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- PDB-5ubo: Mical-oxidized Actin complex with Gelsolin Segment 1 -

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Basic information

Entry
Database: PDB / ID: 5ubo
TitleMical-oxidized Actin complex with Gelsolin Segment 1
Components
  • Actin, alpha skeletal muscle
  • Gelsolin
KeywordsCONTRACTILE PROTEIN / GELSOLIN / ACTIN / METHIONINE OXIDATION
Function / homology
Function and homology information


striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway ...striated muscle atrophy / regulation of establishment of T cell polarity / regulation of plasma membrane raft polarization / regulation of receptor clustering / renal protein absorption / positive regulation of keratinocyte apoptotic process / positive regulation of protein processing in phagocytic vesicle / positive regulation of actin nucleation / phosphatidylinositol 3-kinase catalytic subunit binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / actin cap / sequestering of actin monomers / regulation of podosome assembly / myosin II binding / negative regulation of viral entry into host cell / actin filament severing / actin filament capping / barbed-end actin filament capping / actin filament depolymerization / actin polymerization or depolymerization / cell projection assembly / cardiac muscle cell contraction / podosome / sarcoplasm / Sensory processing of sound by outer hair cells of the cochlea / relaxation of cardiac muscle / cytoskeletal motor activator activity / phagocytosis, engulfment / cortical actin cytoskeleton / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / hepatocyte apoptotic process / actin filament bundle / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / cilium assembly / actin monomer binding / Caspase-mediated cleavage of cytoskeletal proteins / skeletal muscle fiber development / phagocytic vesicle / stress fiber / titin binding / phosphatidylinositol-4,5-bisphosphate binding / response to muscle stretch / actin filament polymerization / filopodium / central nervous system development / actin filament organization / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / protein destabilization / cellular response to type II interferon / calcium-dependent protein binding / actin filament binding / actin cytoskeleton / lamellipodium / cell body / actin binding / blood microparticle / secretory granule lumen / ficolin-1-rich granule lumen / amyloid fibril formation / hydrolase activity / Amyloid fiber formation / protein domain specific binding / focal adhesion / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / magnesium ion binding / extracellular space / extracellular exosome / extracellular region / ATP binding / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / ATPase, substrate binding domain, subdomain 4 ...Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Roll / Alpha-Beta Complex / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Gelsolin / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.39 Å
Model detailsMet 44 and Met47 in the D-loop are oxidized by Mical and disordered
AuthorsGrintsevich, E.E. / Sawaya, M.R. / Reisler, E.
CitationJournal: Nat Commun / Year: 2017
Title: Catastrophic disassembly of actin filaments via Mical-mediated oxidation.
Authors: Elena E Grintsevich / Peng Ge / Michael R Sawaya / Hunkar Gizem Yesilyurt / Jonathan R Terman / Z Hong Zhou / Emil Reisler /
Abstract: Actin filament assembly and disassembly are vital for cell functions. MICAL Redox enzymes are important post-translational effectors of actin that stereo-specifically oxidize actin's M44 and M47 ...Actin filament assembly and disassembly are vital for cell functions. MICAL Redox enzymes are important post-translational effectors of actin that stereo-specifically oxidize actin's M44 and M47 residues to induce cellular F-actin disassembly. Here we show that Mical-oxidized (Mox) actin can undergo extremely fast (84 subunits/s) disassembly, which depends on F-actin's nucleotide-bound state. Using near-atomic resolution cryoEM reconstruction and single filament TIRF microscopy we identify two dynamic and structural states of Mox-actin. Modeling actin's D-loop region based on our 3.9 Å cryoEM reconstruction suggests that oxidation by Mical reorients the side chain of M44 and induces a new intermolecular interaction of actin residue M47 (M47-O-T351). Site-directed mutagenesis reveals that this interaction promotes Mox-actin instability. Moreover, we find that Mical oxidation of actin allows for cofilin-mediated severing even in the presence of inorganic phosphate. Thus, in conjunction with cofilin, Mical oxidation of actin promotes F-actin disassembly independent of the nucleotide-bound state.
History
DepositionDec 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Oct 4, 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 / 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_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
S: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2147
Polymers56,4682
Non-polymers7465
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-66 kcal/mol
Surface area20280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.200, 69.250, 179.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AS

#1: Protein Actin, alpha skeletal muscle / / Alpha-actin-1


Mass: 42128.953 Da / Num. of mol.: 1 / Fragment: unp residues 1-377 / Source method: isolated from a natural source / Details: skeletal / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein Gelsolin / / AGEL / Actin-depolymerizing factor / ADF / Brevin


Mass: 14339.157 Da / Num. of mol.: 1 / Fragment: unp residues 12-138
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSN / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2 cells / References: UniProt: P06396

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Non-polymers , 4 types, 139 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 3.32 Å3/Da / Density % sol: 62.94 % / Description: long plate
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.6 / Details: PEG 6000, NaCl, imidazole, ATP, calcium

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 20, 2016
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.39→89.59 Å / Num. obs: 28998 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 38.1 % / Biso Wilson estimate: 63.88 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 5.7
Reflection shellResolution: 2.39→2.45 Å / Redundancy: 33.4 % / Rmerge(I) obs: 1.711 / Mean I/σ(I) obs: 2.27 / % possible all: 96.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
Cootmodel building
XDSdata processing
MOSFLMdata reduction
X-PLORmodel building
CCP4(TRUNCATE)data scaling
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1EQY

1eqy


Resolution: 2.39→89.59 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.931 / SU R Cruickshank DPI: 0.234 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.24 / SU Rfree Blow DPI: 0.172 / SU Rfree Cruickshank DPI: 0.171
RfactorNum. reflection% reflectionSelection details
Rfree0.191 1405 4.95 %RANDOM
Rwork0.172 ---
obs0.173 28409 99.6 %-
Displacement parametersBiso mean: 80.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.0587 Å20 Å20 Å2
2--16.7253 Å20 Å2
3----16.784 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.39→89.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3843 0 42 134 4019
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013971HARMONIC2
X-RAY DIFFRACTIONt_angle_deg15386HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1365SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes95HARMONIC2
X-RAY DIFFRACTIONt_gen_planes585HARMONIC5
X-RAY DIFFRACTIONt_it3971HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion22.22
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion519SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4740SEMIHARMONIC4
LS refinement shellResolution: 2.39→2.48 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.206 144 5.08 %
Rwork0.2046 2689 -
all0.2046 2833 -
obs--96 %
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)
12.5534-0.7607-0.97974.63580.72042.5542-0.1999-0.50650.30760.95040.34710.07530.05440.1888-0.1472-0.1330.10870.0885-0.2265-0.0794-0.324322.26643.506268.227
21.7849-0.8615-0.6673.97280.11451.7540.09750.23220.053-0.95680.077-0.21250.0286-0.2901-0.17450.1865-0.05490.1157-0.1145-0.0106-0.169927.71591.265237.2505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ S|* }

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