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- PDB-5ve8: Crystal structure of full-length Kluyveromyces lactis Kap123 with... -

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Basic information

Entry
Database: PDB / ID: 5ve8
TitleCrystal structure of full-length Kluyveromyces lactis Kap123 with histone H3 1-28
Components
  • Histone H3
  • Kap123
KeywordsPROTEIN TRANSPORT / Bidding yeast karyopherin / 23 HEAT repeats with a right-handed superhelical solenoid structure / Histone NLS recognition / The extra-long helix of the repeat 23
Function / homology
Function and homology information


nuclear import signal receptor activity / nuclear localization sequence binding / small GTPase binding / protein import into nucleus / nucleosome / protein heterodimerization activity / DNA binding / nucleus / cytoplasm
Similarity search - Function
Importin beta family / TOG domain / TOG / HEAT repeat / HEAT 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. ...Importin beta family / TOG domain / TOG / HEAT repeat / HEAT 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 / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Histone H3 / KLLA0E20769p
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAn, S. / Yoon, J. / Song, J.-J. / Cho, U.-S.
CitationJournal: Elife / Year: 2017
Title: Structure-based nuclear import mechanism of histones H3 and H4 mediated by Kap123.
Authors: An, S. / Yoon, J. / Kim, H. / Song, J.J. / Cho, U.S.
History
DepositionApr 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kap123
B: Kap123
C: Histone H3
E: Histone H3


Theoretical massNumber of molelcules
Total (without water)253,0504
Polymers253,0504
Non-polymers00
Water1,47782
1
A: Kap123
C: Histone H3


Theoretical massNumber of molelcules
Total (without water)126,5252
Polymers126,5252
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-3 kcal/mol
Surface area43450 Å2
MethodPISA
2
B: Kap123
E: Histone H3


Theoretical massNumber of molelcules
Total (without water)126,5252
Polymers126,5252
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-2 kcal/mol
Surface area43080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.098, 88.114, 102.276
Angle α, β, γ (deg.)79.59, 80.77, 70.74
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Kap123


Mass: 123531.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CMF0
#2: Protein/peptide Histone H3


Mass: 2993.515 Da / Num. of mol.: 2 / Fragment: UNP residues 2-29 / Source method: obtained synthetically / Source: (synth.) Kluyveromyces lactis (yeast) / References: UniProt: P61831
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.69 Å3/Da / Density % sol: 54.34 % / Description: brick-shaped crystals
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium cacodylate (pH 6.5), 0.2M sodium acetate, 30% PEG 4000 and 5% Jeffamin M-600

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Data collection

DiffractionMean temperature: 105 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 69157 / % possible obs: 99 % / Redundancy: 4 % / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.042 / Net I/σ(I): 18.8
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 3411 / Rpim(I) all: 0.425 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000HKL2000_v714-Linuxdata processing
HKL-2000HKL2000_v714-Linuxdata scaling
Coot0.8.7model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VCH

5vch


Resolution: 2.7→44.614 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 25.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2297 2000 2.89 %
Rwork0.185 --
obs0.1863 69139 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→44.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16047 0 0 82 16129
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00816283
X-RAY DIFFRACTIONf_angle_d1.01622088
X-RAY DIFFRACTIONf_dihedral_angle_d17.6619983
X-RAY DIFFRACTIONf_chiral_restr0.0542665
X-RAY DIFFRACTIONf_plane_restr0.0072840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6995-2.7670.34361380.28334652X-RAY DIFFRACTION96
2.767-2.84180.3081430.25984810X-RAY DIFFRACTION98
2.8418-2.92540.28811430.23514766X-RAY DIFFRACTION99
2.9254-3.01980.27211410.22934752X-RAY DIFFRACTION99
3.0198-3.12770.30371430.22764799X-RAY DIFFRACTION99
3.1277-3.25290.2821430.22814781X-RAY DIFFRACTION99
3.2529-3.40090.28451440.21224839X-RAY DIFFRACTION99
3.4009-3.58020.24671420.19284803X-RAY DIFFRACTION99
3.5802-3.80440.24491430.18194807X-RAY DIFFRACTION99
3.8044-4.09790.21821440.16854811X-RAY DIFFRACTION99
4.0979-4.50990.17891430.14734806X-RAY DIFFRACTION99
4.5099-5.16170.22491450.15224868X-RAY DIFFRACTION99
5.1617-6.50.21651430.2014812X-RAY DIFFRACTION100
6.5-44.62030.17841450.15814833X-RAY DIFFRACTION99
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)
11.27120.0883-0.61751.3470.31912.313-0.1763-0.0142-0.1979-0.08190.0859-0.1170.13490.2130.06740.19630.03940.0140.3698-0.01290.3563116.3013-30.259452.7611
22.92380.0176-1.07661.9497-0.1971.4018-0.05120.40410.15770.1613-0.00360.2789-0.0359-0.38090.04350.2968-0.0384-0.02330.5662-0.00610.432883.9583-26.505957.2995
30.38-0.63640.31843.574-0.86011.2003-0.0140.01290.03780.04680.11010.341-0.0191-0.0739-0.08320.4507-0.07630.04650.35730.02990.479397.1013-29.7278105.2544
40.83530.27440.17261.24590.72851.45640.1183-0.02680.10690.3638-0.13450.0787-0.02230.0260.01590.5713-0.06780.01240.32330.01350.337888.6281-70.188111.7465
50.6536-0.95850.02222.7783-1.5091.6321-0.0169-0.0023-0.1762-0.1568-0.1068-0.07730.1659-0.09820.06390.56720.0902-0.1270.57120.09590.6378130.8795-65.985278.2831
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 312 through 809 )
2X-RAY DIFFRACTION2chain 'B' and (resid 810 through 1113 )
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 472 )
4X-RAY DIFFRACTION4chain 'A' and (resid 473 through 1113 )
5X-RAY DIFFRACTION5chain 'B' and (resid 41 through 311 )

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