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- PDB-3a6p: Crystal structure of Exportin-5:RanGTP:pre-miRNA complex -

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Basic information

Entry
Database: PDB / ID: 3a6p
TitleCrystal structure of Exportin-5:RanGTP:pre-miRNA complex
Components
  • (pre-microRNA) x 2
  • 13-mer peptide
  • Exportin-5
  • GTP-binding nuclear protein Ran
KeywordsPROTEIN TRANSPORT/NUCLEAR PROTEIN/RNA / EXPORTIN-5 / PRE-MICRORNA / RANGTP / NUCLEAREXPORT / IMPORTIN-BETA FAMILY / Nucleus / Phosphoprotein / Protein transport / RNA-binding / RNA-mediated gene silencing / Transport / tRNA-binding / Cell cycle / Cell division / GTP-binding / Isopeptide bond / Mitosis / Nucleotide-binding / PROTEIN TRANSPORT-NUCLEAR PROTEIN-RNA COMPLEX
Function / homology
Function and homology information


pre-miRNA binding / RISC complex binding / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / nuclear export signal receptor activity / miRNA metabolic process / RISC complex / GTP metabolic process / RNA export from nucleus ...pre-miRNA binding / RISC complex binding / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / nuclear export signal receptor activity / miRNA metabolic process / RISC complex / GTP metabolic process / RNA export from nucleus / MicroRNA (miRNA) biogenesis / mitotic sister chromatid segregation / ribosomal subunit export from nucleus / protein export from nucleus / positive regulation of protein export from nucleus / small GTPase binding / protein import into nucleus / nuclear envelope / melanosome / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / tRNA binding / cell division / GTPase activity / mRNA binding / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Exportin-5, C-terminal domain / Exportin-5 family / 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 ...Exportin-5, C-terminal domain / Exportin-5 family / 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 / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / 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 / Alpha Horseshoe / Armadillo-type fold / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / RNA / RNA (> 10) / GTP-binding nuclear protein Ran / Exportin-5
Similarity search - Component
Biological speciesHomo sapiens (human)
Canis lupus familiaris (dog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.92 Å
AuthorsOkada, C. / Yamashita, E. / Lee, S.J. / Shibata, S. / Katahira, J. / Nakagawa, A. / Yoneda, Y. / Tsukihara, T.
CitationJournal: Science / Year: 2009
Title: A high-resolution structure of the pre-microRNA nuclear export machinery
Authors: Okada, C. / Yamashita, E. / Lee, S.J. / Shibata, S. / Katahira, J. / Nakagawa, A. / Yoneda, Y. / Tsukihara, T.
History
DepositionSep 7, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 25, 2012Group: Database references
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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_asym_id / _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_asym_id / _struct_conn.ptnr2_label_asym_id / _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: Exportin-5
B: 13-mer peptide
C: GTP-binding nuclear protein Ran
D: pre-microRNA
E: pre-microRNA
F: Exportin-5
G: 13-mer peptide
H: GTP-binding nuclear protein Ran
I: pre-microRNA
J: pre-microRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,86214
Polymers354,76710
Non-polymers1,0954
Water00
1
A: Exportin-5
B: 13-mer peptide
C: GTP-binding nuclear protein Ran
D: pre-microRNA
E: pre-microRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,9317
Polymers177,3835
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Exportin-5
G: 13-mer peptide
H: GTP-binding nuclear protein Ran
I: pre-microRNA
J: pre-microRNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,9317
Polymers177,3835
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.157, 304.667, 89.230
Angle α, β, γ (deg.)90.00, 110.79, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12A
22D
13A
23D
14A
24D
15A
25D
16A
26D
17A
27D
18A
28D
19A
29D
110A
210D
111A
211D
112A
212D
113A
213D
114A
214D
115A
215D
116A
216D
117A
217D
118A
218D
119A
219D
120A
220D
121A
221D
122A
222D
123A
223D
124A
224D
125A
225D
126A
226D
127A
227D
128A
228D
129A
229D
130A
230D
131A
231D
132A
232D
133A
233D
134A
234D
135A
235D
136A
236D
137A
237D
138A
238D
139A
239D
140A
240D
141A
241D
142B
242E
143C
243F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A2 - 22
2111D2 - 22
1121A28 - 43
2121D28 - 43
1131A46 - 55
2131D46 - 55
1141A61 - 77
2141D61 - 77
1151A84 - 99
2151D84 - 99
1161A110 - 125
2161D110 - 125
1171A133 - 146
2171D133 - 146
1181A147 - 166
2181D147 - 166
1191A172 - 204
2191D172 - 204
11101A214 - 225
21101D214 - 225
11111A248 - 259
21111D248 - 259
11121A265 - 274
21121D265 - 274
11131A285 - 305
21131D285 - 305
11141A311 - 331
21141D311 - 331
11151A349 - 361
21151D349 - 361
11161A365 - 380
21161D365 - 380
11171A390 - 404
21171D390 - 404
11181A428 - 453
21181D428 - 453
11191A456 - 473
21191D456 - 473
11201A498 - 519
21201D498 - 519
11211A529 - 540
21211D529 - 540
11221A546 - 560
21221D546 - 560
11231A568 - 583
21231D568 - 583
11241A596 - 614
21241D596 - 614
11251A623 - 635
21251D623 - 635
11261A642 - 658
21261D642 - 658
11271A661 - 691
21271D661 - 691
11281A715 - 733
21281D715 - 733
11291A765 - 787
21291D765 - 787
11301A832 - 852
21301D832 - 852
11311A867 - 878
21311D867 - 878
11321A884 - 901
21321D884 - 901
11331A911 - 937
21331D911 - 937
11341A952 - 978
21341D952 - 978
11351A1018 - 1035
21351D1018 - 1035
11361A1041 - 1059
21361D1041 - 1059
11371A1065 - 1081
21371D1065 - 1081
11381A1087 - 1102
21381D1087 - 1102
11391A1109 - 1119
21391D1109 - 1119
11401A1122 - 1136
21401D1122 - 1136
11411A1305 - 1317
21411D1305 - 1317
11421B7 - 176
21421E7 - 176
11431C1 - 63
21431F1 - 63

