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- PDB-6jh9: Crystal structure of an actin monomer in complex with a chimeric ... -

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Basic information

Entry
Database: PDB / ID: 6jh9
TitleCrystal structure of an actin monomer in complex with a chimeric peptide of Cordon-Bleu WH2 mutant and MIM. Lys18Arg
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 / terminal web / embryonic axis specification / notochord development / actin crosslink formation / digestive tract development / collateral sprouting in absence of injury / positive regulation of ruffle assembly ...somite specification / floor plate development / actin filament network formation / terminal web / embryonic axis specification / notochord development / actin crosslink formation / digestive tract development / collateral sprouting in absence of injury / positive regulation of ruffle assembly / positive regulation of dendrite development / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / actin filament bundle / dendritic growth cone / filamentous actin / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / axonal growth cone / stress fiber / titin binding / ruffle / actin filament polymerization / liver development / filopodium / neural tube closure / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / cell body / cell cortex / actin cytoskeleton organization / hydrolase activity / protein domain specific binding / axon / neuronal cell body / dendrite / calcium ion binding / positive regulation of gene expression / perinuclear region of cytoplasm / magnesium ion binding / ATP binding / membrane / identical protein binding / 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 / WH2 domain profile. / 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 / WH2 domain profile. / 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: 1.739 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.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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
B: Cordon-Bleu MIM chimeric peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0506
Polymers45,3712
Non-polymers6794
Water7,116395
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: G-actin sequestration.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3870 Å2
ΔGint-40 kcal/mol
Surface area16790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.350, 56.368, 38.478
Angle α, β, γ (deg.)90.00, 93.66, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-767-

HOH

21A-821-

HOH

31A-840-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 42109.973 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: 3260.667 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

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Non-polymers , 4 types, 399 molecules

#3: 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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 395 / 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: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M sodium acetate trihydrate, pH 4.8, 8% 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: 0.95365 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 19, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95365 Å / Relative weight: 1
ReflectionResolution: 1.739→48.74 Å / Num. obs: 42896 / % possible obs: 99.6 % / Redundancy: 3.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.05 / Rrim(I) all: 0.093 / Net I/σ(I): 8
Reflection shellResolution: 1.739→1.77 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2252 / CC1/2: 0.799 / Rpim(I) all: 0.419 / Rrim(I) all: 0.789 / % possible all: 95.4

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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: 1.739→48.738 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 21.89
RfactorNum. reflection% reflection
Rfree0.2064 2053 4.79 %
Rwork0.1836 --
obs0.1846 42895 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.739→48.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3082 0 7 395 3484
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033228
X-RAY DIFFRACTIONf_angle_d0.6494390
X-RAY DIFFRACTIONf_dihedral_angle_d8.9733348
X-RAY DIFFRACTIONf_chiral_restr0.044488
X-RAY DIFFRACTIONf_plane_restr0.004562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7388-1.77930.34411120.3172619X-RAY DIFFRACTION96
1.7793-1.82380.32961600.29892726X-RAY DIFFRACTION100
1.8238-1.87310.28571370.26992694X-RAY DIFFRACTION100
1.8731-1.92820.32771320.27052727X-RAY DIFFRACTION99
1.9282-1.99040.25011490.24462671X-RAY DIFFRACTION99
1.9904-2.06160.25451390.22292711X-RAY DIFFRACTION100
2.0616-2.14410.23541430.20542719X-RAY DIFFRACTION100
2.1441-2.24170.22051300.19582712X-RAY DIFFRACTION100
2.2417-2.35990.22181500.19282725X-RAY DIFFRACTION100
2.3599-2.50770.21331390.18892709X-RAY DIFFRACTION100
2.5077-2.70130.20811510.18632722X-RAY DIFFRACTION100
2.7013-2.97310.20731320.1782775X-RAY DIFFRACTION100
2.9731-3.40330.20841260.16792743X-RAY DIFFRACTION100
3.4033-4.28740.17211330.14962772X-RAY DIFFRACTION100
4.2874-48.75720.14141200.15282817X-RAY DIFFRACTION99

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