[English] 日本語
Yorodumi
- PDB-3gb8: Crystal structure of CRM1/Snurportin-1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3gb8
TitleCrystal structure of CRM1/Snurportin-1 complex
Components
  • Exportin-1
  • Snurportin-1
KeywordsTRANSPORT PROTEIN / Nuclear Transport Complex / Host-virus interaction / mRNA transport / Nucleus / Phosphoprotein / Protein transport / RNA-binding / Transport
Function / homology
Function and homology information


RNA import into nucleus / HuR (ELAVL1) binds and stabilizes mRNA / annulate lamellae / regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA cap binding / snRNA import into nucleus / regulation of centrosome duplication / nuclear export signal receptor activity / NLS-dependent protein nuclear import complex / regulation of protein export from nucleus ...RNA import into nucleus / HuR (ELAVL1) binds and stabilizes mRNA / annulate lamellae / regulation of proteasomal ubiquitin-dependent protein catabolic process / RNA cap binding / snRNA import into nucleus / regulation of centrosome duplication / nuclear export signal receptor activity / NLS-dependent protein nuclear import complex / regulation of protein export from nucleus / Rev-mediated nuclear export of HIV RNA / NEP/NS2 Interacts with the Cellular Export Machinery / nuclear import signal receptor activity / nucleocytoplasmic transport / Maturation of hRSV A proteins / protein complex oligomerization / ribosomal large subunit export from nucleus / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / protein localization to nucleus / nuclear pore / ribosomal subunit export from nucleus / mRNA export from nucleus / Cajal body / Cyclin A/B1/B2 associated events during G2/M transition / ribosomal small subunit export from nucleus / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / NPAS4 regulates expression of target genes / cytoskeleton organization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Transcriptional and post-translational regulation of MITF-M expression and activity / Resolution of Sister Chromatid Cohesion / protein export from nucleus / Downregulation of TGF-beta receptor signaling / protein tetramerization / Deactivation of the beta-catenin transactivating complex / RHO GTPases Activate Formins / Heme signaling / MAPK6/MAPK4 signaling / small GTPase binding / kinetochore / protein import into nucleus / Separation of Sister Chromatids / nuclear envelope / ribosome biogenesis / snRNP Assembly / nuclear membrane / ribonucleoprotein complex / intracellular membrane-bounded organelle / nucleolus / protein-containing complex / RNA binding / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #450 / Snurportin-1 / Snurportin-1, N-terminal / : / Snurportin1 / Snurportin1, m3G cap-binding domain / DNA ligase/mRNA capping enzyme / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #450 / Snurportin-1 / Snurportin-1, N-terminal / : / Snurportin1 / Snurportin1, m3G cap-binding domain / DNA ligase/mRNA capping enzyme / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1, C-terminal / CRM1 C terminal / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin 1-like protein / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / D-amino Acid Aminotransferase; Chain A, domain 1 / Helix non-globular / Special / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Exportin-1 / Snurportin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsDong, X. / Biswas, A. / Suel, K.E. / Jackson, L.K. / Martinez, R. / Gu, H. / Chook, Y.M.
Citation
Journal: Nature / Year: 2009
Title: Structural basis for leucine-rich nuclear export signal recognition by CRM1.
Authors: Dong, X. / Biswas, A. / Suel, K.E. / Jackson, L.K. / Martinez, R. / Gu, H. / Chook, Y.M.
#1: Journal: To be Published / Year: 2009
Title: Structural basis of assembly and disassembly of the CRM1 nuclear export complex
Authors: Dong, X. / Biswas, A. / Chook, Y.M.
History
DepositionFeb 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Exportin-1
B: Snurportin-1


Theoretical massNumber of molelcules
Total (without water)161,2852
Polymers161,2852
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-11.8 kcal/mol
Surface area55120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)250.400, 250.400, 190.400
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

-
Components

#1: Protein Exportin-1 / Exp1 / Chromosome region maintenance 1 protein homolog


Mass: 123518.359 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRM1, XPO1 / Plasmid: pGEXTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O14980
#2: Protein Snurportin-1 / RNA U transporter 1


Mass: 37766.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RNUT1, SNUPN, SPN1 / Plasmid: pGEXTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95149

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 5.34 Å3/Da / Density % sol: 76.97 %
Description: The structure factor file contains Bijvoet pairs.
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5
Details: 8% PEG 8000, 0.2M Magnesium chloride, 0.1M MES pH 6.5, VAPOR DIFFUSION, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935, 0.97945, 0.97167
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2008
Details: LN2 cooled first crystal, sagital focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979351
20.979451
30.971671
ReflectionResolution: 2.9→50 Å / Num. obs: 73476 / % possible obs: 99.1 % / Redundancy: 7.4 % / Rsym value: 0.083 / Net I/σ(I): 25
Reflection shellResolution: 2.9→3 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.58 / % possible all: 99.6

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.9→47.67 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.877 / Occupancy max: 1 / Occupancy min: 1 / SU B: 24.996 / SU ML: 0.213 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.399 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. The Bijvoet pairs were used in phasing. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 3667 5 %RANDOM
Rwork0.236 ---
obs0.238 69818 94.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 126.05 Å2 / Biso mean: 44.541 Å2 / Biso min: 4.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9750 0 0 0 9750
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229960
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.95313517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21351216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.32724.577461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.45151718
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5661549
X-RAY DIFFRACTIONr_chiral_restr0.1020.21543
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.027481
X-RAY DIFFRACTIONr_nbd_refined0.2460.25051
X-RAY DIFFRACTIONr_nbtor_refined0.3160.26931
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2358
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3180.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.22
X-RAY DIFFRACTIONr_mcbond_it0.6841.56240
X-RAY DIFFRACTIONr_mcangle_it1.24929904
X-RAY DIFFRACTIONr_scbond_it1.61834158
X-RAY DIFFRACTIONr_scangle_it2.7654.53613
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 236 -
Rwork0.306 4608 -
all-4844 -
obs--85.39 %
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)
10.29020.08770.07260.0302-0.02330.56430.0686-0.00520.0408-0.0745-0.04460.06120.1573-0.1551-0.0240.02920.0247-0.0630.22280.00420.0031-5.4843107.95456.8971
25.4897-1.5225-0.84710.50160.38550.41610.35090.7323-0.13220.1028-0.1999-0.06560.0204-0.2163-0.151-0.07020.1-0.0060.2305-0.0238-0.118645.5674109.367567.644
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A53 - 1061
2X-RAY DIFFRACTION2B0 - 293

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more