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- PDB-5vch: Crystal structure of full-length Kluyveromyces lactis Kap123 -

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Basic information

Entry
Database: PDB / ID: 5vch
TitleCrystal structure of full-length Kluyveromyces lactis Kap123
ComponentsKap123
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 / 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 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsAn, S. / Yoon, J. / Song, J.-J. / Cho, U.-S.
Funding support United States, 4items
OrganizationGrant numberCountry
American Diabetes Association1-16-JDF-017 United States
March of dimesN019154-00 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)AG050903 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK111465 United States
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
DepositionMar 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kap123
B: Kap123


Theoretical massNumber of molelcules
Total (without water)247,0632
Polymers247,0632
Non-polymers00
Water7,386410
1
A: Kap123


Theoretical massNumber of molelcules
Total (without water)123,5321
Polymers123,5321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Kap123


Theoretical massNumber of molelcules
Total (without water)123,5321
Polymers123,5321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.050, 88.120, 102.010
Angle α, β, γ (deg.)79.19, 80.03, 70.98
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.68 Å3/Da / Density % sol: 54.18 % / 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-D / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.35→45.52 Å / Num. obs: 105309 / % possible obs: 99.6 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.056 / Net I/σ(I): 21.3
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 7667 / Rpim(I) all: 0.358 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
SHELXDESHELXC/D/Ephasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→33.001 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.06 / Phase error: 24.74 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2349 1999 1.93 %
Rwork0.2099 --
obs0.2104 103373 97.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.35→33.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15824 0 0 410 16234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916076
X-RAY DIFFRACTIONf_angle_d1.0121826
X-RAY DIFFRACTIONf_dihedral_angle_d18.5129851
X-RAY DIFFRACTIONf_chiral_restr0.0552641
X-RAY DIFFRACTIONf_plane_restr0.0072808
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.40880.29611330.29156754X-RAY DIFFRACTION91
2.4088-2.47390.30971350.2846836X-RAY DIFFRACTION92
2.4739-2.54660.31061390.2667020X-RAY DIFFRACTION95
2.5466-2.62880.28811410.25047212X-RAY DIFFRACTION97
2.6288-2.72270.25651430.24357206X-RAY DIFFRACTION98
2.7227-2.83170.2691440.23397333X-RAY DIFFRACTION99
2.8317-2.96050.29691450.2377325X-RAY DIFFRACTION99
2.9605-3.11640.2521450.23367356X-RAY DIFFRACTION100
3.1164-3.31150.2681460.23187385X-RAY DIFFRACTION100
3.3115-3.56690.24971460.2157412X-RAY DIFFRACTION100
3.5669-3.92540.23071460.18797397X-RAY DIFFRACTION100
3.9254-4.49220.16421450.16087388X-RAY DIFFRACTION100
4.4922-5.6550.19831460.16997406X-RAY DIFFRACTION100
5.655-33.00450.16731450.16677344X-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)
12.8312-0.2314-1.31480.97890.11141.5183-0.11780.3252-0.24920.0187-0.00530.29850.0982-0.51870.07760.0962-0.0176-0.01380.3836-0.0640.323289.099-31.574652.8657
20.3293-0.70250.20794.2014-0.59850.7443-0.0686-0.00710.0350.01280.17360.16080.0808-0.0687-0.08040.3267-0.12220.06410.13770.04150.22897.407-25.8261102.2673
30.65610.12430.29150.90370.41810.91520.0631-0.01740.11390.5095-0.0781-0.1035-0.0014-0.06980.00670.5864-0.0317-0.00480.0942-0.0190.174691.9637-68.9543111.2403
41.3329-1.41110.46543.0562-0.85551.551-0.14540.0349-0.1581-0.00850.0264-0.05810.1377-0.2684-0.02970.30870.0795-0.03780.3570.18830.3549131.9804-65.800777.2524
50.952-0.0627-0.20921.05130.30271.5023-0.1726-0.1755-0.1081-0.09990.2545-0.2513-0.12390.34810.0391-0.04530.08920.00820.21620.00190.1561121.5956-25.116754.3796
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 702 through 1113 )
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 429 )
3X-RAY DIFFRACTION3chain 'A' and (resid 430 through 1113 )
4X-RAY DIFFRACTION4chain 'B' and (resid 41 through 311 )
5X-RAY DIFFRACTION5chain 'B' and (resid 312 through 701 )

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