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- PDB-1zuy: High-resolution structure of yeast Myo5 SH3 domain -

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Basic information

Entry
Database: PDB / ID: 1zuy
TitleHigh-resolution structure of yeast Myo5 SH3 domain
ComponentsMyosin-5 isoform
KeywordsCONTRACTILE PROTEIN / SH3 domain
Function / homology
Function and homology information


bipolar cellular bud site selection / myosin I complex / actin cortical patch localization / cellular bud / positive regulation of Arp2/3 complex-mediated actin nucleation / cell tip / fungal-type cell wall organization / actin cortical patch / mating projection tip / vesicle transport along actin filament ...bipolar cellular bud site selection / myosin I complex / actin cortical patch localization / cellular bud / positive regulation of Arp2/3 complex-mediated actin nucleation / cell tip / fungal-type cell wall organization / actin cortical patch / mating projection tip / vesicle transport along actin filament / response to osmotic stress / microfilament motor activity / exocytosis / response to salt stress / receptor-mediated endocytosis / actin filament organization / cell periphery / endocytosis / actin filament binding / actin cytoskeleton / vesicle / hydrolase activity / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Fungal myosin-I, SH3 domain / Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / SH3 Domains ...Fungal myosin-I, SH3 domain / Class I myosin tail homology domain / Class I myosin, motor domain / Unconventional myosin tail, actin- and lipid-binding / Class I myosin tail homology (TH1) domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / SH3 Domains / Kinesin motor domain superfamily / SH3 domain / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Myosin-5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.39 Å
AuthorsWilmanns, M. / Kursula, P. / Gonfloni, S. / Ferracuti, S. / Cesareni, G.
CitationJournal: To be published
Title: High-resolution structure of yeast Myo5 SH3 domain
Authors: Wilmanns, M. / Kursula, P. / Gonfloni, S. / Ferracuti, S. / Cesareni, G.
History
DepositionJun 1, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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-5 isoform
B: Myosin-5 isoform
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,8133
Polymers12,7522
Non-polymers601
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.060, 42.250, 90.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Myosin-5 isoform


Mass: 6376.206 Da / Num. of mol.: 2 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: Q04439
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: ammonium sulfate, isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.813 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 3, 2004
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.813 Å / Relative weight: 1
ReflectionResolution: 1.39→20 Å / Num. all: 21535 / Num. obs: 21535 / % possible obs: 99 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 23 Å2 / Rsym value: 0.04 / Net I/σ(I): 20
Reflection shellResolution: 1.39→1.43 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 1598 / Rsym value: 0.393 / % possible all: 90.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.39→20 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.99 / SU ML: 0.052 / Isotropic thermal model: ANISOTROPIC REFINEMENT / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.074 / ESU R Free: 0.067 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20581 1077 5 %RANDOM
Rwork0.16631 ---
all0.16829 21535 --
obs0.16829 21535 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.972 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20 Å20 Å2
2--0.58 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.39→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms937 0 0 129 1066
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021977
X-RAY DIFFRACTIONr_bond_other_d0.0020.02856
X-RAY DIFFRACTIONr_angle_refined_deg1.7521.9881329
X-RAY DIFFRACTIONr_angle_other_deg0.82932028
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0935124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59624.28635
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.93215157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.445152
X-RAY DIFFRACTIONr_chiral_restr0.1090.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021094
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02188
X-RAY DIFFRACTIONr_nbd_refined0.2290.2174
X-RAY DIFFRACTIONr_nbd_other0.2640.21020
X-RAY DIFFRACTIONr_nbtor_refined0.1930.2465
X-RAY DIFFRACTIONr_nbtor_other0.0920.2548
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2440.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.224
X-RAY DIFFRACTIONr_mcbond_it2.3491.5764
X-RAY DIFFRACTIONr_mcbond_other0.5971.5246
X-RAY DIFFRACTIONr_mcangle_it2.9133987
X-RAY DIFFRACTIONr_scbond_it3.9734.5447
X-RAY DIFFRACTIONr_scangle_it4.8946342
X-RAY DIFFRACTIONr_rigid_bond_restr2.06932263
X-RAY DIFFRACTIONr_sphericity_free6.7563125
X-RAY DIFFRACTIONr_sphericity_bonded2.21531797
LS refinement shellResolution: 1.39→1.426 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 72 -
Rwork0.29 1373 -
obs--90.82 %
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)
13.91030.77310.31542.1051-0.16632.5936-0.02790.1206-0.5046-0.0994-0.0198-0.10810.3905-0.01630.0476-0.0642-0.00210.0168-0.1344-0.0283-0.089510.18-0.54435.997
23.705-0.2139-1.04392.23190.04083.03190.05130.27010.2971-0.2109-0.03260.024-0.2853-0.0565-0.0188-0.0915-0.0041-0.0003-0.12230.0203-0.128615.84917.65132.66
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 591 - 58
2X-RAY DIFFRACTION2BB2 - 591 - 58

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