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- PDB-5m0j: Crystal structure of the cytoplasmic complex with She2p, She3p, a... -

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Basic information

Entry
Database: PDB / ID: 5m0j
TitleCrystal structure of the cytoplasmic complex with She2p, She3p, and the ASH1 mRNA E3-localization element
Components
  • ASH1 E3 (28 nt-loop)
  • SWI5-dependent HO expression protein 2,SWI5-dependent HO expression protein 3
KeywordsRNA BINDING PROTEIN / She2p / She3p / ASH1-mRNA / mRNA transport
Function / homology
Function and homology information


mating type switching / endoplasmic reticulum inheritance / cellular bud tip / intracellular mRNA localization / sequence-specific mRNA binding / mRNA transport / mRNA binding / lipid binding / endoplasmic reticulum membrane / RNA binding ...mating type switching / endoplasmic reticulum inheritance / cellular bud tip / intracellular mRNA localization / sequence-specific mRNA binding / mRNA transport / mRNA binding / lipid binding / endoplasmic reticulum membrane / RNA binding / nucleus / cytoplasm / cytosol
Similarity search - Function
She2 domain / RNA binding protein She2 / She2 domain superfamily / RNA binding protein She2p / SWI5-dependent HO expression protein 3 / SWI5-dependent HO expression protein 3 / Fumarase C; Chain A, domain 2 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA / RNA (> 10) / SWI5-dependent HO expression protein 3 / SWI5-dependent HO expression protein 2 / SWI5-dependent HO expression protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsEdelmann, F.T. / Janowski, R. / Niessing, D.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Molecular architecture and dynamics of ASH1 mRNA recognition by its mRNA-transport complex.
Authors: Edelmann, F.T. / Schlundt, A. / Heym, R.G. / Jenner, A. / Niedner-Boblenz, A. / Syed, M.I. / Paillart, J.C. / Stehle, R. / Janowski, R. / Sattler, M. / Jansen, R.P. / Niessing, D.
History
DepositionOct 5, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Feb 15, 2017Group: Database references
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: SWI5-dependent HO expression protein 2,SWI5-dependent HO expression protein 3
C: SWI5-dependent HO expression protein 2,SWI5-dependent HO expression protein 3
B: SWI5-dependent HO expression protein 2,SWI5-dependent HO expression protein 3
A: SWI5-dependent HO expression protein 2,SWI5-dependent HO expression protein 3
J: SWI5-dependent HO expression protein 2,SWI5-dependent HO expression protein 3
G: SWI5-dependent HO expression protein 2,SWI5-dependent HO expression protein 3
H: SWI5-dependent HO expression protein 2,SWI5-dependent HO expression protein 3
I: SWI5-dependent HO expression protein 2,SWI5-dependent HO expression protein 3
E: ASH1 E3 (28 nt-loop)
F: ASH1 E3 (28 nt-loop)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)307,13014
Polymers307,03310
Non-polymers974
Water3,729207
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24380 Å2
ΔGint-191 kcal/mol
Surface area48500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)219.030, 58.980, 144.680
Angle α, β, γ (deg.)90.00, 126.91, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11D
21C
12D
22B
13D
23A
14C
24B
15C
25A
16B
26A
17J
27G
18E
28F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPGLYGLYDA6 - 2423 - 239
21ASPASPGLYGLYCB6 - 2423 - 239
12ASPASPPHEPHEDA6 - 2413 - 238
22ASPASPPHEPHEBC6 - 2413 - 238
13ASPASPGLYGLYDA6 - 2423 - 239
23ASPASPGLYGLYAD6 - 2423 - 239
14ASPASPLYSLYSCB6 - 2453 - 242
24ASPASPLYSLYSBC6 - 2453 - 242
15ASPASPLYSLYSCB6 - 2433 - 240
25ASPASPLYSLYSAD6 - 2433 - 240
16ASPASPLYSLYSBC6 - 2433 - 240
26ASPASPLYSLYSAD6 - 2433 - 240
17ASNASNVALVALJE338 - 367261 - 290
27ASNASNVALVALGF338 - 367261 - 290
18GGGGEI1 - 281 - 28
28GGGGFJ1 - 281 - 28

NCS ensembles :
ID
1
2
3
4
5
6
7
8

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Components

#1: Protein
SWI5-dependent HO expression protein 2,SWI5-dependent HO expression protein 3


Mass: 36130.492 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: fusion protein
Source: (gene. exp.) Saccharomyces cerevisiae (strain RM11-1a) (yeast), (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: RM11-1a / Gene: SHE2, SCRG_03894, SHE3, SCRG_02838 / Production host: Escherichia coli (E. coli)
References: UniProt: B3LQW9, UniProt: B3LN26, UniProt: P36068*PLUS
#2: RNA chain ASH1 E3 (28 nt-loop)


Mass: 8994.446 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 207 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: 20 % (w/v) PEG3350, 150 mM NaNO3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9175 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9175 Å / Relative weight: 1
ReflectionResolution: 2.8→100 Å / Num. obs: 35077 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.189 / Net I/σ(I): 10.34
Reflection shellResolution: 2.8→2.87 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.02 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XLY

1xly


Resolution: 2.8→50.01 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.904 / SU B: 14.925 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R Free: 0.367 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24614 1828 5 %RANDOM
Rwork0.19447 ---
obs0.19701 35077 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 48.241 Å2
Baniso -1Baniso -2Baniso -3
1--1.05 Å2-0 Å2-0.4 Å2
2--2.73 Å2-0 Å2
3----0.51 Å2
Refinement stepCycle: 1 / Resolution: 2.8→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8158 1192 4 207 9561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0189712
X-RAY DIFFRACTIONr_bond_other_d0.0060.028637
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.85713412
X-RAY DIFFRACTIONr_angle_other_deg1.425319954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.14751004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75524.658395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.423151523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.621540
X-RAY DIFFRACTIONr_chiral_restr0.0820.21545
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029930
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022202
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.7494.8884046
X-RAY DIFFRACTIONr_mcbond_other3.7494.8874045
X-RAY DIFFRACTIONr_mcangle_it6.0997.2875040
X-RAY DIFFRACTIONr_mcangle_other6.0987.2885041
X-RAY DIFFRACTIONr_scbond_it3.2544.9095666
X-RAY DIFFRACTIONr_scbond_other3.254.9095665
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2837.2998373
X-RAY DIFFRACTIONr_long_range_B_refined7.88338.15911201
X-RAY DIFFRACTIONr_long_range_B_other7.87538.18311175
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11D284680.08
12C284680.08
21D278560.09
22B278560.09
31D275060.06
32A275060.06
41C289720.07
42B289720.07
51C273220.08
52A273220.08
61B272840.08
62A272840.08
71J13460.07
72G13460.07
81E43580.1
82F43580.1
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 129 -
Rwork0.301 2547 -
obs--100 %

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