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- PDB-3fwb: Sac3:Sus1:Cdc31 complex -

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Basic information

Entry
Database: PDB / ID: 3fwb
TitleSac3:Sus1:Cdc31 complex
Components
  • Cell division control protein 31
  • Nuclear mRNA export protein SAC3
  • Protein SUS1
Keywordscell cycle / transcription / gene gating / complex / Cell division / Mitosis / mRNA transport / Nuclear pore complex / Nucleus / Phosphoprotein / Protein transport / Translocation / Transport / Transcription regulation
Function / homology
Function and homology information


half bridge of spindle pole body / spindle pole body duplication / actin filament-based process / DUBm complex / mitotic spindle pole body / Golgi vesicle transport / transcription export complex 2 / nuclear pore cytoplasmic filaments / nuclear mRNA surveillance / SLIK (SAGA-like) complex ...half bridge of spindle pole body / spindle pole body duplication / actin filament-based process / DUBm complex / mitotic spindle pole body / Golgi vesicle transport / transcription export complex 2 / nuclear pore cytoplasmic filaments / nuclear mRNA surveillance / SLIK (SAGA-like) complex / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / mRNA 3'-end processing / SAGA complex / poly(A)+ mRNA export from nucleus / nuclear pore / mRNA export from nucleus / transcription-coupled nucleotide-excision repair / protein export from nucleus / transcription elongation by RNA polymerase II / enzyme activator activity / P-body / microtubule cytoskeleton organization / nuclear envelope / protein transport / mitotic cell cycle / regulation of protein localization / chromatin organization / ribosomal small subunit biogenesis / microtubule binding / molecular adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / transcription coactivator activity / cell division / calcium ion binding / chromatin binding / regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1760 / Nuclear mRNA export protein Sac3 / SAC3 helical domain / Leucine permease transcriptional regulator helical domain / ENY2/SUS1 / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 / SAC3/GANP/THP3, conserved domain / SAC3/GANP/THP3 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1760 / Nuclear mRNA export protein Sac3 / SAC3 helical domain / Leucine permease transcriptional regulator helical domain / ENY2/SUS1 / Transcription factor, enhancer of yellow 2 / Transcription factor EnY2 superfamily / Transcription factor e(y)2 / SAC3/GANP/THP3, conserved domain / SAC3/GANP/THP3 / SAC3/GANP family / EF hand domain / Serum Albumin; Chain A, Domain 1 / Proteasome component (PCI) domain / PCI domain profile. / EF-hand / : / Recoverin; domain 1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Cell division control protein 31 / Nuclear mRNA export protein SAC3 / SAGA complex subunit SUS1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsStewart, M. / Jani, D.
CitationJournal: Mol.Cell / Year: 2009
Title: Sus1, Cdc31, and the Sac3 CID region form a conserved interaction platform that promotes nuclear pore association and mRNA export.
Authors: Jani, D. / Lutz, S. / Marshall, N.J. / Fischer, T. / Kohler, A. / Ellisdon, A.M. / Hurt, E. / Stewart, M.
History
DepositionJan 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell division control protein 31
B: Nuclear mRNA export protein SAC3
C: Protein SUS1


Theoretical massNumber of molelcules
Total (without water)36,6363
Polymers36,6363
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-51 kcal/mol
Surface area16970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.535, 60.062, 77.300
Angle α, β, γ (deg.)90.000, 108.670, 90.000
Int Tables number4
Space group name H-MP1211
DetailsSac3:Cdc31:Sus1 component of TREX-2 complex

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Components

#1: Protein Cell division control protein 31 / Nucleoporin CDC31 / Nuclear pore protein CDC31


Mass: 18774.039 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: see publication for complete details
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: CDC31, DSK1, YOR257W / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06704
#2: Protein Nuclear mRNA export protein SAC3 / Leucine permease transcriptional regulator


Mass: 6767.702 Da / Num. of mol.: 1 / Fragment: residues 752-805
Source method: isolated from a genetically manipulated source
Details: see publication for complete details
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: LEP1, SAC3, YD8358.13, YDR159W / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46674
#3: Protein Protein SUS1


Mass: 11094.497 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: see publication for complete details
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SUS1, YBR111W-A / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6WNK7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.21 Å3/Da / Density % sol: 61.73 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES pH6.5, 16% PEG4K, 20% glycerol - see publication for complete details, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2008
RadiationMonochromator: Si (111) channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 16233 / Num. obs: 16233 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 9.7
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0069refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementStarting model: P21 crystal structure obtained as described in publication

Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 1 / SU B: 19.31 / SU ML: 0.186 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic + TLS / Cross valid method: THROUGHOUT / ESU R: 0.327 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23489 815 5 %RANDOM
Rwork0.1882 ---
obs0.19063 15406 99.68 %-
all-16233 --
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: 49.48 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å2-1.37 Å2
2---0.32 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 0 54 2506
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222487
X-RAY DIFFRACTIONr_bond_other_d0.0010.021724
X-RAY DIFFRACTIONr_angle_refined_deg1.0911.9773338
X-RAY DIFFRACTIONr_angle_other_deg0.81734211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2295294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.09625.441136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.8715493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.161515
X-RAY DIFFRACTIONr_chiral_restr0.0640.2366
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022734
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02487
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_it4.404101476
X-RAY DIFFRACTIONr_mcbond_other1.47610598
X-RAY DIFFRACTIONr_mcangle_it6.245152377
X-RAY DIFFRACTIONr_scbond_it5.823101011
X-RAY DIFFRACTIONr_scangle_it8.35115961
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 57 -
Rwork0.299 1128 -
obs--99.66 %
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)
12.7413-0.94181.28561.32510.25722.3088-0.0060.13090.11230.03580.1108-0.1797-0.1380.2493-0.10470.0302-0.0939-0.0647-0.0377-0.0148-0.077512.54-6.6928.589
24.04590.2933-0.63393.88750.46063.18990.14140.1723-0.13560.0551-0.05240.40660.06-0.1103-0.089-0.0432-0.0446-0.0376-0.06760.0033-0.0692-16.381-5.7430.153
33.2677-3.00955.19384.7346-3.89329.92910.1047-0.1818-0.0621-0.02950.0440.31310.231-0.2325-0.14880.1042-0.0083-0.0904-0.05120.01-0.170712.485-41.17339.832
41.1805-3.34652.06449.5107-5.63265.5977-0.0384-0.07830.36160.1995-0.1478-0.1328-0.03210.17660.18620.1227-0.0232-0.1051-0.06160.0357-0.12417.356-27.65325.533
52.4639-4.14593.69277.1514-5.50998.359-0.07090.2772-0.0119-0.03740.00090.00840.3082-0.21110.06990.037-0.0553-0.0788-0.03640.0344-0.02952.24-17.23215.935
62.581-2.99033.74833.5349-4.60516.4227-0.1055-0.11140.2187-0.0250.0068-0.33310.01650.06580.09880.0435-0.0394-0.0497-0.04190.0132-0.0215-3.926-6.4016.42
76.07652.23446.67656.6125-1.760510.4046-0.08740.1199-0.06050.19570.08390.0128-0.32870.0590.0036-0.0339-0.01040.004-0.0341-0.0054-0.0166-11.881.9311.128
89.9091-1.4276-5.57381.8845-3.008211.7870.40220.05940.93690.23980.2454-0.71440.12950.773-0.64770.0367-0.0309-0.19530.00470.0093-0.154421.618-31.99833.154
91.7204-0.21720.68351.4248-0.09093.58940.20780.4216-0.16020.1446-0.2110.22250.24160.35140.00310.0431-0.0457-0.0773-0.020.0065-0.13525.829-31.33817.673
105.0955-2.45550.606110.82376.84287.4098-0.2327-0.25080.38630.31320.02750.5232-0.3895-0.69150.20520.05580.00870.04120.02070.0438-0.0143-9.022-12.40620.247
112.6496-0.2070.38779.53940.33391.8228-0.1131-0.21830.01430.97860.17640.86340.0212-0.2819-0.06320.0908-0.00170.0023-0.02320.0112-0.2262-2.119-24.72825.29
128.9414-3.82544.47363.5803-4.4715.6023-0.09510.6177-0.39440.1821-0.1241-0.06790.34610.53450.21920.09670.0847-0.1077-0.02850.0024-0.129614.164-42.09329.505
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 95
2X-RAY DIFFRACTION2A96 - 161
3X-RAY DIFFRACTION3B752 - 766
4X-RAY DIFFRACTION4B767 - 778
5X-RAY DIFFRACTION5B779 - 787
6X-RAY DIFFRACTION6B788 - 798
7X-RAY DIFFRACTION7B799 - 805
8X-RAY DIFFRACTION8C6 - 16
9X-RAY DIFFRACTION9C17 - 45
10X-RAY DIFFRACTION10C46 - 55
11X-RAY DIFFRACTION11C56 - 80
12X-RAY DIFFRACTION12C81 - 96

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