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- PDB-5hvk: Crystal structure of LIMK1 mutant D460N in complex with full-leng... -

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Basic information

Entry
Database: PDB / ID: 5hvk
TitleCrystal structure of LIMK1 mutant D460N in complex with full-length cofilin-1
Components
  • (Cofilin-1) x 2
  • LIM domain kinase 1
KeywordsTRANSFERASE / kinase substrate actin-remodeling
Function / homology
Function and homology information


cellular response to ether / cofilin-actin rod / positive regulation of protein localization to cell leading edge / positive regulation of establishment of cell polarity regulating cell shape / negative regulation of unidimensional cell growth / positive regulation of barbed-end actin filament capping / neural fold formation / negative regulation of lamellipodium assembly / negative regulation of postsynaptic density organization / actin filament fragmentation ...cellular response to ether / cofilin-actin rod / positive regulation of protein localization to cell leading edge / positive regulation of establishment of cell polarity regulating cell shape / negative regulation of unidimensional cell growth / positive regulation of barbed-end actin filament capping / neural fold formation / negative regulation of lamellipodium assembly / negative regulation of postsynaptic density organization / actin filament fragmentation / positive regulation of actin filament depolymerization / positive regulation of embryonic development / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / positive regulation of synaptic plasticity / negative regulation of actin filament depolymerization / positive regulation of actin filament bundle assembly / actin filament severing / establishment of spindle localization / regulation of dendritic spine morphogenesis / host-mediated activation of viral process / actin filament depolymerization / cell projection organization / negative regulation of cell motility / negative regulation of cell adhesion / RHO GTPases Activate ROCKs / negative regulation of cell size / cellular response to interleukin-6 / regulation of cell morphogenesis / Sema4D induced cell migration and growth-cone collapse / negative regulation of dendritic spine maintenance / axon extension / neural crest cell migration / positive regulation of cell motility / cortical actin cytoskeleton / phosphatidylinositol bisphosphate binding / cellular response to insulin-like growth factor stimulus / stress fiber assembly / establishment of cell polarity / positive regulation of dendritic spine development / Fc-gamma receptor signaling pathway involved in phagocytosis / RHO GTPases activate PAKs / mitotic cytokinesis / lamellipodium membrane / positive regulation of proteolysis / Sema3A PAK dependent Axon repulsion / ubiquitin ligase inhibitor activity / cellular response to interleukin-1 / positive regulation of focal adhesion assembly / response to amino acid / postsynaptic density, intracellular component / positive regulation of axon extension / Rho protein signal transduction / positive regulation of lamellipodium assembly / positive regulation of stress fiber assembly / heat shock protein binding / EPHB-mediated forward signaling / cytoskeleton organization / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cellular response to epidermal growth factor stimulus / synaptic membrane / response to activity / male germ cell nucleus / hippocampus development / filopodium / mitochondrial membrane / Regulation of actin dynamics for phagocytic cup formation / response to virus / ruffle membrane / nuclear matrix / cellular response to hydrogen peroxide / protein import into nucleus / actin filament binding / cell-cell junction / cellular response to tumor necrosis factor / Platelet degranulation / nervous system development / lamellipodium / actin cytoskeleton / growth cone / actin cytoskeleton organization / positive regulation of cell growth / vesicle / protein phosphatase binding / dendritic spine / cytoskeleton / neuron projection / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / postsynapse / nuclear speck / signaling receptor binding / protein serine kinase activity / focal adhesion / neuronal cell body / protein serine/threonine kinase activity / ubiquitin protein ligase binding / negative regulation of apoptotic process / glutamatergic synapse
Similarity search - Function
: / ADF/Cofilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / LIM zinc-binding domain signature. / Severin / Severin / LIM domain ...: / ADF/Cofilin / Actin-depolymerising factor homology domain / Cofilin/tropomyosin-type actin-binding protein / ADF-H domain profile. / Actin depolymerisation factor/cofilin -like domains / LIM zinc-binding domain signature. / Severin / Severin / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / ADF-H/Gelsolin-like domain superfamily / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Cofilin-1 / LIM domain kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsHamill, S. / Boggon, T.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM102262 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103403 United States
CitationJournal: Mol.Cell / Year: 2016
Title: Structural Basis for Noncanonical Substrate Recognition of Cofilin/ADF Proteins by LIM Kinases.
Authors: Hamill, S. / Lou, H.J. / Turk, B.E. / Boggon, T.J.
History
DepositionJan 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 / _struct_conn_type.id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIM domain kinase 1
B: Cofilin-1
C: LIM domain kinase 1
D: Cofilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,9508
Polymers109,8894
Non-polymers1,0614
Water00
1
A: LIM domain kinase 1
B: Cofilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5154
Polymers54,9852
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-31 kcal/mol
Surface area22600 Å2
MethodPISA
2
C: LIM domain kinase 1
D: Cofilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4354
Polymers54,9052
Non-polymers5312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-23 kcal/mol
Surface area22470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.116, 102.283, 141.900
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 LIM domain kinase 1 / LIMK-1


Mass: 36473.191 Da / Num. of mol.: 2 / Fragment: UNP residues 329-638 / Mutation: D460N
Source method: isolated from a genetically manipulated source
Details: Optimized cDNA / Source: (gene. exp.) Homo sapiens (human) / Gene: LIMK1, LIMK / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9
References: UniProt: P53667, non-specific serine/threonine protein kinase
#2: Protein Cofilin-1 / 18 kDa phosphoprotein / p18 / Cofilin / non-muscle isoform


Mass: 18511.342 Da / Num. of mol.: 1 / Mutation: A69T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFL1, CFL / Plasmid: pET-28a / Details (production host): N-terminal His6-SUMO tag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P23528
#3: Protein Cofilin-1 / 18 kDa phosphoprotein / p18 / Cofilin / non-muscle isoform


Mass: 18431.363 Da / Num. of mol.: 1 / Mutation: A69T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFL1, CFL / Plasmid: pET-28a / Details (production host): N-terminal His6-SUMO tag / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P23528
#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
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: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 1.2-1.4 M tri-Sodium citrate, 0.1 M sodium acetate, pH 5.5. 4 crystals used.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 15631 / % possible obs: 100 % / Redundancy: 10.1 % / Biso Wilson estimate: 33.7 Å2 / CC1/2: 0.531 / Rmerge(I) obs: 0.54 / Net I/σ(I): 2.5
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 8.5 % / Mean I/σ(I) obs: 1.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1819refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BEX

4bex


Resolution: 3.5→48.112 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3104 783 5.09 %Random
Rwork0.2734 ---
obs0.2754 15382 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.5→48.112 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7386 0 60 0 7446
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037606
X-RAY DIFFRACTIONf_angle_d0.76310257
X-RAY DIFFRACTIONf_dihedral_angle_d13.0292917
X-RAY DIFFRACTIONf_chiral_restr0.031116
X-RAY DIFFRACTIONf_plane_restr0.0031297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.71920.36741200.33572380X-RAY DIFFRACTION99
3.7192-4.00630.35071260.30432388X-RAY DIFFRACTION100
4.0063-4.40920.34521340.27262392X-RAY DIFFRACTION100
4.4092-5.04660.28581390.2592419X-RAY DIFFRACTION100
5.0466-6.35590.33751350.27992438X-RAY DIFFRACTION100
6.3559-48.11670.22861290.22522582X-RAY DIFFRACTION100

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