[English] 日本語
Yorodumi
- PDB-3tj3: Structure of importin a5 bound to the N-terminus of Nup50 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tj3
TitleStructure of importin a5 bound to the N-terminus of Nup50
Components
  • Importin subunit alpha-1
  • Nuclear pore complex protein Nup50Nuclear pore
KeywordsPROTEIN TRANSPORT / ARMADILLO repeat / nuclear import adaptor / NLS-bearing proteins / nucleo-cytoplasmic shuttling
Function / homology
Function and homology information


satellite cell activation involved in skeletal muscle regeneration / skeletal muscle satellite cell proliferation / Inhibition of nitric oxide production / regulation of DNA recombination / Nuclear Pore Complex (NPC) Disassembly / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA ...satellite cell activation involved in skeletal muscle regeneration / skeletal muscle satellite cell proliferation / Inhibition of nitric oxide production / regulation of DNA recombination / Nuclear Pore Complex (NPC) Disassembly / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / NLS-dependent protein nuclear import complex / Transport of Mature mRNA Derived from an Intronless Transcript / Apoptosis induced DNA fragmentation / postsynapse to nucleus signaling pathway / Rev-mediated nuclear export of HIV RNA / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / regulation of canonical Wnt signaling pathway / nucleocytoplasmic transport / nuclear import signal receptor activity / Viral Messenger RNA Synthesis / nuclear localization sequence binding / NLS-bearing protein import into nucleus / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / Integration of provirus / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA transport / SUMOylation of DNA damage response and repair proteins / nuclear pore / SUMOylation of chromatin organization proteins / Assembly of the ORC complex at the origin of replication / HCMV Late Events / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / HCMV Early Events / protein import into nucleus / Interferon alpha/beta signaling / nuclear envelope / snRNP Assembly / regulation of apoptotic process / nuclear membrane / postsynaptic density / dendrite / glutamatergic synapse / SARS-CoV-2 activates/modulates innate and adaptive immune responses / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear pore complex, NUP2/50/61 / NUP50 (Nucleoporin 50 kDa) / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily ...Nuclear pore complex, NUP2/50/61 / NUP50 (Nucleoporin 50 kDa) / Ran binding protein RanBP1-like / Ran binding domain / RanBP1 domain / Ran binding domain type 1 profile. / Ran-binding domain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / PH-like domain superfamily / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-5 / Nuclear pore complex protein Nup50
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.702 Å
AuthorsPumroy, R. / Nardozzi, J.D. / Hart, D.J. / Root, M.J. / Cingolani, G.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Nucleoporin Nup50 stabilizes closed conformation of armadillo repeat 10 in importin alpha 5.
Authors: Pumroy, R.A. / Nardozzi, J.D. / Hart, D.J. / Root, M.J. / Cingolani, G.
History
DepositionAug 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Importin subunit alpha-1
C: Nuclear pore complex protein Nup50
B: Importin subunit alpha-1
D: Nuclear pore complex protein Nup50


Theoretical massNumber of molelcules
Total (without water)122,4154
Polymers122,4154
Non-polymers00
Water2,342130
1
A: Importin subunit alpha-1
C: Nuclear pore complex protein Nup50


Theoretical massNumber of molelcules
Total (without water)61,2072
Polymers61,2072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-5 kcal/mol
Surface area21350 Å2
MethodPISA
2
B: Importin subunit alpha-1
D: Nuclear pore complex protein Nup50


Theoretical massNumber of molelcules
Total (without water)61,2072
Polymers61,2072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-5 kcal/mol
Surface area21290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.683, 98.291, 135.352
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 82:459 or resseq 466:506 )
211chain B and (resseq 82:459 or resseq 466:506 )
112chain C and (resseq 0:18 or resseq 23:46 )
212chain D and (resseq 0:18 or resseq 23:46 )

NCS ensembles :
ID
1
2
DetailsTHE QUATERNARY STRUCTURE IS A HETERODIMER OF IMPORTIN A5 AND NUP50.

