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- PDB-3wvz: Crystal structure of Hikeshi, a new nuclear transport receptor of... -

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Basic information

Entry
Database: PDB / ID: 3wvz
TitleCrystal structure of Hikeshi, a new nuclear transport receptor of Hsp70
ComponentsProtein Hikeshi
KeywordsTRANSPORT PROTEIN / Nuclear transport receptor
Function / homology
Function and homology information


nuclear import signal receptor activity / Golgi organization / Regulation of HSF1-mediated heat shock response / Hsp70 protein binding / lung development / protein import into nucleus / protein transport / cellular response to heat / nuclear body / nuclear speck ...nuclear import signal receptor activity / Golgi organization / Regulation of HSF1-mediated heat shock response / Hsp70 protein binding / lung development / protein import into nucleus / protein transport / cellular response to heat / nuclear body / nuclear speck / nucleoplasm / nucleus / cytosol
Similarity search - Function
Hikeshi-like domain / OPI10 family / : / Hikeshi-like, N-terminal domain / Hikeshi-like, C-terminal domain
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsSong, J. / Kose, S. / Watanabe, A. / Son, S.Y. / Choi, S. / Hong, R.H. / Yamashita, E. / Park, I.Y. / Imamoto, N. / Lee, S.J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structural and functional analysis of Hikeshi, a new nuclear transport receptor of Hsp70s
Authors: Song, J. / Kose, S. / Watanabe, A. / Son, S.Y. / Choi, S. / Hong, H. / Yamashita, E. / Park, I.Y. / Imamoto, N. / Lee, S.J.
History
DepositionJun 12, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Hikeshi
B: Protein Hikeshi


Theoretical massNumber of molelcules
Total (without water)43,9382
Polymers43,9382
Non-polymers00
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-50 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.138, 137.839, 97.902
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

21B-209-

HOH

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Components

#1: Protein Protein Hikeshi


Mass: 21968.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C11orf73, HSPC138, HSPC179, HSPC248 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53FT3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1M Tris-HCl (pH 7.4), 1M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9192 Å
DetectorDetector: AREA DETECTOR / Date: Nov 8, 2013 / Details: 0.9192
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9192 Å / Relative weight: 1
ReflectionResolution: 1.88→100 Å / Num. all: 32074 / Num. obs: 19445
Reflection shellResolution: 1.88→100 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→39.909 Å / SU ML: 0.22 / σ(F): 1.35 / Phase error: 23.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2278 1697 5.03 %
Rwork0.2071 --
obs0.2082 19445 99.17 %
all-32079 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→39.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 0 226 3097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052949
X-RAY DIFFRACTIONf_angle_d0.8654003
X-RAY DIFFRACTIONf_dihedral_angle_d13.5831036
X-RAY DIFFRACTIONf_chiral_restr0.034437
X-RAY DIFFRACTIONf_plane_restr0.005517
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.88-1.93530.30351380.26152665100
1.9353-1.99780.27691560.24092629100
1.9978-2.06920.2731480.23562636100
2.0692-2.1520.25671420.23082673100
2.152-2.250.26191420.22442664100
2.25-2.36860.26891370.22612683100
2.3686-2.5170.26031250.22762706100
2.517-2.71120.26661450.22892666100
2.7112-2.9840.24951450.21782693100
2.984-3.41560.21821240.20122745100
3.4156-4.30250.1791470.17732713100
4.3025-39.91780.21451480.1962260192
Refinement TLS params.Method: refined / Origin x: 13.6688 Å / Origin y: 25.8113 Å / Origin z: 95.1139 Å
111213212223313233
T0.1608 Å20.0139 Å2-0.0054 Å2-0.1652 Å2-0.0003 Å2--0.1494 Å2
L0.062 °20.0064 °20.032 °2-0.2963 °2-0.1579 °2--0.0514 °2
S-0.0073 Å °-0.0532 Å °0.0213 Å °-0.0452 Å °0.0233 Å °0.0075 Å °0.0001 Å °-0.0267 Å °-0 Å °
Refinement TLS groupSelection details: all

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