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- PDB-1ibr: COMPLEX OF RAN WITH IMPORTIN BETA -

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Basic information

Entry
Database: PDB / ID: 1ibr
TitleCOMPLEX OF RAN WITH IMPORTIN BETA
Components
  • GTP-binding nuclear protein RAN
  • Importin beta-1 subunit
Keywordscell cycle / translation / SMALL GTPASE / NUCLEAR TRANSPORT RECEPTOR
Function / homology
Function and homology information


RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / astral microtubule organization / establishment of mitotic spindle localization / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / manchette ...RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / astral microtubule organization / establishment of mitotic spindle localization / RNA nuclear export complex / pre-miRNA export from nucleus / snRNA import into nucleus / manchette / cellular response to mineralocorticoid stimulus / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / ribosomal protein import into nucleus / Initiation of Nuclear Envelope (NE) Reformation / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / Apoptosis induced DNA fragmentation / 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 / nuclear localization sequence binding / mitotic metaphase chromosome alignment / dynein intermediate chain binding / NLS-bearing protein import into nucleus / mitotic sister chromatid segregation / spermatid development / ribosomal large subunit export from nucleus / mitotic spindle assembly / sperm flagellum / viral process / nuclear pore / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / protein export from nucleus / centriole / Assembly of the ORC complex at the origin of replication / mitotic spindle organization / male germ cell nucleus / hippocampus development / Transcriptional regulation by small RNAs / Hsp90 protein binding / recycling endosome / G protein activity / ISG15 antiviral mechanism / small GTPase binding / positive regulation of protein import into nucleus / specific granule lumen / cytoplasmic stress granule / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / GDP binding / Interferon alpha/beta signaling / 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 / nuclear membrane / ficolin-1-rich granule lumen / cadherin binding / protein heterodimerization activity / protein domain specific binding / cell division / GTPase activity / chromatin binding / Neutrophil degranulation / chromatin / GTP binding / nucleolus / enzyme binding / magnesium ion binding / protein-containing complex / RNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Importin beta family / HEAT-like repeat / 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 / HEAT repeat profile. / HEAT, type 2 ...Importin beta family / HEAT-like repeat / 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 / HEAT repeat profile. / HEAT, type 2 / Armadillo/beta-catenin-like repeat / Leucine-rich Repeat Variant / Armadillo/beta-catenin-like repeats / Armadillo / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTP-binding nuclear protein Ran / Importin subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å
AuthorsVetter, I.R. / Arndt, A. / Kutay, U. / Goerlich, D. / Wittinghofer, A.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 1999
Title: Structural view of the Ran-Importin beta interaction at 2.3 A resolution
Authors: Vetter, I.R. / Arndt, A. / Kutay, U. / Gorlich, D. / Wittinghofer, A.
#1: Journal: Embo J. / Year: 1996
Title: Identification of Different Roles for Rangdp and Rangtp in Nuclear Protein Import
Authors: Goerlich, D. / Pante, N. / Kutay, U. / Aebi, U. / Bischoff, F.R.
#2: Journal: Curr.Biol. / Year: 1995
Title: Two Different Subunits of Importin Cooperate to Recognize Nuclear Envelope Localisation Signals and Bind Them to the Nuclear Pore Envelope
Authors: Goerlich, D. / Kostka, S. / Kraft, R. / Dingwall, C. / Laskey, R.A. / Hartmann, E. / Prehn, S.
#3: Journal: J.Cell Biol. / Year: 1995
Title: Sequence and Characterization of Cytoplasmic Nuclear Protein Import Factor P97
Authors: Chi, N.C. / Adam, E.J. / Adam, S.A.
History
DepositionMay 14, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jun 3, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_conn.ptnr2_label_seq_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 RAN
B: Importin beta-1 subunit
C: GTP-binding nuclear protein RAN
D: Importin beta-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,9528
Polymers151,8594
Non-polymers1,0934
Water5,621312
1
A: GTP-binding nuclear protein RAN
B: Importin beta-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4764
Polymers75,9302
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-19 kcal/mol
Surface area27470 Å2
MethodPISA
2
C: GTP-binding nuclear protein RAN
D: Importin beta-1 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,4764
Polymers75,9302
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.700, 108.950, 114.050
Angle α, β, γ (deg.)90.00, 100.66, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein GTP-binding nuclear protein RAN / RAN / TC4 / Ran GTPase / Androgen receptor-associated protein 24


Mass: 24456.105 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET3D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: P62826
#2: Protein Importin beta-1 subunit / KARYOPHERIN BETA-1 subunit / P95 / Nuclear factor P97 / Importin 90


Mass: 51473.633 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-462 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q14974
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.9 Å3/Da / Density % sol: 50.1 %
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
19.5 %PEG400011
2110 mMcalcium acetate11
3100 mMMES11
40.5 %dioxane11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 25, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.3→28.7 Å / Num. obs: 69758 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.036 / Rsym value: 0.036 / Net I/σ(I): 28.1
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.011 / Mean I/σ(I) obs: 8 / Rsym value: 0.011 / % possible all: 93.8
Reflection
*PLUS
Num. measured all: 354933
Reflection shell
*PLUS
% possible obs: 93.8 % / Mean I/σ(I) obs: 8.02

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Processing

Software
NameVersionClassification
XDSdata scaling
XSCALEdata scaling
MLPHAREphasing
CNS0.5refinement
XDSdata reduction
RefinementMethod to determine structure: MIR / Resolution: 2.3→28.7 Å / Rfactor Rfree error: 0.003 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.272 6821 10.1 %RANDOM
Rwork0.245 ---
all-67812 --
obs-67812 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.89 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 42.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.28 Å20 Å23.99 Å2
2--4.56 Å20 Å2
3----0.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9739 0 66 312 10117
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scbond_it1.652
X-RAY DIFFRACTIONc_scangle_it2.482.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 1091 9.9 %
Rwork0.298 9874 -
obs--94 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3GNP.PAR
X-RAY DIFFRACTION4WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 28.7 Å / σ(F): 0 / % reflection Rfree: 10.1 % / Rfactor obs: 0.246
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 42.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1
X-RAY DIFFRACTIONc_mcbond_it1.131.5
X-RAY DIFFRACTIONc_scbond_it1.652
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scangle_it2.482.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.343 / % reflection Rfree: 9.9 % / Rfactor Rwork: 0.298

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