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- PDB-3m1i: Crystal structure of yeast CRM1 (Xpo1p) in complex with yeast Ran... -

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Basic information

Entry
Database: PDB / ID: 3m1i
TitleCrystal structure of yeast CRM1 (Xpo1p) in complex with yeast RanBP1 (Yrb1p) and yeast RanGTP (Gsp1pGTP)
Components
  • Exportin-1Karyopherin
  • GTP-binding nuclear protein GSP1/CNR1
  • Ran-specific GTPase-activating protein 1
KeywordsPROTEIN TRANSPORT / HEAT REPEAT / EXPORTIN / GTP-binding / Nucleotide-binding / Nucleus / Transport / GTPase activation
Function / homology
Function and homology information


regulation of cell cycle phase transition / positive regulation of mitotic centrosome separation / Postmitotic nuclear pore complex (NPC) reformation / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of nucleocytoplasmic transport / MAPK6/MAPK4 signaling / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / nuclear export signal receptor activity / SUMOylation of SUMOylation proteins ...regulation of cell cycle phase transition / positive regulation of mitotic centrosome separation / Postmitotic nuclear pore complex (NPC) reformation / exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of nucleocytoplasmic transport / MAPK6/MAPK4 signaling / Transport of Mature mRNA derived from an Intron-Containing Transcript / Regulation of HSF1-mediated heat shock response / nuclear export signal receptor activity / SUMOylation of SUMOylation proteins / SUMOylation of RNA binding proteins / spindle pole body / protein localization to kinetochore / U4 snRNA binding / nuclear export / RNA export from nucleus / SUMOylation of chromatin organization proteins / nuclear import signal receptor activity / poly(A)+ mRNA export from nucleus / NLS-bearing protein import into nucleus / nucleus organization / ribosomal large subunit export from nucleus / U5 snRNA binding / ribosomal small subunit export from nucleus / ribosomal subunit export from nucleus / U2 snRNA binding / U6 snRNA binding / mRNA export from nucleus / nuclear pore / U1 snRNA binding / protein export from nucleus / GTPase activator activity / G1/S transition of mitotic cell cycle / kinetochore / small GTPase binding / protein import into nucleus / ubiquitin-dependent protein catabolic process / GTPase activity / GTP binding / perinuclear region of cytoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Ran-specific GTPase-activating protein 1, Ran-binding domain / Exportin-1, C-terminal / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / CRM1 C terminal / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal ...Ran-specific GTPase-activating protein 1, Ran-binding domain / Exportin-1, C-terminal / Exportin-1, repeat 3 / Chromosome region maintenance repeat / Exportin-1, repeat 2 / CRM1 C terminal / Chromosome region maintenance or exportin repeat / CRM1 / Exportin repeat 2 / CRM1 / Exportin repeat 3 / CRM1 C terminal / Exportin-1/5 / Exportin-1/Importin-beta-like / Exportin 1-like protein / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / small GTPase Ran family profile. / Ran GTPase / Importin-beta N-terminal domain profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta, N-terminal domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / 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 / PH-like domain superfamily / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Roll / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Exportin-1 / GTP-binding nuclear protein GSP1/CNR1 / Ran-specific GTPase-activating protein 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKoyama, M. / Matsuura, Y.
CitationJournal: Embo J. / Year: 2010
Title: An allosteric mechanism to displace nuclear export cargo from CRM1 and RanGTP by RanBP1
Authors: Koyama, M. / Matsuura, Y.
History
DepositionMar 5, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 5, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: 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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTP-binding nuclear protein GSP1/CNR1
B: Ran-specific GTPase-activating protein 1
C: Exportin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,6655
Polymers167,1173
Non-polymers5472
Water13,854769
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8450 Å2
ΔGint-25 kcal/mol
Surface area56750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.209, 106.209, 303.602
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe biological assembly is the heterotrimeric complex in the asymmetric unit.

