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- PDB-6jcu: Crystal structure of an actin monomer in complex with a nucleator... -

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Basic information

Entry
Database: PDB / ID: 6jcu
TitleCrystal structure of an actin monomer in complex with a nucleator Cordon-Bleu WH2-motif peptide mutant. T22V, H11R
Components
  • Actin, alpha skeletal muscle
  • Peptide from Protein cordon-bleu
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 / mesenchyme migration / dendritic growth cone / actin filament bundle assembly / skeletal muscle myofibril / 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 / liver development / filopodium / actin filament / neural tube closure / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / actin cytoskeleton organization / cell body / cell cortex / cytoskeleton / 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 / 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 speciesOryctolagus cuniculus (rabbit)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.297 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
DepositionJan 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 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 / struct_conn_type
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.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.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 / _struct_conn_type.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: Peptide from Protein cordon-bleu
C: Actin, alpha skeletal muscle
D: Peptide from Protein cordon-bleu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,2189
Polymers89,0844
Non-polymers1,1355
Water5,062281
1
A: Actin, alpha skeletal muscle
B: Peptide from Protein cordon-bleu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1295
Polymers44,5422
Non-polymers5873
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-39 kcal/mol
Surface area16270 Å2
MethodPISA
2
C: Actin, alpha skeletal muscle
D: Peptide from Protein cordon-bleu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0894
Polymers44,5422
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-31 kcal/mol
Surface area16090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.946, 184.213, 55.673
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-632-

HOH

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Components

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


Mass: 42109.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ACTA1, ACTA / Production host: Escherichia coli (E. coli) / References: UniProt: P68135
#2: Protein/peptide Peptide from Protein cordon-bleu


Mass: 2431.859 Da / Num. of mol.: 2 / Mutation: H11R,T22V
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.: 2 / 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.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.28 Å3/Da / Density % sol: 46.06 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / Details: 0.2M Ammonium nitrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 29, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.297→92.106 Å / Num. obs: 835894 / % possible obs: 98.2 % / Redundancy: 6.7 % / Net I/σ(I): 14.6
Reflection shellResolution: 2.297→2.364 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YPU

5ypu


Resolution: 2.297→19.936 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.97
RfactorNum. reflection% reflection
Rfree0.2298 1659 4.94 %
Rwork0.1801 --
obs0.1825 33589 91.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.297→19.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5984 0 65 281 6330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096193
X-RAY DIFFRACTIONf_angle_d1.2968399
X-RAY DIFFRACTIONf_dihedral_angle_d7.7815101
X-RAY DIFFRACTIONf_chiral_restr0.062936
X-RAY DIFFRACTIONf_plane_restr0.0071066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2966-2.3640.2746690.22571392X-RAY DIFFRACTION49
2.364-2.44020.2828950.2292012X-RAY DIFFRACTION70
2.4402-2.52730.261310.21452415X-RAY DIFFRACTION84
2.5273-2.62820.25631310.2142751X-RAY DIFFRACTION97
2.6282-2.74760.28921340.21472872X-RAY DIFFRACTION100
2.7476-2.8920.25981490.21272881X-RAY DIFFRACTION100
2.892-3.07260.25991270.21132892X-RAY DIFFRACTION100
3.0726-3.30880.24781580.19862885X-RAY DIFFRACTION100
3.3088-3.640.2691520.17732896X-RAY DIFFRACTION100
3.64-4.16250.19041690.15362908X-RAY DIFFRACTION100
4.1625-5.22870.1871740.14312938X-RAY DIFFRACTION100
5.2287-19.9370.21071700.16323088X-RAY DIFFRACTION100

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