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

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Basic information

Entry
Database: PDB / ID: 3cjb
TitleActin dimer cross-linked by V. cholerae MARTX toxin and complexed with Gelsolin-segment 1
Components
  • Actin, alpha skeletal muscle
  • Gelsolin
KeywordsSTRUCTURAL PROTEIN / cross-linked dimer / ATP-binding / Cytoskeleton / Methylation / Muscle protein / Nucleotide-binding / Phosphoprotein / Actin capping / Actin-binding / Alternative initiation / Amyloid / Disease mutation / Secreted
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.21 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 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
G: Gelsolin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7565
Polymers56,1692
Non-polymers5873
Water362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-40.2 kcal/mol
Surface area20510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.696, 69.540, 182.106
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#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 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
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / 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: 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: 3.2 Å3/Da / Density % sol: 61.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 10% Peg MME 5000, 5% Tacsimate, 0.1 M Hepes, pH 7.0, 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 3, 2007
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→120 Å / Num. obs: 9573 / % possible obs: 77.5 % / Observed criterion σ(F): 0 / Redundancy: 2.7 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.236 / Χ2: 1.256 / Net I/σ(I): 3.6
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.418 / Num. unique all: 620 / Χ2: 1.004 / % possible all: 50.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å64.96 Å
Translation4 Å64.96 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: 3.21→90.91 Å / Cor.coef. Fo:Fc: 0.886 / Cor.coef. Fo:Fc free: 0.851 / SU B: 66.704 / SU ML: 0.489 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.623 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.269 464 4.9 %RANDOM
Rwork0.245 ---
obs0.246 9554 77.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.437 Å2
Baniso -1Baniso -2Baniso -3
1-3.72 Å20 Å20 Å2
2---4.59 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 3.21→90.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3818 0 33 2 3853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223938
X-RAY DIFFRACTIONr_bond_other_d0.0010.022659
X-RAY DIFFRACTIONr_angle_refined_deg1.0141.975341
X-RAY DIFFRACTIONr_angle_other_deg2.19636479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8895482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.69624.068177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.2215662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6921522
X-RAY DIFFRACTIONr_chiral_restr0.0560.2582
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214361
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02802
X-RAY DIFFRACTIONr_mcbond_it0.74222407
X-RAY DIFFRACTIONr_mcbond_other2.5242983
X-RAY DIFFRACTIONr_mcangle_it1.27933882
X-RAY DIFFRACTIONr_scbond_it0.34621531
X-RAY DIFFRACTIONr_scangle_it0.60231459
LS refinement shellResolution: 3.21→3.295 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 30 -
Rwork0.395 392 -
all-422 -
obs--47.85 %
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)
10.9133-0.09110.31121.57641.15111.8913-0.19140.0171-0.0436-0.39830.16050.098-0.19470.08340.0309-0.0306-0.0818-0.0413-0.2418-0.04080.0067-5.491-3.848321.5901
22.69940.89050.71532.36211.50541.62460.0598-0.23690.07740.45510.047-0.12690.1266-0.1305-0.10680.0747-0.0108-0.0908-0.2742-0.0084-0.0227-0.3546-0.923453.2612
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 3758 - 377
2X-RAY DIFFRACTION2GB1 - 1251 - 125

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