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- PDB-5j8e: Crystal structure of human Hook3's conserved Hook domain -

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Basic information

Entry
Database: PDB / ID: 5j8e
TitleCrystal structure of human Hook3's conserved Hook domain
ComponentsProtein Hook homolog 3
KeywordsPROTEIN TRANSPORT / calponin homology Hook cargo adaptor
Function / homology
Function and homology information


FHF complex / interkinetic nuclear migration / protein localization to perinuclear region of cytoplasm / microtubule anchoring at centrosome / Golgi localization / dynein light chain binding / neuronal stem cell population maintenance / endosome organization / cytoskeleton-dependent intracellular transport / early endosome to late endosome transport ...FHF complex / interkinetic nuclear migration / protein localization to perinuclear region of cytoplasm / microtubule anchoring at centrosome / Golgi localization / dynein light chain binding / neuronal stem cell population maintenance / endosome organization / cytoskeleton-dependent intracellular transport / early endosome to late endosome transport / cis-Golgi network / dynein light intermediate chain binding / protein localization to centrosome / dynein intermediate chain binding / lysosome organization / endosome to lysosome transport / pericentriolar material / dynactin binding / centriolar satellite / cytoplasmic microtubule organization / negative regulation of neurogenesis / protein transport / microtubule binding / microtubule / centrosome / identical protein binding / cytoplasm
Similarity search - Function
Hook, C-terminal / HOOK protein coiled-coil region / HOOK, N-terminal / HOOK domain / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein Hook homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSchroeder, C.M. / Ekiert, D.C. / Vale, R.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J.Cell Biol. / Year: 2016
Title: Assembly and activation of dynein-dynactin by the cargo adaptor protein Hook3.
Authors: Schroeder, C.M. / Vale, R.D.
History
DepositionApr 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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: Protein Hook homolog 3
B: Protein Hook homolog 3


Theoretical massNumber of molelcules
Total (without water)37,4292
Polymers37,4292
Non-polymers00
Water3,261181
1
A: Protein Hook homolog 3


Theoretical massNumber of molelcules
Total (without water)18,7141
Polymers18,7141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Protein Hook homolog 3


Theoretical massNumber of molelcules
Total (without water)18,7141
Polymers18,7141
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-17 kcal/mol
Surface area14980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.920, 75.880, 111.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-278-

HOH

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Components

#1: Protein Protein Hook homolog 3 / hHK3


Mass: 18714.488 Da / Num. of mol.: 2 / Fragment: UNP residues 1-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HOOK3 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86VS8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 1.92 Å3/Da / Density % sol: 36.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2 M sodium formate, 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.12 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2014
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12 Å / Relative weight: 1
ReflectionResolution: 1.7→45.019 Å / Num. obs: 32558 / % possible obs: 99.7 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.36
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.952 / Mean I/σ(I) obs: 1.1 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WIX

1wix


Resolution: 1.7→45.019 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.95
RfactorNum. reflection% reflectionSelection details
Rfree0.2139 1393 4.28 %Random selection
Rwork0.1842 ---
obs0.1854 32546 99.67 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.7→45.019 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2417 0 0 181 2598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062461
X-RAY DIFFRACTIONf_angle_d0.9123334
X-RAY DIFFRACTIONf_dihedral_angle_d13.933924
X-RAY DIFFRACTIONf_chiral_restr0.035389
X-RAY DIFFRACTIONf_plane_restr0.003431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.76080.33061360.30333039X-RAY DIFFRACTION100
1.7608-1.83130.3341360.28033048X-RAY DIFFRACTION100
1.8313-1.91460.28071380.24093085X-RAY DIFFRACTION100
1.9146-2.01560.24261380.20493107X-RAY DIFFRACTION100
2.0156-2.14180.24551380.18513065X-RAY DIFFRACTION100
2.1418-2.30720.23541380.17163109X-RAY DIFFRACTION100
2.3072-2.53940.20171400.18133110X-RAY DIFFRACTION100
2.5394-2.90680.21681400.17443147X-RAY DIFFRACTION100
2.9068-3.6620.21311430.17393166X-RAY DIFFRACTION100
3.662-45.03470.17831460.1733277X-RAY DIFFRACTION98
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)
11.40990.15920.89260.47181.04432.543-0.1057-0.18210.3616-0.1419-0.02530.0237-0.16350.00580.04650.27740.0066-0.01320.2448-0.05440.318711.440917.398469.4566
21.32530.1970.4010.6193-1.1532.6223-0.02090.13230.3860.15130.0150.043-0.1915-0.06320.05140.2650.02370.02080.22780.05540.31395.277318.05343.7378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1Chain A
2X-RAY DIFFRACTION2Chain B

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