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- PDB-1z9z: Crystal structure of yeast sla1 SH3 domain 3 -

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Basic information

Entry
Database: PDB / ID: 1z9z
TitleCrystal structure of yeast sla1 SH3 domain 3
ComponentsCytoskeleton assembly control protein SLA1
KeywordsSTRUCTURAL PROTEIN / SH3 DOMAIN / yeast / structural genomics
Function / homology
Function and homology information


actin cytoskeleton-regulatory complex / SLAC complex / cargo adaptor activity / RND2 GTPase cycle / RHOQ GTPase cycle / actin cortical patch assembly / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch / regulation of actin filament polymerization ...actin cytoskeleton-regulatory complex / SLAC complex / cargo adaptor activity / RND2 GTPase cycle / RHOQ GTPase cycle / actin cortical patch assembly / regulation of Arp2/3 complex-mediated actin nucleation / negative regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch / regulation of actin filament polymerization / cellular bud neck / mating projection tip / ubiquitin binding / recycling endosome / cell wall organization / endocytosis / actin binding / cell cortex / endosome membrane / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
SLA1 homology domain 1, SHD1 / Sla1, first SH3 domain / Sla1, third SH3 domain / SLA1 homology domain 1, SHD1 / Variant SH3 domain / SH3 Domains / Sterile alpha motif/pointed domain superfamily / SH3 domain / SH3 type barrels. / Src homology 3 domains ...SLA1 homology domain 1, SHD1 / Sla1, first SH3 domain / Sla1, third SH3 domain / SLA1 homology domain 1, SHD1 / Variant SH3 domain / SH3 Domains / Sterile alpha motif/pointed domain superfamily / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
Actin cytoskeleton-regulatory complex protein SLA1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKursula, P. / Kursula, I. / Salmazo, A.P.T. / Zou, P. / Song, Y.H. / Lehmann, F. / Wilmanns, M.
CitationJournal: To be Published
Title: Yeast SH3 domain three-dimensional proteome
Authors: Kursula, P. / Kursula, I. / Salmazo, A.P.T. / Zou, P. / Song, Y.H. / Lehmann, F. / Wilmanns, M.
History
DepositionApr 5, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 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 1.4Feb 14, 2024Group: 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_struct_special_symmetry / struct_ncs_dom_lim / struct_ref_seq_dif / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _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: Cytoskeleton assembly control protein SLA1
B: Cytoskeleton assembly control protein SLA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7643
Polymers13,6682
Non-polymers961
Water3,279182
1
A: Cytoskeleton assembly control protein SLA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9302
Polymers6,8341
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytoskeleton assembly control protein SLA1


Theoretical massNumber of molelcules
Total (without water)6,8341
Polymers6,8341
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Cytoskeleton assembly control protein SLA1
hetero molecules

A: Cytoskeleton assembly control protein SLA1
hetero molecules

B: Cytoskeleton assembly control protein SLA1

B: Cytoskeleton assembly control protein SLA1


Theoretical massNumber of molelcules
Total (without water)27,5276
Polymers27,3354
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation4_454y-1/2,-x+1/2,z-1/41
crystal symmetry operation5_545-x+1/2,y-1/2,-z+1/41
Buried area4450 Å2
ΔGint-37 kcal/mol
Surface area12630 Å2
MethodPISA
4
A: Cytoskeleton assembly control protein SLA1
hetero molecules

B: Cytoskeleton assembly control protein SLA1


Theoretical massNumber of molelcules
Total (without water)13,7643
Polymers13,6682
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_545-x+1/2,y-1/2,-z+1/41
Buried area950 Å2
ΔGint-13 kcal/mol
Surface area7590 Å2
MethodPISA
5
B: Cytoskeleton assembly control protein SLA1

B: Cytoskeleton assembly control protein SLA1


Theoretical massNumber of molelcules
Total (without water)13,6682
Polymers13,6682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area1060 Å2
ΔGint-7 kcal/mol
Surface area7250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.990, 83.990, 50.140
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-264-

HOH

21B-126-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 3 - 58 / Label seq-ID: 3 - 58

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Cytoskeleton assembly control protein SLA1


Mass: 6833.769 Da / Num. of mol.: 2 / Fragment: SH3 domain 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SLA1 / Plasmid: pET24d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Ril / References: UniProt: P32790
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.69 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ammonium sulphate, sodium citrate, potassium/sodium tartrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9781 / Wavelength: 0.9781 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 23, 2004 / Details: mirrors, double crystal
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9781 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 12025 / Num. obs: 12025 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.066 / Net I/σ(I): 23.44
Reflection shellResolution: 1.9→10 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.64 / SU ML: 0.09 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22902 633 5 %RANDOM
Rwork0.17787 ---
obs0.18036 12025 93.23 %-
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: 26.158 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.95→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms956 0 5 182 1143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221008
X-RAY DIFFRACTIONr_bond_other_d0.0010.02906
X-RAY DIFFRACTIONr_angle_refined_deg1.351.981357
X-RAY DIFFRACTIONr_angle_other_deg0.74432137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8295119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.76326.52246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55815200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.271152
X-RAY DIFFRACTIONr_chiral_restr0.0730.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021087
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02179
X-RAY DIFFRACTIONr_nbd_refined0.2030.2155
X-RAY DIFFRACTIONr_nbd_other0.1750.2878
X-RAY DIFFRACTIONr_nbtor_refined0.1780.2451
X-RAY DIFFRACTIONr_nbtor_other0.0830.2568
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.210.2119
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1930.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.217
X-RAY DIFFRACTIONr_mcbond_it0.8231.5782
X-RAY DIFFRACTIONr_mcbond_other0.1931.5252
X-RAY DIFFRACTIONr_mcangle_it0.9592982
X-RAY DIFFRACTIONr_scbond_it1.7063490
X-RAY DIFFRACTIONr_scangle_it2.3094.5375
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 837 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
medium positional0.460.5
medium thermal0.592
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 49 -
Rwork0.224 925 -
obs--99.8 %
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)
12.74240.6906-1.38384.08430.41053.47610.0608-0.0617-0.03260.1935-0.0413-0.05230.07190.0182-0.0195-0.0963-0.0194-0.0126-0.1505-0.012-0.147224.604630.289810.4819
23.38840.02660.71324.0607-0.13162.83030.08430.09280.0273-0.282-0.03420.23670.0898-0.0633-0.0501-0.09210.0254-0.008-0.1463-0.0074-0.115724.487750.83774.4659
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 601 - 60
2X-RAY DIFFRACTION2BB1 - 601 - 60

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