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- PDB-6jh8: Crystal structure of an actin monomer in complex with a chimeric ... -

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Basic information

Entry
Database: PDB / ID: 6jh8
TitleCrystal structure of an actin monomer in complex with a chimeric peptide of Cordon-Bleu WH2 mutant and MIM.
Components
  • Actin, alpha skeletal muscle
  • Cordon-Bleu MIM chimeric peptide
KeywordsSTRUCTURAL PROTEIN/PROTEIN BINDING / WH2 / actin / sequestering / PROTEIN BINDING / STRUCTURAL PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


somite specification / floor plate development / actin filament network formation / embryonic axis specification / actin crosslink formation / notochord development / collateral sprouting in absence of injury / digestive tract development / positive regulation of ruffle assembly / positive regulation of dendrite development ...somite specification / floor plate development / actin filament network formation / embryonic axis specification / actin crosslink formation / notochord development / collateral sprouting in absence of injury / digestive tract development / positive regulation of ruffle assembly / positive regulation of dendrite development / cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / dendritic growth cone / mesenchyme migration / skeletal muscle myofibril / actin filament bundle assembly / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / axonal growth cone / skeletal muscle fiber development / stress fiber / titin binding / ruffle / actin filament polymerization / neural tube closure / actin filament / filopodium / liver development / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / actin cytoskeleton organization / cell cortex / cytoskeleton / hydrolase activity / protein domain specific binding / axon / neuronal cell body / calcium ion binding / dendrite / positive regulation of gene expression / perinuclear region of cytoplasm / magnesium ion binding / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
Cordon-bleu, ubiquitin-like domain / Protein cordon-bleu-like / Cordon-bleu ubiquitin-like domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH2 domain profile. / WH2 domain / Actins signature 1. / Actin, conserved site / Actins signature 2. ...Cordon-bleu, ubiquitin-like domain / Protein cordon-bleu-like / Cordon-bleu ubiquitin-like domain / Wiskott Aldrich syndrome homology region 2 / WH2 motif / WH2 domain profile. / WH2 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
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Actin, alpha skeletal muscle / Protein cordon-bleu
Similarity search - Component
Biological speciesMus musculus (house mouse)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.149 Å
AuthorsScipion, C.P.M. / Robinson, R.C.
CitationJournal: To Be Published
Title: Design of an actin-severing peptide.
Authors: Scipion, C.P.M. / Robinson, R.C.
History
DepositionFeb 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle
B: Cordon-Bleu MIM chimeric peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,8885
Polymers45,3012
Non-polymers5873
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: G-actin sequestering.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-40 kcal/mol
Surface area16640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.439, 56.073, 38.432
Angle α, β, γ (deg.)90.00, 93.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-631-

HOH

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Components

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


Mass: 42067.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P68135
#2: Protein/peptide Cordon-Bleu MIM chimeric peptide


Mass: 3232.653 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cobl, Kiaa0633 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5NBX1
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate trihydrate, pH 4.6, 10% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.149→42.47 Å / Num. obs: 22798 / % possible obs: 99.2 % / Redundancy: 3.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.075 / Rrim(I) all: 0.145 / Net I/σ(I): 7.3
Reflection shellResolution: 2.149→2.21 Å / Redundancy: 3.7 % / Num. unique obs: 1810 / CC1/2: 0.702 / Rpim(I) all: 0.524 / % possible all: 96.7

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YPU

5ypu


Resolution: 2.149→42.467 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.86
RfactorNum. reflection% reflection
Rfree0.2293 1067 4.71 %
Rwork0.1748 --
obs0.1773 22660 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.149→42.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3083 0 1 234 3318
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013148
X-RAY DIFFRACTIONf_angle_d1.044269
X-RAY DIFFRACTIONf_dihedral_angle_d9.5741903
X-RAY DIFFRACTIONf_chiral_restr0.056476
X-RAY DIFFRACTIONf_plane_restr0.006544
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1485-2.24630.3041260.26452647X-RAY DIFFRACTION98
2.2463-2.36470.28511520.23422651X-RAY DIFFRACTION99
2.3647-2.51290.25931400.21462701X-RAY DIFFRACTION100
2.5129-2.70690.27931410.1992655X-RAY DIFFRACTION99
2.7069-2.97920.26071330.1872745X-RAY DIFFRACTION100
2.9792-3.41020.26031260.16792697X-RAY DIFFRACTION100
3.4102-4.29580.18061310.14362720X-RAY DIFFRACTION99
4.2958-42.47490.17891180.14842777X-RAY DIFFRACTION99

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