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- PDB-2hl3: Crystal structure of the A49M mutant CAP-Gly domain of human Dyna... -

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Basic information

Entry
Database: PDB / ID: 2hl3
TitleCrystal structure of the A49M mutant CAP-Gly domain of human Dynactin-1 (p150-Glued) in complex with human EB1 C-terminal hexapeptide
Components
  • Dynactin-1
  • Microtubule-associated protein RP/EB family member 1
KeywordsSTRUCTURAL PROTEIN / microtubule binding / dynactin / cytoskeleton associated protein / p150Glued / EB1 / +TIP protein Complex structure / EEY/F-COO- sequence motif / CLIP-170 / alpha-tubulin
Function / homology
Function and homology information


protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / cell cortex region / mitotic spindle astral microtubule end / centriolar subdistal appendage / positive regulation of neuromuscular junction development / centriole-centriole cohesion / microtubule anchoring at centrosome / protein localization to microtubule ...protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / cell cortex region / mitotic spindle astral microtubule end / centriolar subdistal appendage / positive regulation of neuromuscular junction development / centriole-centriole cohesion / microtubule anchoring at centrosome / protein localization to microtubule / maintenance of synapse structure / ventral spinal cord development / cell projection membrane / microtubule plus-end / mitotic spindle microtubule / nuclear membrane disassembly / XBP1(S) activates chaperone genes / positive regulation of microtubule nucleation / attachment of mitotic spindle microtubules to kinetochore / melanosome transport / microtubule bundle formation / microtubule plus-end binding / non-motile cilium assembly / protein localization to centrosome / dynein complex / retrograde transport, endosome to Golgi / COPI-independent Golgi-to-ER retrograde traffic / microtubule associated complex / nuclear migration / neuromuscular process / mitotic spindle pole / spindle midzone / negative regulation of microtubule polymerization / neuromuscular junction development / motor behavior / cell leading edge / microtubule polymerization / microtubule organizing center / establishment of mitotic spindle orientation / regulation of microtubule polymerization or depolymerization / intercellular bridge / COPI-mediated anterograde transport / cytoplasmic microtubule / spindle assembly / positive regulation of microtubule polymerization / neuron projection maintenance / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / protein serine/threonine kinase binding / AURKA Activation by TPX2 / regulation of mitotic spindle organization / Resolution of Sister Chromatid Cohesion / centriole / tubulin binding / RHO GTPases Activate Formins / neuron cellular homeostasis / kinetochore / tau protein binding / spindle / spindle pole / The role of GTSE1 in G2/M progression after G2 checkpoint / mitotic spindle / Separation of Sister Chromatids / Signaling by ALK fusions and activated point mutants / intracellular protein localization / Regulation of PLK1 Activity at G2/M Transition / nuclear envelope / cell migration / nervous system development / mitotic cell cycle / microtubule cytoskeleton / cell cortex / microtubule binding / microtubule / neuron projection / cilium / ciliary basal body / cadherin binding / axon / cell division / focal adhesion / neuronal cell body / centrosome / protein kinase binding / Golgi apparatus / RNA binding / membrane / identical protein binding / cytoplasm / cytosol
Similarity search - Function
CAP Gly-rich-like domain / Dynein associated protein / Dynein associated protein / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / CAP-Gly domain signature. / CAP Gly-rich domain ...CAP Gly-rich-like domain / Dynein associated protein / Dynein associated protein / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Dynactin subunit 1 / Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 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 6, 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: Version format compliance
Revision 1.3Jul 29, 2015Group: Database references / Structure summary
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). IN THE CRYSTAL STRUCTURE, THE BIOLOGICAL UNIT IS COMPRISED OF CHAINS A, B AND C. HOWEVER, THE ACTIVE BIOLOGICAL UNIT IS A COMPLEX OF CHAINS A AND C.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dynactin-1
B: Dynactin-1
C: Microtubule-associated protein RP/EB family member 1


Theoretical massNumber of molelcules
Total (without water)21,5653
Polymers21,5653
Non-polymers00
Water1,20767
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.062, 55.068, 66.221
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 10369.531 Da / Num. of mol.: 2 / Fragment: CAP-Gly domain / Mutation: A49M
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: Protein/peptide Microtubule-associated protein RP/EB family member 1 / APC-binding protein EB1 / End-binding protein 1 / EB1


Mass: 825.773 Da / Num. of mol.: 1 / Fragment: C-terminal hexapeptide / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human).
References: UniProt: Q15691
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 1.82 Å3/Da / Density % sol: 32.42 %
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: Jan 8, 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: 2.03→42.33 Å / Num. all: 10303 / Num. obs: 10303 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.03→2.085 Å / % possible all: 92.17

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→42.33 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.683 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.197 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22339 488 4.7 %RANDOM
Rwork0.18302 ---
obs0.18483 9814 97.03 %-
all-9814 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.088 Å2
Baniso -1Baniso -2Baniso -3
1-1.35 Å20 Å20 Å2
2---0.49 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.03→42.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1169 0 0 67 1236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221213
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.9311622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5515149
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.20422.85756
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56715209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9181510
X-RAY DIFFRACTIONr_chiral_restr0.0760.2173
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02906
X-RAY DIFFRACTIONr_nbd_refined0.1890.2504
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2807
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.292
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.212
X-RAY DIFFRACTIONr_mcbond_it1.9592761
X-RAY DIFFRACTIONr_mcangle_it3.1231182
X-RAY DIFFRACTIONr_scbond_it4.8254.5512
X-RAY DIFFRACTIONr_scangle_it7.156440
LS refinement shellResolution: 2.03→2.085 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 32 -
Rwork0.188 674 -
obs--92.17 %

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