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein GTP-binding nuclear protein GSP1/CNR1 / RanGTP / Gsp1pGTP / GTPase Ran homolog / Genetic suppressor of PRP20-1 / Chromosome stability protein 17


Mass: 24825.357 Da / Num. of mol.: 1 / Mutation: Q71L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: GSP1 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / References: UniProt: P32835
#2: Protein Ran-specific GTPase-activating protein 1 / Yrb1p / Ran-binding protein 1 / RANBP1 / Perinuclear array-localized protein / Chromosome stability protein 20


Mass: 21893.789 Da / Num. of mol.: 1 / Mutation: A deletion mutant (residues 1-10 deleted)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YRB1 / Plasmid: pET30a / Production host: Escherichia coli (E. coli) / References: UniProt: P41920
#3: Protein Exportin-1 / Karyopherin / CRM1 / Xpo1p / Chromosome region maintenance protein 1 / Karyopherin-124


Mass: 120398.195 Da / Num. of mol.: 1 / Mutation: A deletion mutant (residues 377-413 deleted)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: XPO1 / Plasmid: pET30a-TEV / Production host: Escherichia coli (E. coli) / References: UniProt: P30822

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Non-polymers , 3 types, 771 molecules

#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 769 / 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: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.6
Details: 0.1M Bis-Tris, 0.2M ammonium nitrate, 18% PEG3350, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 26, 2009
RadiationMonochromator: Rotated-inclined double-crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→45.33 Å / Num. all: 118072 / Num. obs: 117954 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Biso Wilson estimate: 35.68 Å2 / Rmerge(I) obs: 0.087 / Rsym value: 0.084 / Net I/σ(I): 5.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 10 % / Rmerge(I) obs: 0.876 / Mean I/σ(I) obs: 2.9 / Num. unique all: 16944 / Rsym value: 0.834 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
BSSdata collection
PROCESSdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RRP, 1W9C, 2H4M

