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- PDB-4ae3: Crystal structure of ammosamide 272:myosin-2 motor domain complex -

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Basic information

Entry
Database: PDB / ID: 4ae3
TitleCrystal structure of ammosamide 272:myosin-2 motor domain complex
ComponentsMYOSIN-2 HEAVY CHAIN
KeywordsHYDROLASE / ATPASE / CONTRACTILE PROTEIN / ACTIN BINDING / MOTOR PROTEIN
Function / homology
Function and homology information


calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / equatorial cell cortex / contractile actin filament bundle assembly / cell trailing edge / contractile vacuole organization ...calcium-dependent ATPase activity / pseudopodium retraction / uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / equatorial cell cortex / contractile actin filament bundle assembly / cell trailing edge / contractile vacuole organization / myosin filament assembly / aggregation involved in sorocarp development / culmination involved in sorocarp development / RHO GTPases activate PAKs / adenyl nucleotide binding / response to differentiation-inducing factor 1 / hypotonic response / uropod / mitotic actomyosin contractile ring / actomyosin contractile ring / mitotic actomyosin contractile ring contraction / actin-myosin filament sliding / detection of mechanical stimulus / apical cortex / negative regulation of actin filament polymerization / bleb assembly / actomyosin / substrate-dependent cell migration, cell extension / myosin filament / filopodium assembly / early phagosome / cortical actin cytoskeleton organization / myosin II complex / cortical actin cytoskeleton / microfilament motor activity / pseudopodium / cytoskeletal motor activity / cleavage furrow / mitotic cytokinesis / response to mechanical stimulus / 14-3-3 protein binding / response to cAMP / extracellular matrix / muscle contraction / cell motility / response to hydrogen peroxide / protein localization / chemotaxis / actin filament binding / cell cortex / regulation of cell shape / cytoplasmic vesicle / cytoskeleton / calmodulin binding / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. ...Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
AMMOSAMIDE 272 / ADP ORTHOVANADATE / Myosin-2 heavy chain
Similarity search - Component
Biological speciesDICTYOSTELIUM DISCOIDEUM (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChinthalapudi, K. / Heissler, S.M. / Fenical, W. / Manstein, D.J.
CitationJournal: To be Published
Title: Structural Basis for Ammosamide Mediated Myosin Motor Activity Inhibition
Authors: Chinthalapudi, K. / Heissler, S.M. / Fenical, W. / Manstein, D.J.
History
DepositionJan 5, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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.pdbx_dist_value / _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_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_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: MYOSIN-2 HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8759
Polymers88,5141
Non-polymers1,3618
Water7,909439
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.050, 145.520, 153.830
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2301-

HOH

21A-2305-

HOH

31A-2367-

HOH

41A-2377-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein MYOSIN-2 HEAVY CHAIN / MYOSIN II HEAVY CHAIN


Mass: 88513.969 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN, RESIDUES 2-761
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Strain: AX4 / Plasmid: PDXA-3H / Production host: DICTYOSTELIUM DISCOIDEUM (eukaryote) / Strain (production host): AX4 / References: UniProt: P08799, EC: 3.6.4.1

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Non-polymers , 5 types, 447 molecules

#2: Chemical ChemComp-AOV / ADP ORTHOVANADATE


Mass: 544.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N5O14P2V / Comment: energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-27X / AMMOSAMIDE 272


Mass: 272.259 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H12N4O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 439 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsAMMOSAMIDE 272 (27X): AMMOSAMIDE 272 ADP ORTHOVANADATE (AOV) (AOV): ADP LINKED TO VO4
Sequence detailsRESIDUES FROM 750 ARE NOT RESOLVED IN THE MOTOR DOMAIN.

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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: 3.02 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growDetails: 50 MM HEPES PH 7.6, 140 MM NACL, 11% W/V PEG5K-MME, 2% (V/V) MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER X8 PROTEUM / Wavelength: 1.5418
DetectorType: BRUKER / Detector: CCD / Date: Sep 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→41.91 Å / Num. obs: 34133 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 76.61 % / Biso Wilson estimate: 47.465 Å2 / Rmerge(I) obs: 0.57 / Net I/σ(I): 16.68
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 49.39 % / Mean I/σ(I) obs: 2.16 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PROTEUM2data reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YV3

1yv3


Resolution: 2.5→41.914 Å / SU ML: 0.35 / σ(F): 0 / Phase error: 25.63 / Stereochemistry target values: ML
Details: LEVER ARM RESIDUES(FROM 700 TO 748) ARE HIGHLY MOBILE.
RfactorNum. reflection% reflection
Rfree0.2536 1721 5 %
Rwork0.2138 --
obs0.2158 34133 98.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.103 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.5819 Å20 Å20 Å2
2--6.4747 Å20 Å2
3----10.0566 Å2
Refinement stepCycle: LAST / Resolution: 2.5→41.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5963 0 89 439 6491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126172
X-RAY DIFFRACTIONf_angle_d1.5548340
X-RAY DIFFRACTIONf_dihedral_angle_d15.922334
X-RAY DIFFRACTIONf_chiral_restr0.103902
X-RAY DIFFRACTIONf_plane_restr0.0091076
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.57360.34491320.27112701X-RAY DIFFRACTION100
2.5736-2.65660.25731170.25192711X-RAY DIFFRACTION99
2.6566-2.75150.30011610.24792675X-RAY DIFFRACTION99
2.7515-2.86170.36021310.25742658X-RAY DIFFRACTION99
2.8617-2.99190.34091530.25422673X-RAY DIFFRACTION100
2.9919-3.14960.2941480.22642686X-RAY DIFFRACTION98
3.1496-3.34680.23851400.22692641X-RAY DIFFRACTION98
3.3468-3.60510.23561400.20022667X-RAY DIFFRACTION98
3.6051-3.96770.22551500.19262668X-RAY DIFFRACTION98
3.9677-4.54120.21371390.17712704X-RAY DIFFRACTION98
4.5412-5.71910.23271680.19512745X-RAY DIFFRACTION99
5.7191-41.91990.24031420.21512883X-RAY DIFFRACTION100

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