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- PDB-4c0q: Transportin 3 in complex with Ran(Q69L)GTP -

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Basic information

Entry
Database: PDB / ID: 4c0q
TitleTransportin 3 in complex with Ran(Q69L)GTP
Components
  • GTP-BINDING NUCLEAR PROTEIN RAN
  • TRANSPORTIN-3
KeywordsTRANSPORT PROTEIN/GTP-BINDING PROTEIN / TRANSPORT PROTEIN-GTP-BINDING PROTEIN COMPLEX / NUCLEAR IMPORT / HEAT REPEAT / IMPORTIN BETA
Function / homology
Function and homology information


annulate lamellae / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / 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 ...annulate lamellae / pre-miRNA export from nucleus / RNA nuclear export complex / snRNA import into nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / 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 / nuclear import signal receptor activity / MicroRNA (miRNA) biogenesis / DNA metabolic process / mitotic sister chromatid segregation / ribosomal large subunit export from nucleus / viral process / ribosomal subunit export from nucleus / nuclear pore / ribosomal small subunit export from nucleus / centriole / mitotic spindle organization / protein export from nucleus / Transcriptional regulation by small RNAs / recycling endosome / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / nuclear envelope / melanosome / positive regulation of protein binding / mitotic cell cycle / G protein activity / midbody / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cadherin binding / protein heterodimerization activity / cell division / intracellular membrane-bounded organelle / GTPase activity / chromatin binding / nucleolus / GTP binding / chromatin / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / Exportin-1/Importin-beta-like / Exportin 1-like protein / small GTPase Ran family profile. / Ran GTPase / 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 ...: / Exportin-1/Importin-beta-like / Exportin 1-like protein / small GTPase Ran family profile. / Ran GTPase / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / GTP-binding nuclear protein Ran / Transportin-3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.42 Å
AuthorsMaertens, G. / Hare, S. / Cherepanov, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural Basis for Nuclear Import of Splicing Factors by Human Transportin 3.
Authors: Maertens, G.N. / Cook, N.J. / Wang, W. / Hare, S. / Gupta, S.S. / Oztop, I. / Lee, K. / Pye, V.E. / Cosnefroy, O. / Snijders, A.P. / Kewalramani, V.N. / Fassati, A. / Engelman, A. / Cherepanov, P.
History
DepositionAug 6, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references / Structure summary
Revision 1.2Feb 5, 2014Group: Database references
Revision 1.3Mar 5, 2014Group: Database references
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSPORTIN-3
B: TRANSPORTIN-3
C: GTP-BINDING NUCLEAR PROTEIN RAN
D: GTP-BINDING NUCLEAR PROTEIN RAN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,4988
Polymers259,4044
Non-polymers1,0954
Water00
1
A: TRANSPORTIN-3
C: GTP-BINDING NUCLEAR PROTEIN RAN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,2494
Polymers129,7022
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRANSPORTIN-3
D: GTP-BINDING NUCLEAR PROTEIN RAN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,2494
Polymers129,7022
Non-polymers5472
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.950, 93.514, 104.713
Angle α, β, γ (deg.)78.43, 68.29, 68.28
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.72047, 0.04323, 0.69214), (0.1001, -0.98112, 0.16547), (0.68622, 0.1885, 0.70254)6.7149, 17.72964, 50.93138
2given(-0.72638, 0.04996, 0.68548), (0.05247, -0.99041, 0.12779), (0.68529, 0.12879, 0.71679)6.48357, 16.08058, 52.20178

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Components

#1: Protein TRANSPORTIN-3 / IMPORTIN-12 / IMP12 / TRANSPORTIN-SR / TRN-SR / TRANSPORTIN 3


Mass: 105391.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETSUMO-TNPO3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 LACI / References: UniProt: Q9Y5L0
#2: Protein GTP-BINDING NUCLEAR PROTEIN RAN / ANDROGEN RECEPTOR-ASSOCIATED PROTEIN 24 / GTPASE RAN / RAS-LIKE PROTEIN TC4 / RAS-RELATED NUCLEAR ...ANDROGEN RECEPTOR-ASSOCIATED PROTEIN 24 / GTPASE RAN / RAS-LIKE PROTEIN TC4 / RAS-RELATED NUCLEAR PROTEIN / RAN


