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- PDB-3nc1: Crystal structure of the CRM1-RanGTP complex -

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Basic information

Entry
Database: PDB / ID: 3nc1
TitleCrystal structure of the CRM1-RanGTP complex
Components
  • Exportin-1
  • GTP-binding nuclear protein Ran
KeywordsGTP-binding protein/transport protein / protein transport / GTP-binding protein-transport protein complex
Function / homology
Function and homology information


Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Cyclin A/B1/B2 associated events during G2/M transition / HuR (ELAVL1) binds and stabilizes mRNA / Heme signaling / Deactivation of the beta-catenin transactivating complex / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Transcriptional and post-translational regulation of MITF-M expression and activity / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion ...Estrogen-dependent nuclear events downstream of ESR-membrane signaling / Cyclin A/B1/B2 associated events during G2/M transition / HuR (ELAVL1) binds and stabilizes mRNA / Heme signaling / Deactivation of the beta-catenin transactivating complex / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Transcriptional and post-translational regulation of MITF-M expression and activity / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / annulate lamellae / RHO GTPases Activate Formins / regulation of proteasomal ubiquitin-dependent protein catabolic process / Separation of Sister Chromatids / MAPK6/MAPK4 signaling / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / regulation of centrosome duplication / nuclear export signal receptor activity / Regulation of cholesterol biosynthesis by SREBP (SREBF) / regulation of protein export from nucleus / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / NEP/NS2 Interacts with the Cellular Export Machinery / GTP metabolic process / tRNA processing in the nucleus / Postmitotic nuclear pore complex (NPC) reformation / MicroRNA (miRNA) biogenesis / DNA metabolic process / regulation of protein catabolic process / mitotic sister chromatid segregation / ribosomal large subunit export from nucleus / protein localization to nucleus / viral process / nuclear pore / ribosomal subunit export from nucleus / mRNA export from nucleus / Cajal body / ribosomal small subunit export from nucleus / centriole / protein export from nucleus / mitotic spindle organization / Transcriptional regulation by small RNAs / recycling endosome / small GTPase binding / kinetochore / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / positive regulation of protein binding / nuclear envelope / melanosome / mitotic cell cycle / G protein activity / midbody / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / nuclear membrane / cadherin binding / protein heterodimerization activity / ribonucleoprotein complex / cell division / GTPase activity / chromatin binding / GTP binding / chromatin / nucleolus / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
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, 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 / small GTPase Ran family profile. / Ran GTPase / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Armadillo-like helical / Small GTP-binding protein domain / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / GTP-binding nuclear protein Ran / Exportin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.35 Å
AuthorsGuttler, T. / Madl, T. / Neumann, P. / Deichsel, D. / Corsini, L. / Monecke, T. / Ficner, R. / Sattler, M. / Gorlich, D.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: NES consensus redefined by structures of PKI-type and Rev-type nuclear export signals bound to CRM1.
Authors: Guttler, T. / Madl, T. / Neumann, P. / Deichsel, D. / Corsini, L. / Monecke, T. / Ficner, R. / Sattler, M. / Gorlich, D.
History
DepositionJun 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_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.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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: GTP-binding nuclear protein Ran
A: Exportin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,6534
Polymers144,1052
Non-polymers5472
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-16 kcal/mol
Surface area51350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.802, 216.158, 123.818
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein GTP-binding nuclear protein Ran / GTPase Ran / Ras-related nuclear protein / Ras-like protein TC4 / Androgen receptor-associated protein 24


Mass: 20738.096 Da / Num. of mol.: 1 / Mutation: Q69L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARA24, OK/SW-cl.81, RAN, RAN (GeneID: 5901) / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: P62826
#2: Protein Exportin-1 / Exp1 / Chromosome region maintenance 1 protein homolog


