[English] 日本語
Yorodumi
- PDB-1m5n: Crystal structure of HEAT repeats (1-11) of importin b bound to t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1m5n
TitleCrystal structure of HEAT repeats (1-11) of importin b bound to the non-classical NLS(67-94) of PTHrP
Components
  • Importin beta-1 subunit
  • Parathyroid hormone-related protein
KeywordsPROTEIN TRANSPORT / all helical protein / HEAT repeats
Function / homology
Function and homology information


negative regulation of chondrocyte development / regulation of chondrocyte differentiation / RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / astral microtubule organization / cAMP metabolic process / establishment of mitotic spindle localization / Transport of Ribonucleoproteins into the Host Nucleus ...negative regulation of chondrocyte development / regulation of chondrocyte differentiation / RNA import into nucleus / Inhibition of nitric oxide production / mitotic chromosome movement towards spindle pole / endoplasmic reticulum tubular network / astral microtubule organization / cAMP metabolic process / establishment of mitotic spindle localization / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / importin-alpha family protein binding / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / Apoptosis induced DNA fragmentation / nuclear localization sequence binding / ribosomal protein import into nucleus / Initiation of Nuclear Envelope (NE) Reformation / Nuclear import of Rev protein / Class B/2 (Secretin family receptors) / negative regulation of chondrocyte differentiation / Postmitotic nuclear pore complex (NPC) reformation / osteoblast development / nuclear import signal receptor activity / mitotic metaphase chromosome alignment / peptide hormone receptor binding / bone mineralization / mitotic spindle assembly / epidermis development / nuclear pore / Assembly of the ORC complex at the origin of replication / skeletal system development / Hsp90 protein binding / positive regulation of cholesterol biosynthetic process / female pregnancy / hormone activity / small GTPase binding / ISG15 antiviral mechanism / specific granule lumen / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cytoplasmic stress granule / protein import into nucleus / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / nuclear envelope / cell-cell signaling / regulation of gene expression / nuclear membrane / G alpha (s) signalling events / ficolin-1-rich granule lumen / protein domain specific binding / negative regulation of cell population proliferation / positive regulation of cell population proliferation / Neutrophil degranulation / enzyme binding / Golgi apparatus / extracellular space / RNA binding / extracellular exosome / extracellular region / zinc ion binding / nucleoplasm / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Parathyroid hormone-related protein / Parathyroid hormone/parathyroid hormone-related protein / Parathyroid hormone family / Parathyroid hormone family signature. / Parathyroid hormone / Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. ...Parathyroid hormone-related protein / Parathyroid hormone/parathyroid hormone-related protein / Parathyroid hormone family / Parathyroid hormone family signature. / Parathyroid hormone / Importin beta family / HEAT-like repeat / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / HEAT repeat profile. / HEAT, type 2 / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Parathyroid hormone-related protein / Importin subunit beta-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsCingolani, G. / Bednenko, J. / Gillespie, M.T. / Gerace, L.
CitationJournal: Mol.Cell / Year: 2002
Title: Molecular basis for the recognition of a nonclassical nuclear localization signal by importin beta
Authors: Cingolani, G. / Bednenko, J. / Gillespie, M.T. / Gerace, L.
History
DepositionJul 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
S: Importin beta-1 subunit
Q: Parathyroid hormone-related protein


Theoretical massNumber of molelcules
Total (without water)57,1702
Polymers57,1702
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.792, 105.447, 146.738
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThere is one biological assembly [importin b(1-485):PTHrP(67-94)] per asymmetryc unit

-
Components

#1: Protein Importin beta-1 subunit / Karyopherin beta-1 subunit / Nuclear factor P97 / Importin 90


Mass: 53899.285 Da / Num. of mol.: 1 / Fragment: N-terminal domain (Residues 1-485)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTYB4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q14974
#2: Protein/peptide Parathyroid hormone-related protein / PTHrP / PTH-rP


Mass: 3270.812 Da / Num. of mol.: 1 / Fragment: Residues 67-94 / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN HOMO SAPIENS (HUMAN).
References: UniProt: P12272
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 3.14 Å3/Da / Density % sol: 60.8 %
Crystal growTemperature: 298 K / pH: 6
Details: MES, PEG 4000, sodium chloride, Tween, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 6.00
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Conti, E., (1998) Cell, 94, 193.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118-20 %(w/v)PEG40001reservoir
2200 mMsodium acetate1reservoir
3100 mMHEPES1reservoir
420 mM1reservoirCoCl2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.005
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 17, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 16459 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 18.03 % / Biso Wilson estimate: 67.9 Å2 / Rmerge(I) obs: 0.0116 / Rsym value: 0.0116 / Net I/σ(I): 17.32
Reflection shellHighest resolution: 2.9 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.469 / % possible all: 99.3
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 50 Å / Num. measured all: 296796
Reflection shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 3 Å / % possible obs: 99.3 % / Rmerge(I) obs: 0.469

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QGK

1qgk


Resolution: 2.9→50 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1435 -RANDOM
Rwork0.25 ---
obs0.25 14452 10 %-
all-16459 --
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3983 0 0 37 4020
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.9→3 Å /
RfactorNum. reflection
Rfree0.3815 105
Rwork0.3645 -
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor Rwork: 0.25
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.009

+
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