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43

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Components

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Protein , 2 types, 4 molecules AFCH

#1: Protein Exportin-5 / Exp5 / Ran-binding protein 21


Mass: 136454.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XPO5, KIAA1291, RANBP21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HAV4
#3: Protein GTP-binding nuclear protein Ran / RanGTP / GTPase Ran / Ras-related nuclear protein / Ras-like protein TC4


Mass: 24456.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Gene: RAN / Production host: Escherichia coli (E. coli) / References: UniProt: P62825

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Protein/peptide , 1 types, 2 molecules BG

#2: Protein/peptide 13-mer peptide


Mass: 1124.378 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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RNA chain , 2 types, 4 molecules DIEJ

#4: RNA chain pre-microRNA


Mass: 7692.639 Da / Num. of mol.: 2 / Source method: obtained synthetically
#5: RNA chain pre-microRNA


Mass: 7655.519 Da / Num. of mol.: 2 / Source method: obtained synthetically

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Non-polymers , 2 types, 4 molecules

#6: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg

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Details

Has protein modificationY
Sequence detailsTHE AUTHOR COULDN'T TRACE THE RESIDUES AT POSITIONS 1305-1317 (CHAINS B, G) BECAUSE ELECTRON ...THE AUTHOR COULDN'T TRACE THE RESIDUES AT POSITIONS 1305-1317 (CHAINS B, G) BECAUSE ELECTRON DENSITY IS BROKEN. THERE IS DISCONTINUOUS ELECTRON DENSITY, SO THE AUTHOR COULDN'T SPECIFY THE AMINO ACID.