Mass: 123367.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Crm1, Xpo1, Xpo1 (GeneID: 103573) / Production host: Escherichia coli (E. coli) / Strain (production host): BLR / References: UniProt: Q6P5F9
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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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: 3.64 Å3/Da / Density % sol: 66.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris/HCl, 12% (w/v) PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.92 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 13, 2008 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3.35→37.37 Å / Num. all: 30619 / Num. obs: 28804 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.12 % / Biso Wilson estimate: 115.503 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.0399 / Net I/σ(I): 18.06
Reflection shellResolution: 3.35→3.45 Å / Redundancy: 2.66 % / Rmerge(I) obs: 0.4998 / Mean I/σ(I) obs: 2.1 / Num. measured obs: 6713 / Num. unique all: 1682 / Num. unique obs: 1679 / Rsym value: 0.5521 / % possible all: 66.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CRM1 and RANGTP molecules taken from PDB entry 3GJX

3gjx


Resolution: 3.35→36.521 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.757 / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 0.04 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1328 5.02 %RANDOM
Rwork0.219 ---
obs0.221 26438 86.47 %-
all-28804 --
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 93.229 Å2 / ksol: 0.271 e/Å3
Displacement parametersBiso max: 333.6 Å2 / Biso mean: 151.245 Å2 / Biso min: 69.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.4 Å
Luzzati d res low-8 Å
Luzzati sigma a0.53 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 3.35→36.521 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9716 0 33 0 9749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029958
X-RAY DIFFRACTIONf_angle_d0.52813490
X-RAY DIFFRACTIONf_chiral_restr0.0391535
X-RAY DIFFRACTIONf_plane_restr0.0021711
X-RAY DIFFRACTIONf_dihedral_angle_d13.4553708
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.35-3.3920.42300.38164967962
3.392-3.4370.387420.39871876067
3.437-3.4840.455310.3769172266
3.484-3.5340.424220.35867069262
3.534-3.5870.374310.32758261354
3.587-3.6430.276350.31966970463
3.643-3.7020.364460.3251068111499
3.702-3.7660.423370.28867371064
3.766-3.8350.344460.29381586176
3.835-3.9080.316660.268951101791
3.908-3.9880.265450.25884488980
3.988-4.0740.261530.25191897186
4.074-4.1690.312600.234985104592
4.169-4.2730.314470.221994104194
4.273-4.3890.25570.2011014107195
4.389-4.5170.242600.1841022108297
4.517-4.6630.179350.1781079111497
4.663-4.8290.237580.1821047110598
4.829-5.0220.222470.1871065111299
5.022-5.250.264750.2051035111098
5.25-5.5260.264620.2091066112898
5.526-5.8710.298490.2161074112398
5.871-6.3220.286490.2191065111499
6.322-6.9540.306510.2141091114299
6.954-7.9510.241580.2031101115999
7.951-9.9840.206660.1431091115799
9.984-36.5230.141700.1681133120398
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)
11.6172-0.1774-0.23792.7173-1.49460.88030.2141-0.4404-0.3653-0.57620.02870.4488-0.1288-0.039-0.02461.085-0.14790.02081.5048-0.33420.7427-34.485872.6885-21.4425
21.57150.6513-1.33820.82390.02473.1729-0.18050.17771.3335-2.02570.3928-0.6475-1.70911.644-0.37892.42720.0848-0.20072.0582-0.3982.0839-1.276786.3294-45.3636
