[English] 日本語
Yorodumi
- PDB-2v55: Mechanism of multi-site phosphorylation from a ROCK-I:RhoE comple... -

+
Open data


ID or keywords:

Loading...

-
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 / ROCK-subfamily protein kinase / myoblast migration / membrane to membrane docking / Rho-dependent protein serine/threonine kinase activity / negative regulation of membrane protein ectodomain proteolysis / regulation of keratinocyte differentiation / positive regulation of connective tissue replacement ...apical constriction / podocyte cell migration / regulation of angiotensin-activated signaling pathway / ROCK-subfamily protein kinase / myoblast migration / membrane to membrane docking / Rho-dependent protein serine/threonine kinase activity / negative regulation of membrane protein ectodomain proteolysis / regulation of keratinocyte differentiation / positive regulation of connective tissue replacement / response to transforming growth factor beta / regulation of cell junction assembly / negative regulation of amyloid precursor protein catabolic process / embryonic morphogenesis / bleb assembly / regulation of cell motility / positive regulation of amyloid-beta clearance / leukocyte tethering or rolling / neuron projection arborization / negative regulation of biomineral tissue development / bleb / response to angiotensin / regulation of establishment of endothelial barrier / negative regulation of motor neuron apoptotic process / regulation of synapse maturation / regulation of stress fiber assembly / RHO GTPases Activate ROCKs / actomyosin structure organization / Sema4D induced cell migration and growth-cone collapse / cortical actin cytoskeleton organization / aortic valve morphogenesis / RND3 GTPase cycle / motor neuron apoptotic process / regulation of neuron differentiation / RHOBTB1 GTPase cycle / leukocyte migration / regulation of focal adhesion assembly / RHOB GTPase cycle / EPHA-mediated growth cone collapse / leukocyte cell-cell adhesion / tau-protein kinase activity / Apoptotic cleavage of cellular proteins / small GTPase-mediated signal transduction / negative regulation of bicellular tight junction assembly / regulation of establishment of cell polarity / positive regulation of cardiac muscle hypertrophy / RHOC GTPase cycle / mRNA destabilization / negative regulation of amyloid-beta formation / mitotic cytokinesis / smooth muscle contraction / RHOH GTPase cycle / epithelial to mesenchymal transition / RHOA GTPase cycle / positive regulation of focal adhesion assembly / negative regulation of protein binding / regulation of synaptic vesicle endocytosis / regulation of cell adhesion / Rho protein signal transduction / ruffle / EPHB-mediated forward signaling / positive regulation of autophagy / regulation of cell migration / negative regulation of angiogenesis / blood vessel diameter maintenance / peptidyl-serine phosphorylation / regulation of microtubule cytoskeleton organization / actin filament organization / protein localization to plasma membrane / regulation of actin cytoskeleton organization / centriole / VEGFA-VEGFR2 Pathway / tau protein binding / Schaffer collateral - CA1 synapse / small GTPase binding / cytoplasmic stress granule / neuron projection development / lamellipodium / G alpha (12/13) signalling events / actin cytoskeleton organization / secretory granule lumen / Potential therapeutics for SARS / cytoskeleton / positive regulation of MAPK cascade / cell adhesion / intracellular signal transduction / Golgi membrane / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / GTPase activity / Neutrophil degranulation / positive regulation of gene expression / protein kinase binding / GTP binding / signal transduction / extracellular region / zinc ion binding / ATP binding / plasma membrane
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. / : / MRCK kinase PH domain / : / HR1 rho-binding domain ...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. / : / MRCK kinase PH domain / : / HR1 rho-binding domain / REM-1 domain profile. / Small GTPase Rho / Small GTPase Rho 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 / 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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more