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- PDB-5tqc: Crystal structure of transport factor karyopherin-beta 2 in compl... -

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Basic information

Entry
Database: PDB / ID: 5tqc
TitleCrystal structure of transport factor karyopherin-beta 2 in complex with the PY-NLS of ribosomal protein L4 (RpL4)
Components
  • 60S ribosomal protein L4-like protein
  • Transportin-1,Transportin-1
KeywordsRIBOSOMAL PROTEIN / Karyopherin
Function / homology
Function and homology information


Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / nuclear localization sequence binding / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / small GTPase binding / protein import into nucleus / cilium / structural constituent of ribosome / ribosome ...Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA / Intraflagellar transport / nuclear localization sequence binding / Postmitotic nuclear pore complex (NPC) reformation / nuclear import signal receptor activity / small GTPase binding / protein import into nucleus / cilium / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / nucleolus / RNA binding / extracellular exosome / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Importin beta family / HEAT-like repeat / HEAT repeat / HEAT repeat / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant ...Importin beta family / HEAT-like repeat / HEAT repeat / HEAT repeat / Importin-beta N-terminal domain / Importin-beta N-terminal domain / Importin-beta N-terminal domain profile. / Importin-beta, N-terminal domain / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L4, eukaryotic and archaeal type / Armadillo-like helical / Alpha Horseshoe / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L4/L1 family / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
60S ribosomal protein L4-like protein / Transportin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Chaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHuber, F.M. / Hoelz, A.
Funding support United States, 2items
OrganizationGrant numberCountry
Heritage Medical Research Institute United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nat Commun / Year: 2017
Title: Molecular basis for protection of ribosomal protein L4 from cellular degradation.
Authors: Huber, F.M. / Hoelz, A.
History
DepositionOct 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transportin-1,Transportin-1
B: 60S ribosomal protein L4-like protein


Theoretical massNumber of molelcules
Total (without water)101,3042
Polymers101,3042
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-4 kcal/mol
Surface area38620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.630, 130.700, 174.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Transportin-1,Transportin-1 / Importin beta-2 / Karyopherin beta-2 / M9 region interaction protein / MIP


Mass: 98139.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNPO1, KPNB2, MIP1, TRN / Production host: Escherichia coli (E. coli) / References: UniProt: Q92973
#2: Protein/peptide 60S ribosomal protein L4-like protein


Mass: 3164.839 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0061540 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SFC3

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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: 3.84 Å3/Da / Density % sol: 67.94 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.5 M Sodium citrate tribasic 0.1 M BIS-TRIS-propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 32119 / % possible obs: 99.9 % / Redundancy: 13.2 % / CC1/2: 0.999 / Net I/σ(I): 20.7
Reflection shellHighest resolution: 3 Å / Redundancy: 13.7 % / Mean I/σ(I) obs: 1.64 / CC1/2: 0.757 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JLQ

4jlq


Resolution: 3→45.671 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2379 1606 5.01 %
Rwork0.2081 --
obs0.2096 32065 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→45.671 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6750 0 0 0 6750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026894
X-RAY DIFFRACTIONf_angle_d0.6659363
X-RAY DIFFRACTIONf_dihedral_angle_d8.4362594
X-RAY DIFFRACTIONf_chiral_restr0.0431075
X-RAY DIFFRACTIONf_plane_restr0.0031204
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.09680.35431420.31412688X-RAY DIFFRACTION99
3.0968-3.20750.30781440.28972745X-RAY DIFFRACTION100
3.2075-3.33590.33831430.27992712X-RAY DIFFRACTION100
3.3359-3.48760.3331440.28312731X-RAY DIFFRACTION100
3.4876-3.67140.32391450.2522757X-RAY DIFFRACTION100
3.6714-3.90140.30341460.22882757X-RAY DIFFRACTION100
3.9014-4.20240.21971450.2122755X-RAY DIFFRACTION100
4.2024-4.62490.26271460.20162775X-RAY DIFFRACTION100
4.6249-5.29330.24761470.20532800X-RAY DIFFRACTION100
5.2933-6.66570.23621480.22232799X-RAY DIFFRACTION100
6.6657-45.67630.16021560.15372940X-RAY DIFFRACTION99

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