30.9261-0.72110.04612.6692-2.18262.1307-0.19290.25140.71720.1683-0.499-0.1557-0.21020.68720.19151.6301-0.28570.09741.5053-0.10260.9733-8.631376.9423-49.0647
40.82160.5188-0.0342.498-0.88571.64-0.46120.9238-0.2224-0.9377-0.08330.37730.7862-0.52750.35671.4706-0.10810.22781.2272-0.03960.8666-6.035863.3028-47.5371
53.6099-0.0729-0.77055.5998-2.47765.014-0.27260.4035-0.2695-0.075-0.0487-0.1057-0.0436-0.07180.36471.2053-0.24060.08971.21-0.24420.5368-15.725945.8183-36.9819
63.20870.30751.7573.98760.63362.9529-0.2743-0.1139-0.6950.09860.23660.06960.0623-0.16660.21171.1764-0.18740.16281.32510.04930.599-25.156633.2588-16.7017
73.49720.5962-2.01073.26872.84534.2738-0.28310.5823-0.5936-0.1520.517-0.31580.57240.8254-0.11621.5366-0.07410.07731.68310.06560.5763-21.035143.27487.3794
88.8097-0.2551-0.06821.89460.50642.4929-0.2044-0.261-1.15211.27650.30810.16370.0210.570.3471.2304-0.08320.30081.3511-0.02160.0999-21.508161.971816.1704
93.236-1.5711-0.83162.7996-0.27980.52111.27841.3078-0.9102-1.4516-0.37740.2345-1.3817-0.4354-0.24961.2933-0.07180.23271.4392-0.07270.6199-14.764968.77181.1196
100.0142-0.0963-0.09590.92650.69310.51450.04940.656-0.3527-1.21130.0085-0.1928-0.12510.7662-0.24171.1165-0.0024-0.07131.7194-0.02781.247-28.956854.464-10.5541
110.77-0.99640.03381.299-0.08360.0628-0.7342-1.2997-0.14281.51020.89310.6972-0.3607-0.5359-0.18821.608-0.2004-0.13752.1542-0.29350.711-12.632978.771810.235
122.0967-1.72981.77073.199-1.23561.47290.3169-0.74630.38940.0496-0.4021-0.74510.1052-0.38850.09041.6186-0.01720.15461.6963-0.42070.8173-15.438885.10521.1067
133.1747-0.25770.22812.1743-2.02681.8865-0.70770.30060.79010.07660.41470.2211-0.2248-0.16750.28811.8445-0.0603-0.00181.6604-0.77591.2708-19.316498.0888-4.9758
142.2899-0.69180.531.03060.63834.7465-0.23510.82860.2085-0.3811-0.1419-0.32640.54-0.01460.42541.5637-0.3782-0.02791.0157-0.15051.0639-20.3845102.0067-27.3983
152.92780.24480.47830.8756-0.16464.32620.5826-1.4667-0.0084-0.5844-0.50320.211.32411.6873-0.63281.7483-0.1299-0.08151.319-0.33931.1832-29.709897.0536-35.4796
161.95251.219-1.00330.8844-0.27680.79780.24050.17441.515-1.565-0.1707-0.08790.45490.78010.00351.701-0.0184-0.16831.6042-0.15141.3109-34.902697.2898-42.4099
172.4972-0.61511.23482.3209-0.60214.8126-0.3638-0.3926-0.15481.25440.53581.25031.7091-0.8035-0.3951.2646-0.1108-0.33040.7908-0.28560.8135-46.10383.1853-45.1905
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain CC8 - 180
2X-RAY DIFFRACTION2chain A and resid 1028:1059A1028 - 1059
3X-RAY DIFFRACTION3chain A and resid 969:1027A969 - 1027
4X-RAY DIFFRACTION4chain A and resid 908:963A908 - 963
5X-RAY DIFFRACTION5chain A and resid 767:907A767 - 907
6X-RAY DIFFRACTION6chain A and resid 627:766A627 - 766
7X-RAY DIFFRACTION7chain A and resid 533:626A533 - 626
8X-RAY DIFFRACTION8chain A and resid 468:532A468 - 532
9X-RAY DIFFRACTION9chain A and resid 449:467A449 - 467
10X-RAY DIFFRACTION10chain A and resid 425:448A425 - 448
11X-RAY DIFFRACTION11chain A and resid 402:424A402 - 424
12X-RAY DIFFRACTION12chain A and resid 311:401A311 - 401
13X-RAY DIFFRACTION13chain A and resid 240:310A240 - 310
14X-RAY DIFFRACTION14chain A and resid 145:239A145 - 239
15X-RAY DIFFRACTION15chain A and resid 120:144A120 - 144
16X-RAY DIFFRACTION16chain A and resid 67:119A67 - 119
17X-RAY DIFFRACTION17chain A and resid 4:66A4 - 66

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