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- PDB-1zuk: Yeast BBC1 Sh3 domain complexed with a peptide from Las17 -

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Basic information

Entry
Database: PDB / ID: 1zuk
TitleYeast BBC1 Sh3 domain complexed with a peptide from Las17
Components
  • Myosin tail region-interacting protein MTI1
  • Proline-rich protein LAS17
KeywordsCONTRACTILE PROTEIN / SH3 domain / PxxP peptide
Function / homology
Function and homology information


SLAC complex / myosin I binding / actin cortical patch localization / positive regulation of Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / actin nucleation / actin cortical patch / positive regulation of actin filament bundle assembly / mating projection tip / cytoskeleton organization ...SLAC complex / myosin I binding / actin cortical patch localization / positive regulation of Arp2/3 complex-mediated actin nucleation / Arp2/3 complex binding / actin nucleation / actin cortical patch / positive regulation of actin filament bundle assembly / mating projection tip / cytoskeleton organization / actin filament polymerization / actin filament organization / actin binding / actin cytoskeleton organization / nucleolus / cytoplasm
Similarity search - Function
Actin nucleation-promoting factor WAS / Mti1, SH3 domain / WASP family, EVH1 domain / WH2 motif / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / WH2 domain / WH2 domain profile. ...Actin nucleation-promoting factor WAS / Mti1, SH3 domain / WASP family, EVH1 domain / WH2 motif / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / WH2 domain / WH2 domain profile. / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Myosin tail region-interacting protein MTI1 / Proline-rich protein LAS17
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKursula, P. / Kursula, I. / Lehmann, F. / Zou, P. / Song, Y.H. / Wilmanns, M.
CitationJournal: To be Published
Title: Structural genomics of yeast SH3 domains
Authors: Kursula, P. / Kursula, I. / Lehmann, F. / Zou, P. / Song, Y.H. / Wilmanns, M.
History
DepositionMay 31, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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 tail region-interacting protein MTI1
B: Myosin tail region-interacting protein MTI1
C: Proline-rich protein LAS17
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9086
Polymers16,8243
Non-polymers843
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-35 kcal/mol
Surface area8240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.770, 78.500, 35.460
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
11B-2003-

HOH

21B-2039-

HOH

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Components

#1: Protein Myosin tail region-interacting protein MTI1 / BBC1 protein


Mass: 7821.465 Da / Num. of mol.: 2 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pDEST-17 / Production host: Escherichia coli (E. coli) / References: UniProt: P47068
#2: Protein/peptide Proline-rich protein LAS17


Mass: 1181.368 Da / Num. of mol.: 1 / Fragment: PxxP motif / Source method: obtained synthetically / Details: synthetic peptide / References: UniProt: Q12446
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.3 Å3/Da / Density % sol: 42.511078 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 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: Apr 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.813 Å / Relative weight: 1
ReflectionResolution: 1.86→20 Å / Num. all: 12659 / Num. obs: 12659 / % possible obs: 98.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 27.4 Å2 / Rsym value: 0.065 / Net I/σ(I): 15.3
Reflection shellResolution: 1.86→1.95 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.8 / Rsym value: 0.334 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TG0

1tg0


Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.332 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS refinement / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.162 / ESU R Free: 0.151 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22599 594 5 %RANDOM
Rwork0.1739 ---
all0.17645 11879 --
obs0.17645 11879 99.85 %-
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: 28.698 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2---1.34 Å20 Å2
3---2.29 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1154 0 3 179 1336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221210
X-RAY DIFFRACTIONr_bond_other_d0.0010.021002
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.9551652
X-RAY DIFFRACTIONr_angle_other_deg0.76232368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5445142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26226.19771
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5615181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.752152
X-RAY DIFFRACTIONr_chiral_restr0.0730.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021380
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02240
X-RAY DIFFRACTIONr_nbd_refined0.1790.2218
X-RAY DIFFRACTIONr_nbd_other0.1760.21019
X-RAY DIFFRACTIONr_nbtor_refined0.1820.2610
X-RAY DIFFRACTIONr_nbtor_other0.0910.2623
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2134
X-RAY DIFFRACTIONr_metal_ion_refined0.0330.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0870.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2370.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.226
X-RAY DIFFRACTIONr_mcbond_it1.0972935
X-RAY DIFFRACTIONr_mcbond_other0.1862285
X-RAY DIFFRACTIONr_mcangle_it1.29131183
X-RAY DIFFRACTIONr_scbond_it1.6964644
X-RAY DIFFRACTIONr_scangle_it2.0045469
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 42 -
Rwork0.199 809 -
obs--99.88 %
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)
13.80631.35860.25694.12211.21134.76930.1273-0.5552-0.02050.3125-0.14820.0707-0.0509-0.21790.0209-0.1443-0.0150.0284-0.0843-0.0113-0.211513.57857.678515.1
24.3824-0.27370.79115.95320.92081.79-0.0505-0.07120.35830.0081-0.03470.0216-0.1327-0.10260.0852-0.1717-0.00120.0236-0.17010.0102-0.15310.1144-13.27030.9755
329.784514.0064-5.26589.5498-2.28855.0298-0.1746-0.4065-1.0159-0.3136-0.1869-0.32980.3542-0.29240.3615-0.07490.03260.0187-0.1672-0.0359-0.1468.9249-0.29644.8174
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 663 - 66
2X-RAY DIFFRACTION2BB3 - 663 - 66
3X-RAY DIFFRACTION3CC1 - 111 - 11

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