[English] 日本語
Yorodumi
- PDB-4c0q: Transportin 3 in complex with Ran(Q69L)GTP -

+
Open data


ID or keywords:

Loading...

-
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 / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / manchette / cellular response to mineralocorticoid stimulus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / protein localization to nucleolus / Rev-mediated nuclear export of HIV RNA ...annulate lamellae / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / manchette / cellular response to mineralocorticoid stimulus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / 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 / nuclear import signal receptor activity / DNA metabolic process / dynein intermediate chain binding / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / sperm flagellum / viral process / nuclear pore / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / protein export from nucleus / centriole / mitotic spindle organization / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / recycling endosome / G protein activity / small GTPase binding / positive regulation of protein import into nucleus / protein import into nucleus / GDP binding / melanosome / positive regulation of protein binding / nuclear envelope / mitotic cell cycle / midbody / actin cytoskeleton organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / intracellular membrane-bounded organelle / GTPase activity / chromatin binding / chromatin / nucleolus / GTP binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / membrane / nucleus / 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 / Alpha Horseshoe / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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)

+
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