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- PDB-3cjc: Actin dimer cross-linked by V. cholerae MARTX toxin and complexed... -

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Basic information

Entry
Database: PDB / ID: 3cjc
TitleActin dimer cross-linked by V. cholerae MARTX toxin and complexed with DNase I and Gelsolin-segment 1
Components
  • Actin, alpha skeletal muscle
  • Deoxyribonuclease-1
  • Gelsolin
KeywordsStructural protein/Hydrolase / cross-linked dimer / ATP-binding / Cytoskeleton / Methylation / Muscle protein / Nucleotide-binding / Phosphoprotein / Structural protein / Actin-binding / Apoptosis / Endonuclease / Glycoprotein / Hydrolase / Nuclease / Nucleus / Secreted / Actin capping / Alternative initiation / Amyloid / Disease mutation / Structural protein-Hydrolase COMPLEX
Function / homology
Function and homology information


regulation of neutrophil mediated cytotoxicity / zymogen granule / regulation of acute inflammatory response / deoxyribonuclease I / 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 ...regulation of neutrophil mediated cytotoxicity / zymogen granule / regulation of acute inflammatory response / deoxyribonuclease I / 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 / deoxyribonuclease I activity / neutrophil activation involved in immune response / 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 / DNA catabolic process / 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 / nuclear envelope / 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 / apoptotic process / calcium ion binding / Neutrophil degranulation / positive regulation of gene expression / magnesium ion binding / DNA binding / extracellular space / extracellular exosome / extracellular region / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Deoxyribonuclease I / Deoxyribonuclease I, active site / Deoxyribonuclease I, conservied site / Deoxyribonuclease I signature 2. / Deoxyribonuclease I signature 1. / deoxyribonuclease I / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / Villin/Gelsolin / Gelsolin homology domain ...Deoxyribonuclease I / Deoxyribonuclease I, active site / Deoxyribonuclease I, conservied site / Deoxyribonuclease I signature 2. / Deoxyribonuclease I signature 1. / deoxyribonuclease I / Actin; Chain A, domain 2 / Actin; Chain A, domain 2 / Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Deoxyribonuclease I; Chain A / Endonuclease/exonuclease/phosphatase / Gelsolin-like domain / Gelsolin repeat / Endonuclease/exonuclease/phosphatase / Endonuclease/Exonuclease/phosphatase family / ADF-H/Gelsolin-like domain superfamily / Endonuclease/exonuclease/phosphatase 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 / 4-Layer Sandwich / 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 / Deoxyribonuclease-1 / Gelsolin / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
Oryctolagus cuniculus (rabbit)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.9 Å
AuthorsSawaya, M.R. / Kudryashov, D.S. / Pashkov, I. / Reisler, E. / Yeates, T.O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Connecting actin monomers by iso-peptide bond is a toxicity mechanism of the Vibrio cholerae MARTX toxin.
Authors: Kudryashov, D.S. / Durer, Z.A. / Ytterberg, A.J. / Sawaya, M.R. / Pashkov, I. / Prochazkova, K. / Yeates, T.O. / Loo, R.R. / Loo, J.A. / Satchell, K.J. / Reisler, E.
History
DepositionMar 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
D: Deoxyribonuclease-1
G: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,84913
Polymers85,2613
Non-polymers1,58810
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6610 Å2
ΔGint-124.4 kcal/mol
Surface area31230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.303, 108.566, 133.761
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 3 molecules ADG

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


Mass: 42096.953 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: skeletal muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein Deoxyribonuclease-1 / / Deoxyribonuclease I / DNase I


Mass: 29092.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: pancreatic / Source: (natural) Bos taurus (cattle) / References: UniProt: P00639, deoxyribonuclease I
#3: Protein Gelsolin / / Actin-depolymerizing factor / ADF / Brevin / AGEL


Mass: 14071.831 Da / Num. of mol.: 1 / Fragment: segment 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSN / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P06396

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Sugars , 1 types, 1 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 11 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: 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
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.8 Å3/Da / Density % sol: 67.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.5 M (NH4)SO4, 0.1 M Bis-Tris, 0.1 M NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 27, 2007
RadiationMonochromator: KOHZU: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.9→90 Å / Num. obs: 12337 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.207 / Χ2: 1.073 / Net I/σ(I): 4
Reflection shellResolution: 3.9→4.04 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.481 / Num. unique all: 1193 / Χ2: 1.127 / % possible all: 97.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å84.29 Å
Translation4 Å84.29 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
BOSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.9→74.33 Å / Cor.coef. Fo:Fc: 0.897 / Cor.coef. Fo:Fc free: 0.86 / SU B: 93.365 / SU ML: 0.617 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: A peptide cross-link is formed by the toxin between Lys50 and Glu270 of neighboring actin molecules. The cross-link is not modeled in the coordinate set due to disorder. HYDROGENS HAVE BEEN ...Details: A peptide cross-link is formed by the toxin between Lys50 and Glu270 of neighboring actin molecules. The cross-link is not modeled in the coordinate set due to disorder. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Ellipsoidal truncation and anisotropic scale factors have been applied to the structure factors and used in refinement. The ellipsoid has principle axes of 5.8, 3.9, and 3.9 reciprocal angstroms along a*, b*, and c*, respectively. The submitted structure factor archive contains the truncated/scaled structure factors and the original, unmodified intensities.
RfactorNum. reflection% reflectionSelection details
Rfree0.278 400 4.7 %RANDOM
Rwork0.223 ---
obs0.226 8450 68.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.869 Å2
Baniso -1Baniso -2Baniso -3
1--13.77 Å20 Å20 Å2
2--6.73 Å20 Å2
3---7.04 Å2
Refine analyzeLuzzati coordinate error free: 1.083 Å
Refinement stepCycle: LAST / Resolution: 3.9→74.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5936 0 91 2 6029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226159
X-RAY DIFFRACTIONr_bond_other_d0.0070.024082
X-RAY DIFFRACTIONr_angle_refined_deg0.9281.9698372
X-RAY DIFFRACTIONr_angle_other_deg0.783.0019931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8535751
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.61524.143280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.866151007
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.3531534
X-RAY DIFFRACTIONr_chiral_restr0.0540.2928
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0216808
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021252
X-RAY DIFFRACTIONr_mcbond_it1.10323753
X-RAY DIFFRACTIONr_mcbond_other0.0521526
X-RAY DIFFRACTIONr_mcangle_it1.58736063
X-RAY DIFFRACTIONr_scbond_it0.32322406
X-RAY DIFFRACTIONr_scangle_it0.56732309
LS refinement shellResolution: 3.9→3.998 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 10 -
Rwork0.263 137 -
all-147 -
obs--16.63 %
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)
10.5605-0.33930.13221.02720.12810.49170.0390.04790.0470.0318-0.0318-0.12740.05210.0355-0.00710.18820.0021-0.0018-0.16060.0396-0.2401-4.90537.904-5.469
23.7029-0.3763-0.32730.8785-0.1163.06520.03480.14580.0265-0.0355-0.03460.0663-0.0287-0.1009-0.00020.1538-0.0265-0.0135-0.3667-0.0538-0.26826.7754-3.7914-19.2784
33.4750.10810.65091.51010.65170.55880.0964-0.16660.4189-0.13740.3237-0.8476-0.42370.3738-0.42010.1995-0.08350.1071-0.30650.00510.01848.031967.792-3.3341
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 3723 - 374
2X-RAY DIFFRACTION2DB1 - 2601 - 260
3X-RAY DIFFRACTION3GC1 - 1251 - 125

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