ANTIGEN NY-REN-35


Mass: 47020.234 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 1-406
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PHTB / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: Q13464, non-specific serine/threonine protein kinase
#2: Protein RHO-RELATED GTP-BINDING PROTEIN RHOE / RHOE / RHO FAMILY GTPASE 3 / RND3 / RHO8 / MEMB PROTEIN


Mass: 22427.449 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P61587

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Non-polymers , 4 types, 9 molecules

#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 6.3 Å3/Da / Density % sol: 85 % / Description: NONE
Crystal growpH: 6.5
Details: 0.6 - 1 M NA/K TARTRATE, 0.1 M MES [PH 5-6], 0.2 M LISO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→131 Å / Num. obs: 39411 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 74.95 Å2 / Rmerge(I) obs: 0.19 / Net I/σ(I): 8.4
Reflection shellResolution: 3.7→3.9 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2ETR AND 1GWN

2etr

1gwn


Resolution: 3.705→49.288 Å / SU ML: 0.5 / σ(F): 1.36 / Phase error: 21.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2689 809 2.06 %
Rwork0.2376 --
obs0.2382 39321 98.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.719 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso mean: 81.67 Å2
Baniso -1Baniso -2Baniso -3
1-1.6465 Å20 Å20 Å2
2--1.6465 Å2-0 Å2
3----3.2931 Å2
Refinement stepCycle: LAST / Resolution: 3.705→49.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9053 0 135 0 9188
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d09397
X-RAY DIFFRACTIONf_angle_d1.312791
X-RAY DIFFRACTIONf_dihedral_angle_d23.233370
X-RAY DIFFRACTIONf_chiral_restr0.081398
X-RAY DIFFRACTIONf_plane_restr01636
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3082X-RAY DIFFRACTIONPOSITIONAL
12C3082X-RAY DIFFRACTIONPOSITIONAL0.049
21B1366X-RAY DIFFRACTIONPOSITIONAL
22D1366X-RAY DIFFRACTIONPOSITIONAL0.044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7049-3.9370.31641180.27936307X-RAY DIFFRACTION99
3.937-4.24080.2641390.25196395X-RAY DIFFRACTION100
4.2408-4.66730.29961430.21946356X-RAY DIFFRACTION99
4.6673-5.3420.26211410.22096417X-RAY DIFFRACTION99
5.342-6.72760.24421240.22236476X-RAY DIFFRACTION98
6.7276-49.29220.21451440.21036561X-RAY DIFFRACTION94
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)
10.58930.8654-0.32691.3668-0.19510.26350.0137-0.01570.10780.23430.10330.09450.0801-0.0567-0.07210.33490.15920.01430.4950.08170.4485-19.894542.258434.6998
22.2816-1.53291.1231.36770.23650.99160.06610.38920.09680.107-0.1845-0.1222-0.31140.07580.14770.30070.12740.06040.65380.09080.5818-38.431671.773113.0245
31.5920.54830.26791.11780.3240.173-0.2142-0.11190.1710.03810.14770.0724-0.0228-0.12070.05640.31110.2103-0.05190.6461-0.03950.486610.408323.724255.5134
41.7514-0.77210.94180.9539-0.01610.6567-0.15260.5107-0.122-0.3869-0.09290.2356-0.03680.2250.12240.37970.23120.09060.369-0.02150.311545.197920.999376.7684
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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