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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: 2.55 Å3/Da / Density % sol: 51.74 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Dec 12, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionHighest resolution: 2.9 Å / Num. obs: 74959

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Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.92→39.84 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.887 / SU B: 26.177 / SU ML: 0.481 / Cross valid method: THROUGHOUT / ESU R Free: 0.518 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31242 3826 5.1 %RANDOM
Rwork0.24734 ---
obs0.25061 71062 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 96.699 Å2
Baniso -1Baniso -2Baniso -3
1-5.16 Å20 Å2-5.32 Å2
2---6.54 Å20 Å2
3----2.4 Å2
Refinement stepCycle: LAST / Resolution: 2.92→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20044 1942 66 0 22052
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02222684
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8282.08331156
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17552496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.45124.239920
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.336153702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.63615126
X-RAY DIFFRACTIONr_chiral_restr0.1020.23636
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216138
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.210801
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.215770
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2610
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined00.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3130.2109
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3180.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9691.512873
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.732220316
X-RAY DIFFRACTIONr_scbond_it2.339311091
X-RAY DIFFRACTIONr_scangle_it3.5214.510840
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A156tight positional0.070.05
2A146tight positional0.060.05
3A70tight positional0.070.05
4A142tight positional0.090.05
5A132tight positional0.090.05
6A129tight positional0.090.05
7A107tight positional0.080.05
8A161tight positional0.080.05
9A287tight positional0.070.05
10A86tight positional0.060.05
11A94tight positional0.070.05
12A66tight positional0.060.05
13A160tight positional0.070.05
14A170tight positional0.080.05
15A108tight positional0.070.05
16A135tight positional0.070.05
17A118tight positional0.070.05
18A208tight positional0.070.05
19A152tight positional0.080.05
20A186tight positional0.080.05
21A93tight positional0.070.05
22A110tight positional0.080.05
23A133tight positional0.10.05
24A151tight positional0.10.05
25A112tight positional0.10.05
26A130tight positional0.10.05
27A259tight positional0.080.05
28A146tight positional0.080.05
29A188tight positional0.070.05
30A182tight positional0.060.05
31A88tight positional0.070.05
32A155tight positional0.060.05
33A228tight positional0.070.05
34A217tight positional0.060.05
35A138tight positional0.060.05
36A152tight positional0.060.05
37A131tight positional0.060.05
38A124tight positional0.060.05
39A89tight positional0.050.05
40A122tight positional0.060.05
41A66tight positional0.040.05
42B1386tight positional0.080.05
43C971tight positional0.060.05
1A156tight thermal9.6650
2A146tight thermal9.4250
3A70tight thermal7.9650
4A142tight thermal10.8450
5A132tight thermal7.9450
6A129tight thermal12.2350
7A107tight thermal9.8550
8A161tight thermal12.1450
9A287tight thermal14.250
10A86tight thermal7.1450
11A94tight thermal11.7650
12A66tight thermal13.3450
13A160tight thermal18.8650
14A170tight thermal8.8950
15A108tight thermal13.8950
16A135tight thermal10.6550
17A118tight thermal9.1150
18A208tight thermal8.3250
19A152tight thermal12.1550
20A186tight thermal7.150
21A93tight thermal2.2950
22A110tight thermal4.4950
23A133tight thermal5.2750
24A151tight thermal5.8250
25A112tight thermal650
26A130tight thermal4.8550
27A259tight thermal11.1150
28A146tight thermal8.6850
29A188tight thermal13.5950
30A182tight thermal11.6450
31A88tight thermal10.0850
32A155tight thermal10.4850
33A228tight thermal18.5450
34A217tight thermal13.450
35A138tight thermal9.3850
36A152tight thermal9.3350
37A131tight thermal8.1350
38A124tight thermal11.4850
39A89tight thermal7.1950
40A122tight thermal6.8950
41A66tight thermal13.2250
42B1386tight thermal6.1850
43C971tight thermal26.550
LS refinement shellResolution: 2.925→3 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.411 240 -
Rwork0.355 4255 -
obs--100 %

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