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- PDB-1m5n: Crystal structure of HEAT repeats (1-11) of importin b bound to t... -

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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 subunitImportin
  • 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 / establishment of mitotic spindle localization / astral microtubule organization / cAMP metabolic process / 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 / establishment of mitotic spindle localization / astral microtubule organization / cAMP metabolic process / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of cholesterol biosynthesis by SREBP (SREBF) / ribosomal protein import into nucleus / importin-alpha family protein binding / NS1 Mediated Effects on Host Pathways / Initiation of Nuclear Envelope (NE) Reformation / NLS-dependent protein nuclear import complex / Apoptosis induced DNA fragmentation / Nuclear import of Rev protein / negative regulation of chondrocyte differentiation / Class B/2 (Secretin family receptors) / Postmitotic nuclear pore complex (NPC) reformation / osteoblast development / nuclear import signal receptor activity / peptide hormone receptor binding / nuclear localization sequence binding / NLS-bearing protein import into nucleus / mitotic metaphase chromosome alignment / bone mineralization / mitotic spindle assembly / epidermis development / nuclear pore / Assembly of the ORC complex at the origin of replication / skeletal system development / female pregnancy / Hsp90 protein binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / hormone activity / ISG15 antiviral mechanism / small GTPase binding / cytoplasmic stress granule / protein import into nucleus / specific granule lumen / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / cell-cell signaling / nuclear envelope / G alpha (s) signalling events / regulation of gene expression / nuclear membrane / ficolin-1-rich granule lumen / protein domain specific binding / negative regulation of cell population proliferation / positive regulation of cell population proliferation / Neutrophil degranulation / Golgi apparatus / enzyme binding / extracellular space / RNA binding / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
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 profile. / Importin-beta N-terminal domain / Importin-beta N-terminal domain ...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 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

#1: Protein Importin beta-1 subunit / Importin / 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 / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 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

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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

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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

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