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- PDB-2hkn: Crystal structure of the CAP-Gly domain of human Dynactin-1 (p150... -

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Basic information

Entry
Database: PDB / ID: 2hkn
TitleCrystal structure of the CAP-Gly domain of human Dynactin-1 (p150-Glued)
ComponentsDynactin-1
KeywordsSTRUCTURAL PROTEIN / microtubule binding / cytoskeleton associated protein / p150-glued / Strand swap / EB1 and CLIP-170 binding protein
Function / homology
Function and homology information


cell cortex region / centriolar subdistal appendage / ventral spinal cord development / centriole-centriole cohesion / positive regulation of neuromuscular junction development / microtubule anchoring at centrosome / maintenance of synapse structure / lysosome to ER cholesterol transport / mitotic nuclear membrane disassembly / XBP1(S) activates chaperone genes ...cell cortex region / centriolar subdistal appendage / ventral spinal cord development / centriole-centriole cohesion / positive regulation of neuromuscular junction development / microtubule anchoring at centrosome / maintenance of synapse structure / lysosome to ER cholesterol transport / mitotic nuclear membrane disassembly / XBP1(S) activates chaperone genes / positive regulation of microtubule nucleation / microtubule plus-end / non-motile cilium assembly / motor behavior / neuron cellular homeostasis / retrograde transport, endosome to Golgi / COPI-independent Golgi-to-ER retrograde traffic / microtubule associated complex / nuclear migration / neuromuscular process / intercellular bridge / cell leading edge / neuromuscular junction development / COPI-mediated anterograde transport / positive regulation of microtubule polymerization / cholesterol homeostasis / neuron projection maintenance / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / centriole / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / AURKA Activation by TPX2 / regulation of mitotic spindle organization / establishment of mitotic spindle orientation / tubulin binding / tau protein binding / kinetochore / spindle / microtubule cytoskeleton / Signaling by ALK fusions and activated point mutants / nervous system development / mitotic cell cycle / Regulation of PLK1 Activity at G2/M Transition / nuclear envelope / spindle pole / ciliary basal body / microtubule / cell cortex / microtubule binding / neuron projection / endosome membrane / axon / centrosome / neuronal cell body / protein kinase binding / protein-containing complex / membrane / cytosol / cytoplasm
Similarity search - Function
CAP Gly-rich-like domain / : / Domain of unknown function (DUF8221) / Dynein associated protein / Dynein associated protein / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. ...CAP Gly-rich-like domain / : / Domain of unknown function (DUF8221) / Dynein associated protein / Dynein associated protein / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsHonnappa, S. / Winkler, F.K. / Steinmetz, M.O.
CitationJournal: Mol.Cell / Year: 2006
Title: Key interaction modes of dynamic +TIP networks.
Authors: Honnappa, S. / Okhrimenko, O. / Jaussi, R. / Jawhari, H. / Jelesarov, I. / Winkler, F.K. / Steinmetz, M.O.
History
DepositionJul 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 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
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). IN THE CRYSTAL STRUCTURE, THE BIOLOGICAL UNIT IS A STRAND SWAPPED DIMER DUE TO LOW BUFFER PH AND HIGH PEG CONCENTRATION. HOWEVER, THE MOLECULE IS ACTIVE BIOLOGICALLY AS A MONOMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dynactin-1
B: Dynactin-1


Theoretical massNumber of molelcules
Total (without water)20,6192
Polymers20,6192
Non-polymers00
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3240 Å2
ΔGint-14 kcal/mol
Surface area9190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.300, 55.200, 66.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a Monomer, But in the crystal structure it forms a strand swapped dimer, due to low buffer pH and high PEG concentration

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Components

#1: Protein Dynactin-1 / 150 kDa dynein-associated polypeptide / DP-150 / DAP-150 / p150-glued / p135


Mass: 10309.413 Da / Num. of mol.: 2 / Fragment: CAP-Gly domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCTN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14203
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.93 Å3/Da / Density % sol: 36.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 25% PEG 3350, 0.05M sodium citrate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 21, 2005 / Details: Osmic mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→42.49 Å / Num. obs: 25448 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.86→2 Å / % possible all: 95

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→42.49 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.196 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.144 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25056 684 5 %RANDOM
Rwork0.19932 ---
obs0.20182 13030 99.21 %-
all-13030 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2---0.29 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.87→42.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1132 0 0 60 1192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221145
X-RAY DIFFRACTIONr_angle_refined_deg1.1981.9211534
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6545145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.35722.450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33715193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9161510
X-RAY DIFFRACTIONr_chiral_restr0.0760.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02850
X-RAY DIFFRACTIONr_nbd_refined0.20.2409
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2755
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.272
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3340.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4040.217
X-RAY DIFFRACTIONr_mcbond_it1.9672730
X-RAY DIFFRACTIONr_mcangle_it2.84731134
X-RAY DIFFRACTIONr_scbond_it4.7044.5465
X-RAY DIFFRACTIONr_scangle_it7.3736400
LS refinement shellResolution: 1.87→1.914 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 56 -
Rwork0.255 847 -
obs--90.66 %
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)
10.5147-0.2077-0.53522.5534-3.2095.3064-0.19060.1085-0.153-0.3658-0.0544-0.1690.44970.10960.245-0.0359-0.00170.0324-0.0756-0.0253-0.066213.477119.20013.633
20.9495-0.42220.70981.1749-1.66663.08240.0475-0.1451-0.0205-0.0264-0.0501-0.02750.0903-0.0110.0026-0.1362-0.00520.0036-0.0825-0.0387-0.082710.711237.8184-2.465
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA26 - 9612 - 82
2X-RAY DIFFRACTION2BB26 - 9612 - 82

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