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- PDB-2hkq: Crystal structure of the C-terminal domain of human EB1 in comple... -

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Basic information

Entry
Database: PDB / ID: 2hkq
TitleCrystal structure of the C-terminal domain of human EB1 in complex with the CAP-Gly domain of human Dynactin-1 (p150-Glued)
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
Function / homology
Function and homology information


cell cortex region / protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / centriolar subdistal appendage / positive regulation of neuromuscular junction development / mitotic spindle astral microtubule end / centriole-centriole cohesion / microtubule anchoring at centrosome / maintenance of synapse structure ...cell cortex region / protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / centriolar subdistal appendage / positive regulation of neuromuscular junction development / mitotic spindle astral microtubule end / centriole-centriole cohesion / microtubule anchoring at centrosome / maintenance of synapse structure / ventral spinal cord development / protein localization to microtubule / microtubule plus-end / mitotic spindle microtubule / nuclear membrane disassembly / cell projection membrane / positive regulation of microtubule nucleation / XBP1(S) activates chaperone genes / attachment of mitotic spindle microtubules to kinetochore / melanosome transport / microtubule bundle formation / microtubule plus-end binding / non-motile cilium assembly / dynein complex / retrograde transport, endosome to Golgi / protein localization to centrosome / COPI-independent Golgi-to-ER retrograde traffic / microtubule associated complex / neuromuscular process / nuclear migration / negative regulation of microtubule polymerization / mitotic spindle pole / neuromuscular junction development / spindle midzone / cell leading edge / motor behavior / microtubule organizing center / microtubule polymerization / establishment of mitotic spindle orientation / regulation of microtubule polymerization or depolymerization / intercellular bridge / spindle assembly / COPI-mediated anterograde transport / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of microtubule polymerization / neuron projection maintenance / Mitotic Prometaphase / centriole / EML4 and NUDC in mitotic spindle formation / 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 / tubulin binding / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein serine/threonine kinase binding / regulation of mitotic spindle organization / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / RHO GTPases Activate Formins / neuron cellular homeostasis / kinetochore / tau protein binding / spindle / The role of GTSE1 in G2/M progression after G2 checkpoint / Signaling by ALK fusions and activated point mutants / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / spindle pole / mitotic spindle / intracellular protein localization / 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 / identical protein binding / membrane / cytosol / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / 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. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / 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. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / SH3 type barrels. / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
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: 1.86 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)19,5212
Polymers19,5212
Non-polymers00
Water1,33374
1
A: Microtubule-associated protein RP/EB family member 1
B: Dynactin-1

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


Theoretical massNumber of molelcules
Total (without water)39,0434
Polymers39,0434
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)53.156, 79.597, 38.935
Angle α, β, γ (deg.)90.00, 109.29, 90.00
Int Tables number5
Space group name H-MC121
DetailsBiological assambly is dimer of EB1-C (chain A) binds two monomers of Cap-Gly domain(chain B) The biological assembly is generated from the heterodimer in asymmetric unit by the operation: -X+1, Y, -Z

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Components

#1: Protein Microtubule-associated protein RP/EB family member 1 / APC-binding protein EB1 / End-binding protein 1 / EB1


Mass: 9212.031 Da / Num. of mol.: 1 / Fragment: C-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPRE1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15691
#2: Protein Dynactin-1 / 150 kDa dynein-associated polypeptide / DP-150 / DAP-150 / p150-glued / p135


Mass: 10309.413 Da / Num. of mol.: 1 / 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 1.99 Å3/Da / Density % sol: 38.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.3 M Trisodium Citrate, 0.1M HEPES Buffer, pH 7.5, 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 11, 2005
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→42.45 Å / Num. obs: 12595 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.86→1.908 Å / % possible all: 96

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→42.45 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.398 / SU ML: 0.108 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21732 616 4.9 %RANDOM
Rwork0.17686 ---
obs0.17887 11978 97.93 %-
all-11978 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.413 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20 Å2-0.32 Å2
2---0.29 Å20 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.86→42.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1074 0 0 74 1148
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221089
X-RAY DIFFRACTIONr_angle_refined_deg1.441.951465
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5265134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.19224.64356
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.90715195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.66158
X-RAY DIFFRACTIONr_chiral_restr0.1250.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02819
X-RAY DIFFRACTIONr_nbd_refined0.1990.2476
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2769
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.282
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.217
X-RAY DIFFRACTIONr_mcbond_it1.9952674
X-RAY DIFFRACTIONr_mcangle_it3.13731067
X-RAY DIFFRACTIONr_scbond_it4.7934.5451
X-RAY DIFFRACTIONr_scangle_it6.8216398
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 48 -
Rwork0.288 823 -
obs--95.19 %
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)
11.05490.34830.23656.5902-0.76541.44220.0065-0.0526-0.0479-0.1563-0.14140.08850.2498-0.00960.1349-0.16470.02920.0457-0.0588-0.0077-0.165924.27311.92862.001
26.3021.2565-0.25811.41270.36944.34390.07140.00640.27880.0251-0.03980.2559-0.0122-0.3711-0.0316-0.1195-0.0102-0.0073-0.1051-0.0163-0.12398.1514-2.039813.095
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA194 - 2556 - 67
2X-RAY DIFFRACTION2BB26 - 9712 - 83

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