-
Components

#1: Protein Importin subunit alpha-1 / / importin alpha 5 / Karyopherin subunit alpha-1 / Nucleoprotein interactor 1 / NPI-1 / RAG cohort ...importin alpha 5 / Karyopherin subunit alpha-1 / Nucleoprotein interactor 1 / NPI-1 / RAG cohort protein 2 / SRP1-beta


Mass: 49401.328 Da / Num. of mol.: 2 / Fragment: UNP residues 66-512
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPNA1, RCH2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52294
#2: Protein Nuclear pore complex protein Nup50 / Nuclear pore / 50 kDa nucleoporin / Nuclear pore-associated protein 60 kDa-like / Nucleoporin Nup50


Mass: 11806.040 Da / Num. of mol.: 2 / Fragment: N-terminal domain (UNP residues 1-109)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NUP50, NPAP60L, PRO1146 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKX7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 24% PEG3350, 100 mM Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X6A10.976
SYNCHROTRONNSLS X2521.1
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDJun 20, 2011
DECTRIS PILATUS 6M2PIXELApr 15, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.9761
21.11
ReflectionResolution: 2.7→79.532 Å / Num. all: 29294 / Num. obs: 29294 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rsym value: 0.086 / Net I/σ(I): 26.86
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.15 / Num. unique all: 2820 / Rsym value: 0.618 / % possible all: 94.1

