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- PDB-4x2h: Sac3N peptide bound to Mex67:Mtr2 -

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Basic information

Entry
Database: PDB / ID: 4x2h
TitleSac3N peptide bound to Mex67:Mtr2
Components
  • Putative mRNA export protein
  • Putative uncharacterized protein
  • SER-SER-VAL-PHE-GLY-ALA-PRO-ALA
KeywordsTRANSCRIPTION / mRNA nuclear export / TREX-2
Function / homology
Function and homology information


transcription export complex 2 / poly(A)+ mRNA export from nucleus / mRNA export from nucleus / RNA binding / nucleus / cytoplasm
Similarity search - Function
SAC3/GANP/THP3 / SAC3/GANP/THP3, conserved domain / SAC3/GANP family / Mex67, RNA recognition motif / RNA recognition motif / TAP C-terminal (TAP-C) domain / TAP C-terminal domain / TAP C-terminal (TAP-C) domain profile. / C-terminal domain of vertebrate Tap protein / Nuclear RNA export factor ...SAC3/GANP/THP3 / SAC3/GANP/THP3, conserved domain / SAC3/GANP family / Mex67, RNA recognition motif / RNA recognition motif / TAP C-terminal (TAP-C) domain / TAP C-terminal domain / TAP C-terminal (TAP-C) domain profile. / C-terminal domain of vertebrate Tap protein / Nuclear RNA export factor / Nuclear transport factor 2, eukaryote / Nuclear transport factor 2 domain profile. / Nuclear Transport Factor 2; Chain: A, - #50 / UBA-like superfamily / NTF2-like domain superfamily / Leucine-rich repeat profile. / Nuclear Transport Factor 2; Chain: A, / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Putative mRNA export protein / NTF2 domain-containing protein / Putative SAC3 family protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsAibara, S. / Valkov, E. / Stewart, M.
CitationJournal: Structure / Year: 2015
Title: Structural Characterization of the Chaetomium thermophilum TREX-2 Complex and its Interaction with the mRNA Nuclear Export Factor Mex67:Mtr2.
Authors: Dimitrova, L. / Valkov, E. / Aibara, S. / Flemming, D. / McLaughlin, S.H. / Hurt, E. / Stewart, M.
History
DepositionNov 26, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2015Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative mRNA export protein
B: Putative uncharacterized protein
C: SER-SER-VAL-PHE-GLY-ALA-PRO-ALA


Theoretical massNumber of molelcules
Total (without water)44,6123
Polymers44,6123
Non-polymers00
Water5,639313
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-26 kcal/mol
Surface area17320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.019, 74.195, 54.816
Angle α, β, γ (deg.)90.00, 112.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative mRNA export protein


Mass: 21617.295 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0059630 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SET4
#2: Protein Putative uncharacterized protein


Mass: 20909.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0065500 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SG92
#3: Protein/peptide SER-SER-VAL-PHE-GLY-ALA-PRO-ALA