Mass: 24309.938 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCPH6P-RAN(Q69L) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P62826
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: 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
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growpH: 6.5
Details: 13.5% (W/V) PEG3350, 8.5% (W/V) BENZAMIDINE HYDROCHLORIDE, 0.2M SODIUM ACETATE, PH6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9798
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 26, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3.42→40 Å / Num. obs: 34998 / % possible obs: 99.2 % / Redundancy: 5.8 % / Biso Wilson estimate: 133.66 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.6
Reflection shellResolution: 3.42→3.6 Å / Redundancy: 5.9 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 1.5 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C0P

4c0p


Resolution: 3.42→39.946 Å / SU ML: 0.56 / σ(F): 1.96 / Phase error: 37.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.29 1764 5.1 %
Rwork0.2677 --
obs0.2689 34962 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 137.75 Å2
Refinement stepCycle: LAST / Resolution: 3.42→39.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15700 0 66 0 15766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00316086
X-RAY DIFFRACTIONf_angle_d0.74921819
X-RAY DIFFRACTIONf_dihedral_angle_d15.6815911
X-RAY DIFFRACTIONf_chiral_restr0.0282531
X-RAY DIFFRACTIONf_plane_restr0.0032746
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.42-3.51240.42881340.42162571X-RAY DIFFRACTION99
3.5124-3.61570.40691290.38052562X-RAY DIFFRACTION99
3.6157-3.73230.39131350.37872533X-RAY DIFFRACTION99
3.7323-3.86560.35871360.32872564X-RAY DIFFRACTION99
3.8656-4.02030.33321320.3172565X-RAY DIFFRACTION99
4.0203-4.2030.3071420.29582580X-RAY DIFFRACTION100
4.203-4.42440.33761440.28582536X-RAY DIFFRACTION99
4.4244-4.70120.29321490.27792553X-RAY DIFFRACTION100
4.7012-5.06350.31991300.26582557X-RAY DIFFRACTION100
5.0635-5.57180.30741110.27912603X-RAY DIFFRACTION100
5.5718-6.37530.31791480.29562544X-RAY DIFFRACTION100
6.3753-8.02150.31441340.26962579X-RAY DIFFRACTION99
8.0215-39.94830.2071400.19452451X-RAY DIFFRACTION96
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)
11.96920.56340.87911.65640.12880.4928-0.05-0.33851.165-0.3062-0.03460.2004-0.2713-0.0594-0.16330.79330.0843-0.03910.3131-0.0441.0692-23.162825.6136-28.858
21.1364-0.13560.24911.22550.0980.47810.0445-0.5338-1.1891-0.0170.07480.4023-0.05340.09220.09720.71020.1476-0.07990.767-0.02321.622-21.982-23.1298-21.2183
31.29750.4659-0.52231.13620.41780.76050.0021-0.0215-0.19750.17090.0137-0.0641-0.0485-0.0691-00.65890.21290.04621.1291-0.03590.637413.4193-1.7785-19.3242
41.3492-0.4093-1.16950.8615-0.12323.03290.1248-0.2847-0.62840.1185-0.46610.18050.80091.16370.06111.2897-0.1942-0.2420.92720.40611.04559.9759-8.693318.6689
50.4418-0.60880.330.7025-0.31720.41570.0903-0.35480.6044-0.4602-0.1829-0.2756-0.6224-0.1242-0.00071.4135-0.0878-0.02371.4010.0991.92895.340636.931712.1103
61.36480.0959-0.38480.3964-0.23152.54180.2737-1.2070.51320.54250.07380.23410.1502-0.821.81231.38760.0070.1143.5092-0.45090.9354-16.731818.881745.1132
70.9635-0.4666-0.21931.07160.11621.009-0.06830.2632-0.6703-0.57220.12520.87950.20850.01200.8817-0.0382-0.31510.7507-0.0091.057-18.81651.0541-36.565
81.348-0.9271-0.11541.56520.16351.03760.38-0.25160.24080.0886-0.2213-0.2197-0.1692-0.46340.00370.7813-0.12530.01531.1626-0.01730.4678-4.85649.363913.2253
90.0036-0.01550.00630.0664-0.02770.01340.1169-0.1822-0.2648-0.02040.0897-0.1758-0.15350.1836-0.00070.97810.23890.07471.628-0.18480.743-5.70394.9424-12.045
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 5:286)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 287:736)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 737:922)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 5:369)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 370:702)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 703:922)
7X-RAY DIFFRACTION7(CHAIN C AND RESID 9:177)
8X-RAY DIFFRACTION8(CHAIN D AND RESID 9:177)
9X-RAY DIFFRACTION9(CHAIN D AND RESID 183:188)

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