1rrp

1w9c

2h4m


Resolution: 2→43.51 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 1 / SU B: 7.432 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.151 / ESU R Free: 0.145 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22 5918 5 %RANDOM
Rwork0.175 ---
all0.178 118072 --
obs0.178 117821 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 131.04 Å2 / Biso mean: 41.996 Å2 / Biso min: 17.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2---0.41 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 2→43.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10832 0 33 769 11634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.02211081
X-RAY DIFFRACTIONr_angle_refined_deg2.0421.96115021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4451349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.14225.029511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.015151988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4411548
X-RAY DIFFRACTIONr_chiral_restr0.2070.21729
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0218220
X-RAY DIFFRACTIONr_mcbond_it1.2951.56763
X-RAY DIFFRACTIONr_mcangle_it2.319210970
X-RAY DIFFRACTIONr_scbond_it3.934318
X-RAY DIFFRACTIONr_scangle_it6.2174.54051
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 442 -
Rwork0.245 8131 -
all-8573 -
obs--100 %
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)
11.7638-0.1140.41591.14570.0581.20490.0064-0.0060.26690.0246-0.0124-0.0652-0.18010.12280.0060.101-0.02310.0170.0565-0.01970.2027-4.9894-43.6646-33.9733
20.9533-0.465-0.07822.1295-0.74632.02270.0847-0.07040.24580.0866-0.02060.281-0.2196-0.1176-0.06410.0867-0.0142-0.00270.05820.00170.2121-15.9592-45.6306-38.1454
31.7758-0.17270.43271.29050.12631.6263-0.0078-0.02140.06610.0004-0.01880.05660.1238-0.03360.02660.1121-0.01490.01740.08360.00370.1651-11.8434-57.511-38.361
41.95550.37731.20160.6703-0.64342.0338-0.02490.19090.27560.1288-0.06980.0676-0.20350.29330.09460.1333-0.05020.02120.1669-0.02420.28598.5645-44.8811-35.048
56.0257-0.9843-1.52511.2873-4.50258.44190.07-0.3222-0.09250.52350.02340.4503-0.3016-0.2838-0.09340.1609-0.05940.14580.103-0.07620.15093.9762-47.222-8.7733
614.04443.020311.39190.86752.20579.5189-1.00572.24430.712-0.4050.34910.1332-0.67392.07090.65660.262-0.10530.01580.82110.1260.264320.4151-43.5096-40.8238
79.2068-1.6691-2.45213.64831.59244.6620.07010.19270.28820.2457-0.19410.1848-0.1753-0.16130.1240.1883-0.067-0.00750.12290.01510.164510.6001-46.3649-17.9252
82.569-0.027-0.22711.69290.27241.8250.0239-0.07080.13410.1742-0.0805-0.0779-0.10470.32140.05660.0928-0.092-0.02340.14520.00720.160518.3025-43.955-23.1223
93.32911.3976-1.61813.290.12633.5353-0.0019-0.24930.29470.2952-0.02830.1521-0.1670.14740.03020.1544-0.0826-0.01030.1102-0.03670.156311.9603-44.4639-14.2993
1010.26318.4949-1.393416.4097-1.21713.0039-0.064-0.3891-0.28110.43550.0134-0.7554-0.03820.78460.05070.1334-0.0294-0.09830.3216-0.02170.110525.7379-46.5586-12.8613
112.04280.70820.13322.1848-0.03621.781-0.0202-0.04450.21520.10050.09560.3109-0.1705-0.1191-0.07540.13380.04080.01880.01960.02140.2653-26.3925-29.2769-42.3064
121.0973-0.4423-0.40590.97220.36231.07880.0060.19250.1574-0.2019-0.02720.06880.0021-0.03010.02120.1278-0.0066-0.05850.14820.06190.1606-28.7283-53.6434-60.3686
130.8827-0.31950.4410.9919-0.49871.1257-0.04950.0183-0.00480.02610.0423-0.12880.02790.11130.00720.16010.01060.03120.1488-0.00010.08762.2718-78.4242-46.6592
141.22080.0936-0.15931.59240.41722.31450.0218-0.12490.01450.1329-0.0553-0.11960.03660.20850.03350.16570.0381-0.06630.18760.02970.09179.6832-85.015-9.9638
151.6312-0.77270.03771.2852-0.06420.23170.0677-0.0291-0.12340.1754-0.03660.1968-0.0629-0.0284-0.03110.21380.00220.04630.1544-0.02790.0382-14.0381-68.339-1.8816
162.6494-0.00740.62381.4836-0.81382.7590.0357-0.2646-0.12780.1660.16090.41840.0791-0.1335-0.19660.13340.03710.07350.1018-0.00780.2353-42.545-62.9815-14.8265
171.7692-0.5157-0.28852.5924-0.34553.0412-0.02980.1223-0.2695-0.05870.01230.21310.1507-0.19040.01740.09460.01050.00010.0954-0.04370.2281-45.175-56.1025-31.2635
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 71
2X-RAY DIFFRACTION2A72 - 95
3X-RAY DIFFRACTION3A96 - 159
4X-RAY DIFFRACTION4A160 - 201
5X-RAY DIFFRACTION5A202 - 217
6X-RAY DIFFRACTION6B71 - 83
7X-RAY DIFFRACTION7B84 - 103
8X-RAY DIFFRACTION8B104 - 146
9X-RAY DIFFRACTION9B147 - 182
10X-RAY DIFFRACTION10B183 - 201
11X-RAY DIFFRACTION11C-1 - 87
12X-RAY DIFFRACTION12C88 - 273
13X-RAY DIFFRACTION13C274 - 570
14X-RAY DIFFRACTION14C571 - 694
15X-RAY DIFFRACTION15C695 - 901
16X-RAY DIFFRACTION16C902 - 991
17X-RAY DIFFRACTION17C992 - 1058

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