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JDQ

2jdq


Resolution: 2.702→15.028 Å / SU ML: 0.75 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 28.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2553 1350 5 %RANDOM
Rwork0.2149 ---
all0.217 ---
obs0.217 26999 88.96 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.132 Å2 / ksol: 0.301 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--11.2301 Å20 Å20 Å2
2---0.0863 Å2-0 Å2
3---11.3164 Å2
Refinement stepCycle: LAST / Resolution: 2.702→15.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7415 0 0 130 7545
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057517
X-RAY DIFFRACTIONf_angle_d0.79510189
X-RAY DIFFRACTIONf_dihedral_angle_d15.7492795
X-RAY DIFFRACTIONf_chiral_restr0.0521189
X-RAY DIFFRACTIONf_plane_restr0.0031313
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3254X-RAY DIFFRACTIONPOSITIONAL
12B3254X-RAY DIFFRACTIONPOSITIONAL0.028
21C352X-RAY DIFFRACTIONPOSITIONAL
22D352X-RAY DIFFRACTIONPOSITIONAL0.026
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.702-2.79810.36841040.35092027X-RAY DIFFRACTION71
2.7981-2.90940.41911200.34022213X-RAY DIFFRACTION78
2.9094-3.04070.39521270.31532317X-RAY DIFFRACTION81
3.0407-3.19960.31941320.29022518X-RAY DIFFRACTION89
3.1996-3.39790.36111390.26952731X-RAY DIFFRACTION95
3.3979-3.65680.28411420.25322739X-RAY DIFFRACTION95
3.6568-4.01840.22421410.20542650X-RAY DIFFRACTION93
4.0184-4.58530.2031400.16542671X-RAY DIFFRACTION92
4.5853-5.72340.21721480.17442840X-RAY DIFFRACTION97
5.7234-15.02830.19391570.16342943X-RAY DIFFRACTION97
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)
12.89370.9047-0.24816.0222-2.11913.306-0.2591-0.1673-0.31460.43120.1374-0.259-0.14350.0120.08180.333-0.0022-0.12270.1597-0.03670.201521.62017.8822-20.4581
22.66241.7361-0.15187.3589-0.1271.3797-0.34150.60120.1441-0.89760.39420.2557-0.02990.0624-0.02810.5087-0.14470.05420.55680.0310.324412.1008-26.2877-19.5491
36.4314-2.72430.11961.784-0.79964.484-0.1642-0.4648-0.5114-0.10230.2241-0.16160.4355-0.0043-0.14040.6095-0.07160.21770.4215-0.12140.598125.8628-53.4049-10.3664
49.322-1.7133-3.47550.95271.19091.7734-0.49550.42541.39990.56450.71721.9989-0.4566-0.2858-1.26250.69280.17730.21481.9218-0.22591.139512.7962-42.0755-1.0021
54.59871.9679-4.45313.5572-0.95754.68110.1539-1.0405-0.19590.9237-0.03540.0690.50690.41630.00440.6875-0.14650.05370.58810.12850.337318.2447-33.359-9.119
69.1817-1.48641.7942.0691-2.69299.0488-0.10761.293-0.1279-0.89720.058-1.07990.66560.68940.83020.8172-0.12040.11831.02110.08840.615724.4274-20.4846-19.8535
77.733-7.00151.88926.3395-1.75550.5618-0.1171-0.2399-1.07550.64470.30291.47410.2931-1.753-0.38471.3306-0.04690.52441.41510.49311.552332.5263-26.443-24.5239
88.4122-3.1280.09679.4608-0.98846.43950.2918-0.16640.29010.9401-0.1166-1.315-0.8480.92580.55930.6123-0.26110.22570.7533-0.24351.20943.7651-46.271-5.626
90.62350.64961.26755.08453.55179.11590.82430.628-0.30461.31390.5177-1.45051.31780.9864-1.2410.73090.2640.1950.9636-0.11231.138936.1464-62.9098-5.8441
105.9887-2.84120.07674.19120.4622.9666-0.3127-0.76041.2170.32520.2093-0.3768-0.597-0.14710.02340.77030.0206-0.26680.457-0.06740.823514.71216.750422.2687
111.6844-0.3222-0.16896.0341.7191.421-0.16960.0758-0.0148-0.31430.1888-0.17510.26740.1024-0.00340.31840.02760.03690.3582-0.01780.227824.2707-27.304119.4064
125.55272.7031.54063.59040.44783.6292-0.28730.2381-0.6560.27260.16270.21390.23050.0780.01730.58030.04530.1940.23640.09880.456114.1863-50.440111.3938
139.1278-2.36581.22784.7264-0.57697.72580.26240.4794-0.7719-0.58350.11260.2010.6033-0.1637-0.26160.5762-0.04550.15950.2890.03940.60275.6056-57.74145.1099
145.9817-0.31173.01290.1550.00341.7067-0.60180.49411.1264-0.2531-0.4715-0.3207-0.3058-1.1725-0.03150.91030.06920.43121.68910.11151.262423.516-41.9266-0.1856
152.316-2.4587-3.83275.26363.68546.4343-1.0530.11660.0438-1.0725-0.75510.97990.285-0.96370.22821.38450.1049-0.11910.5485-0.27760.347718.121-33.82758.4207
161.38562.69592.45125.42984.30558.7869-0.5287-1.73490.5229-1.3607-0.77161.247-1.2111-1.74091.4420.74710.1860.04510.7728-0.18261.153811.9823-21.622219.9358
172.43611.79921.29793.90782.2131.8160.2522-0.23681.68160.9489-0.04650.05980.21220.3148-0.71461.6668-0.36080.74140.8209-0.44352.35383.3854-28.677523.7102
185.46484.84263.68229.49992.67414.14311.8679-0.97351.21521.4217-0.5397-0.0788-2.198-0.284-0.91191.2087-0.0690.82560.56750.07261.5523-1.6295-40.475216.5879
199.30012.29620.20632.0816-0.38418.48460.71492.64790.6551-0.6183-0.68182.1089-0.0148-0.71480.28810.9960.4448-0.2110.9262-0.00021.0932-9.3298-48.4276-0.1075
206.8628-0.1296-2.17441.2136-1.93365.84260.7653-0.5941-0.7471-1.228-0.98540.4951.51680.86250.13010.91150.08230.24510.47040.10121.0015-0.2385-62.72682.7814
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 82:225)
2X-RAY DIFFRACTION2chain 'A' and (resseq 226:393)
3X-RAY DIFFRACTION3chain 'A' and (resseq 394:508)
4X-RAY DIFFRACTION4chain 'C' and (resseq -3:1)
5X-RAY DIFFRACTION5chain 'C' and (resseq 2:6)
6X-RAY DIFFRACTION6chain 'C' and (resseq 7:16)
7X-RAY DIFFRACTION7chain 'C' and (resseq 17:21)
8X-RAY DIFFRACTION8chain 'C' and (resseq 22:37)
9X-RAY DIFFRACTION9chain 'C' and (resseq 38:47)
10X-RAY DIFFRACTION10chain 'B' and (resseq 82:225)
11X-RAY DIFFRACTION11chain 'B' and (resseq 226:393)
12X-RAY DIFFRACTION12chain 'B' and (resseq 394:460)
13X-RAY DIFFRACTION13chain 'B' and (resseq 461:507)
14X-RAY DIFFRACTION14chain 'D' and (resseq -3:1)
15X-RAY DIFFRACTION15chain 'D' and (resseq 2:6)
16X-RAY DIFFRACTION16chain 'D' and (resseq 7:16)
17X-RAY DIFFRACTION17chain 'D' and (resseq 17:21)
18X-RAY DIFFRACTION18chain 'D' and (resseq 22:26)
19X-RAY DIFFRACTION19chain 'D' and (resseq 27:37)
20X-RAY DIFFRACTION20chain 'D' and (resseq 38:46)

+
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