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- PDB-5m0i: Crystal structure of the nuclear complex with She2p and the ASH1 ... -

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Basic information

Entry
Database: PDB / ID: 5m0i
TitleCrystal structure of the nuclear complex with She2p and the ASH1 mRNA E3-localization element
Components
  • (SWI5-dependent HO expression protein ...) x 2
  • ASH1-E3 element, RNA (28-MER)
KeywordsTRANSPORT PROTEIN / She2p / 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 / cytosol / cytoplasm
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
ACETATE ION / RNA / RNA (> 10) / SWI5-dependent HO expression protein 2 / SWI5-dependent HO expression protein 2 / SWI5-dependent HO expression protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Saccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_seq_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.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_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
C: SWI5-dependent HO expression protein 2
B: SWI5-dependent HO expression protein 2
A: SWI5-dependent HO expression protein 2
E: ASH1-E3 element, RNA (28-MER)
F: ASH1-E3 element, RNA (28-MER)
H: SWI5-dependent HO expression protein 3
J: SWI5-dependent HO expression protein 3
I: SWI5-dependent HO expression protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,89132
Polymers137,7089
Non-polymers1,18323
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21850 Å2
ΔGint-130 kcal/mol
Surface area47360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)220.520, 58.340, 146.010
Angle α, β, γ (deg.)90.00, 126.98, 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
17E
27F

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
11LEULEUGLYGLYDA3 - 2423 - 242
21LEULEUGLYGLYCB3 - 2423 - 242
12GLYGLYPHEPHEDA4 - 2414 - 241
22GLYGLYPHEPHEBC4 - 2414 - 241
13LEULEUGLYGLYDA3 - 2423 - 242
23LEULEUGLYGLYAD3 - 2423 - 242
14GLYGLYLYSLYSCB4 - 2454 - 245
24GLYGLYLYSLYSBC4 - 2454 - 245
15LEULEULYSLYSCB3 - 2433 - 243
25LEULEULYSLYSAD3 - 2433 - 243
16GLYGLYLYSLYSBC4 - 2434 - 243
26GLYGLYLYSLYSAD4 - 2434 - 243
17GGGGEE1 - 281 - 28
27GGGGFF1 - 281 - 28

NCS ensembles :
ID
1
2
3
4
5
6
7

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Components

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SWI5-dependent HO expression protein ... , 2 types, 7 molecules DCBAHJI

#1: Protein
SWI5-dependent HO expression protein 2


Mass: 28037.736 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: RM11-1a / Gene: SHE2, SCRG_03894 / Production host: Escherichia coli (E. coli) / References: UniProt: B3LQW9, UniProt: P36068*PLUS
#3: Protein/peptide SWI5-dependent HO expression protein 3


Mass: 2522.745 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: SHE3, YBR130C, YBR1005 / Production host: Escherichia coli (E. coli) / References: UniProt: P38272

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RNA chain , 1 types, 2 molecules EF

#2: RNA chain ASH1-E3 element, RNA (28-MER)


Mass: 8994.446 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast)

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Non-polymers , 4 types, 356 molecules

#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 100 mM Bis Tris propane, pH 6.5, 200 mM NaF, 20 % (w/v) PEG 3350,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0716 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0716 Å / Relative weight: 1
ReflectionResolution: 2.41→100 Å / Num. obs: 49733 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 10.37
Reflection shellResolution: 2.41→2.47 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 2.13 / % possible all: 91

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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: 2.41→50.01 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.933 / SU B: 17.421 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.417 / ESU R Free: 0.258 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23458 2571 4.9 %RANDOM
Rwork0.18946 ---
obs0.19175 49733 90.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.211 Å2
Baniso -1Baniso -2Baniso -3
1--1.67 Å20 Å21.52 Å2
2---1.39 Å2-0 Å2
3---0.36 Å2
Refinement stepCycle: 1 / Resolution: 2.41→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7731 1192 74 333 9330
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0189263
X-RAY DIFFRACTIONr_bond_other_d0.0110.028217
X-RAY DIFFRACTIONr_angle_refined_deg1.8811.85612779
X-RAY DIFFRACTIONr_angle_other_deg1.716318993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9685949
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.83425.096365
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.59151431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.5921529
X-RAY DIFFRACTIONr_chiral_restr0.1130.21479
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.029389
X-RAY DIFFRACTIONr_gen_planes_other0.010.022048
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_it3.0754.0153835
X-RAY DIFFRACTIONr_mcbond_other3.0424.0093828
X-RAY DIFFRACTIONr_mcangle_it4.8345.9774767
X-RAY DIFFRACTIONr_mcangle_other4.8345.9794768
X-RAY DIFFRACTIONr_scbond_it3.0663.9865428
X-RAY DIFFRACTIONr_scbond_other3.0663.9865429
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8575.8938013
X-RAY DIFFRACTIONr_long_range_B_refined7.76231.16810857
X-RAY DIFFRACTIONr_long_range_B_other7.76231.1710858
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)
11D281660.09
12C281660.09
21D275080.1
22B275080.1
31D280540.06
32A280540.06
41C283960.08
42B283960.08
51C276660.09
52A276660.09
61B268660.1
62A268660.1
71E43480.1
72F43480.1
LS refinement shellResolution: 2.41→2.472 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 165 -
Rwork0.301 3685 -
obs--91.08 %
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)
11.44370.0428-0.00880.4101-0.20310.10330.06420.5297-0.15720.1011-0.1228-0.119-0.03870.05750.05860.0765-0.0221-0.06890.651-0.05410.0779171.987474.2437137.2393
21.86210.11790.21050.2631-0.24930.3381-0.26570.54050.29030.14330.0002-0.1905-0.12530.09580.26550.2809-0.1618-0.2050.51450.16250.2219167.045194.5095145.5823
30.90810.1854-0.26730.14640.04060.69710.0177-0.08220.0286-0.04050.01770.0561-0.0244-0.0639-0.03540.2011-0.0049-0.0790.32130.02480.0898110.549676.0214155.497
41.06210.39750.01570.44870.09730.24090.04380.02-0.17010.05310.0394-0.00820.0061-0.0246-0.08320.1955-0.036-0.12840.27050.04180.1713114.922254.7184150.5167
50.32760.21730.40770.33480.09180.67520.1014-0.1401-0.02350.1775-0.1853-0.12790.0068-0.07980.08390.2962-0.0437-0.18170.36750.00210.1311153.175276.4913169.7478
60.3607-0.0169-0.67560.00170.00422.53790.00380.2879-0.0395-0.002-0.04920.0069-0.37160.08480.04540.2904-0.1373-0.13060.5357-0.03490.0855126.121283.1382127.2303
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 242
2X-RAY DIFFRACTION2B3 - 245
3X-RAY DIFFRACTION3C3 - 245
4X-RAY DIFFRACTION4D3 - 242
5X-RAY DIFFRACTION5E1 - 28
6X-RAY DIFFRACTION6F1 - 28

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