Mass: 2085.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Chaetomium thermophilum (fungus) / References: UniProt: G0SGL4*PLUS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 400, 0.1M NaCl, 0.1M MgCl2, 0.1 M Na Citrate, pH 5.5. See publication for complete details.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→44.9 Å / Num. obs: 36313 / % possible obs: 99.9 % / Redundancy: 4.5 % / Net I/σ(I): 9.3
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 1.8 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.8→44.9 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.187 1839 5.07 %
Rwork0.1642 --
obs0.1654 36278 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→44.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2981 0 0 313 3294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043068
X-RAY DIFFRACTIONf_angle_d0.8894184
X-RAY DIFFRACTIONf_dihedral_angle_d13.7261123
X-RAY DIFFRACTIONf_chiral_restr0.035450
X-RAY DIFFRACTIONf_plane_restr0.004549
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84870.24741250.2572630X-RAY DIFFRACTION100
1.8487-1.90310.24851410.22662653X-RAY DIFFRACTION100
1.9031-1.96450.22881410.20292624X-RAY DIFFRACTION100
1.9645-2.03470.23811380.19362650X-RAY DIFFRACTION100
2.0347-2.11620.21591550.1812637X-RAY DIFFRACTION100
2.1162-2.21250.20871460.1732619X-RAY DIFFRACTION100
2.2125-2.32910.22241110.172663X-RAY DIFFRACTION100
2.3291-2.47510.18571450.16342659X-RAY DIFFRACTION100
2.4751-2.66610.17791500.16662623X-RAY DIFFRACTION100
2.6661-2.93440.1851540.16032654X-RAY DIFFRACTION100
2.9344-3.35890.16531340.15312659X-RAY DIFFRACTION100
3.3589-4.23130.15941620.13882659X-RAY DIFFRACTION100
4.2313-44.91350.16161370.14112709X-RAY DIFFRACTION100
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)
10.3766-0.03440.06710.2998-0.02430.14330.0346-0.00290.0739-0.0389-0.006-0.0739-0.05130.09040.00010.1319-0.0133-0.01110.1267-0.00140.1551-59.8414-219.56668.3787
2-0.0021-0.00630.00790.00080.00520.0043-0.2227-0.0661-0.2237-0.1407-0.12340.06030.0240.0547-00.27110.0373-0.01250.27760.01580.3741-56.5839-233.763680.2217
30.35350.14080.05940.2488-0.01480.09340.0270.02950.07430.0451-0.0202-0.097-0.04120.0426-0.00320.1044-0.0082-0.00820.12330.00780.1306-62.1391-217.529168.7441
40.1089-0.01-0.1292-0.01660.02680.1724-0.08490.0333-0.04520.0353-0.0674-0.02240.2516-0.0098-0.02560.16980.010.00490.10090.0010.1379-75.134-237.55268.6105
50.137-0.0275-0.01930.0219-0.05050.0675-0.06380.09620.01310.0277-0.00120.02470.0375-0.12570.00030.1072-0.0084-0.00030.1151-0.01450.1211-87.2476-227.738669.52
60.0626-0.05920.0830.1224-0.13220.1133-0.04440.00940.0217-0.0539-0.03180.0431-0.0326-0.1427-0.04910.1053-0.0015-0.02640.1591-0.02110.125-83.3976-229.55952.252
70.0880.21640.06360.31220.06030.1159-0.0069-0.0113-0.06170.0302-0.0278-0.00740.0469-0.0161-0.00350.090.01510.00290.0864-0.00140.0773-74.1085-231.627469.0241
80.06580.0310.00220.035-0.00570.00250.0517-0.1628-0.07950.14480.03970.091-0.0061-0.13050.00610.1407-0.03680.02220.13260.04420.1443-85.7886-239.01279.5036
90.038-0.0208-0.00070.00730.02230.02050.03780.02540.076-0.01330.060.01680.02080.0036-0.00150.1138-0.00340.01050.09280.00580.1163-76.5915-225.472764.5293
100.0091-0.0014-0.00270.0038-0.00680.014-0.07190.04370.11570.10340.0218-0.0399-0.0282-0.1-0.00010.26850.01650.03010.1734-0.00110.1557-77.3678-209.63581.8458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 365 through 439 )
2X-RAY DIFFRACTION2chain 'A' and (resid 440 through 453 )
3X-RAY DIFFRACTION3chain 'A' and (resid 454 through 556 )
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 20 )
5X-RAY DIFFRACTION5chain 'B' and (resid 21 through 48 )
6X-RAY DIFFRACTION6chain 'B' and (resid 49 through 84 )
7X-RAY DIFFRACTION7chain 'B' and (resid 85 through 157 )
8X-RAY DIFFRACTION8chain 'B' and (resid 158 through 172 )
9X-RAY DIFFRACTION9chain 'B' and (resid 173 through 183 )
10X-RAY DIFFRACTION10chain 'C' and (resid 15 through 20 )

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