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- PDB-4ll7: Structure of She3p amino terminus. -

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Basic information

Entry
Database: PDB / ID: 4ll7
TitleStructure of She3p amino terminus.
ComponentsSWI5-dependent HO expression protein 3
KeywordsTRANSPORT PROTEIN / She3p / myosin cargo adaptor protein / mRNA translocation
Function / homology
Function and homology information


mating type switching / endoplasmic reticulum inheritance / intracellular mRNA localization / cellular bud tip / sequence-specific mRNA binding / mRNA transport / mRNA binding / endoplasmic reticulum membrane / cytoplasm
Similarity search - Function
SWI5-dependent HO expression protein 3 / SWI5-dependent HO expression protein 3
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / : / ISOPROPYL ALCOHOL / : / SWI5-dependent HO expression protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.31 Å
AuthorsShi, H. / Singh, N. / Esselborn, F. / Blobel, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure of a myosinbulletadaptor complex and pairing by cargo.
Authors: Shi, H. / Singh, N. / Esselborn, F. / Blobel, G.
History
DepositionJul 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 2.0Jul 31, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description
Category: atom_site / chem_comp ...atom_site / chem_comp / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _chem_comp.formula / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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: SWI5-dependent HO expression protein 3
B: SWI5-dependent HO expression protein 3
C: SWI5-dependent HO expression protein 3
D: SWI5-dependent HO expression protein 3
E: SWI5-dependent HO expression protein 3
F: SWI5-dependent HO expression protein 3
G: SWI5-dependent HO expression protein 3
H: SWI5-dependent HO expression protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,51383
Polymers90,3828
Non-polymers9,13175
Water3,513195
1
A: SWI5-dependent HO expression protein 3
C: SWI5-dependent HO expression protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,58626
Polymers22,5962
Non-polymers2,99124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-119 kcal/mol
Surface area17440 Å2
MethodPISA
2
B: SWI5-dependent HO expression protein 3
D: SWI5-dependent HO expression protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,78320
Polymers22,5962
Non-polymers2,18818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-121 kcal/mol
Surface area17210 Å2
MethodPISA
3
E: SWI5-dependent HO expression protein 3
H: SWI5-dependent HO expression protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,62518
Polymers22,5962
Non-polymers2,03016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
ΔGint-76 kcal/mol
Surface area16860 Å2
MethodPISA
4
F: SWI5-dependent HO expression protein 3
G: SWI5-dependent HO expression protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,51819
Polymers22,5962
Non-polymers1,92217
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint-97 kcal/mol
Surface area17040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.069, 49.576, 149.950
Angle α, β, γ (deg.)89.960, 84.670, 89.980
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
SWI5-dependent HO expression protein 3


Mass: 11297.770 Da / Num. of mol.: 8 / Fragment: UNP residues 42-137
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: SHE3, YBR130C, YBR1005 / Production host: Escherichia coli (E. coli) / References: UniProt: P38272

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Non-polymers , 7 types, 270 molecules

#2: Chemical...
ChemComp-DY / DYSPROSIUM ION


Mass: 162.500 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Dy
#3: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Pt
#5: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 46.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES, pH 6.5, 0.45M Ammonium sulfate, 10% (v/v) 2-propanol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.105 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 25, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.105 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. all: 35520 / Num. obs: 34442 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3

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Processing

Software
NameClassification
CBASSdata collection
SHELXSphasing
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementResolution: 2.31→29.86 Å / σ(F): 3805
RfactorNum. reflection% reflection
Rfree0.2644 3193 7.8 %
Rwork0.2314 25362 -
obs-28170 78.7 %
Solvent computationBsol: 63.1719 Å2
Displacement parametersBiso max: 174.9 Å2 / Biso mean: 76.8162 Å2 / Biso min: 3.85 Å2
Baniso -1Baniso -2Baniso -3
1-2.862 Å2-4.425 Å2-0.411 Å2
2--19.937 Å2-2.843 Å2
3----22.799 Å2
Refinement stepCycle: LAST / Resolution: 2.31→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5986 0 237 195 6418
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.142
X-RAY DIFFRACTIONc_mcbond_it5.7741.5
X-RAY DIFFRACTIONc_scbond_it8.4942
X-RAY DIFFRACTIONc_mcangle_it6.712
X-RAY DIFFRACTIONc_scangle_it10.9082.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.31-2.380.30821920.26581576176849.2
2.38-2.480.32522070.26021922212959.6
2.48-2.590.26522450.19222180242566.5
2.59-2.730.24622680.20142368263675.4
2.73-2.90.27152800.22372545282579.2
2.9-3.120.2452880.22612730301882.9
3.12-3.440.24583260.21652837316389.7
3.44-3.930.2263560.19693018337493.7
3.93-4.950.2663440.2193031337595.4
4.95-500.30743020.29273155345796.2
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION6iso.param

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