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- PDB-3tq7: EB1c/EB3c heterodimer in complex with the CAP-Gly domain of P150glued -

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Basic information

Entry
Database: PDB / ID: 3tq7
TitleEB1c/EB3c heterodimer in complex with the CAP-Gly domain of P150glued
Components
  • Dynactin subunit 1
  • Microtubule-associated protein RP/EB family member 1
  • Microtubule-associated protein RP/EB family member 3
KeywordsPROTEIN BINDING / CAP-Gly domain / protein-protein interaction / microtubule binding / cytoskeleton
Function / homology
Function and homology information


protein localization to astral microtubule / cell cortex region / protein localization to mitotic spindle / neuron to neuron synapse / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / centriolar subdistal appendage / centriole-centriole cohesion / positive regulation of neuromuscular junction development / microtubule anchoring at centrosome ...protein localization to astral microtubule / cell cortex region / protein localization to mitotic spindle / neuron to neuron synapse / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / centriolar subdistal appendage / centriole-centriole cohesion / positive regulation of neuromuscular junction development / microtubule anchoring at centrosome / lysosome to ER cholesterol transport / maintenance of synapse structure / ventral spinal cord development / protein localization to microtubule / dynein complex / cell projection membrane / microtubule plus-end / mitotic spindle microtubule / mitotic nuclear membrane disassembly / XBP1(S) activates chaperone genes / positive regulation of microtubule nucleation / positive regulation of dendritic spine morphogenesis / attachment of mitotic spindle microtubules to kinetochore / non-motile cilium assembly / microtubule bundle formation / microtubule plus-end binding / motor behavior / retrograde transport, endosome to Golgi / neuromuscular process / COPI-independent Golgi-to-ER retrograde traffic / microtubule associated complex / nuclear migration / mitotic spindle pole / intercellular bridge / spindle midzone / establishment of mitotic spindle orientation / negative regulation of microtubule polymerization / cell leading edge / neuromuscular junction development / microtubule polymerization / microtubule organizing center / regulation of microtubule polymerization / Dengue Virus Attachment and Entry / regulation of microtubule polymerization or depolymerization / positive regulation of microtubule polymerization / COPI-mediated anterograde transport / cytoplasmic microtubule / spindle assembly / behavioral response to cocaine / cholesterol homeostasis / neuron projection maintenance / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / 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 / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / AURKA Activation by TPX2 / Resolution of Sister Chromatid Cohesion / protein serine/threonine kinase activator activity / regulation of mitotic spindle organization / protein serine/threonine kinase binding / neuron cellular homeostasis / tubulin binding / RHO GTPases Activate Formins / tau protein binding / spindle / kinetochore / spindle pole / intracellular protein localization / The role of GTSE1 in G2/M progression after G2 checkpoint / Signaling by ALK fusions and activated point mutants / Separation of Sister Chromatids / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / nuclear envelope / mitotic cell cycle / cell migration / nervous system development / midbody / cell cortex / microtubule binding / ciliary basal body / microtubule / endosome membrane / neuron projection / cadherin binding / axon / cell division / focal adhesion / neuronal cell body / centrosome / protein kinase binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / CAP Gly-rich-like domain / : / Domain of unknown function (DUF8221) / 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. ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / CAP Gly-rich-like domain / : / Domain of unknown function (DUF8221) / 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 / Microtubule-associated protein RP/EB family member 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDe Groot, C.O. / Scharer, M.A. / Capitani, G. / Steinmetz, M.O.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Interaction of mammalian end binding proteins with CAP-Gly domains of CLIP-170 and p150(glued).
Authors: Bjelic, S. / De Groot, C.O. / Scharer, M.A. / Jaussi, R. / Bargsten, K. / Salzmann, M. / Frey, D. / Capitani, G. / Kammerer, R.A. / Steinmetz, M.O.
History
DepositionSep 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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 / 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: Microtubule-associated protein RP/EB family member 3
P: Dynactin subunit 1
Q: Dynactin subunit 1


Theoretical massNumber of molelcules
Total (without water)34,1494
Polymers34,1494
Non-polymers00
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-45 kcal/mol
Surface area14020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.150, 103.560, 48.130
Angle α, β, γ (deg.)90.00, 113.64, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN P AND (RESSEQ 27:97 ) AND (NOT ELEMENT H)
211CHAIN Q AND (RESSEQ 27:97 ) AND (NOT ELEMENT H)
112CHAIN A AND (RESSEQ 203:207 OR RESSEQ 210:218 OR RESSEQ...
212CHAIN B AND (RESSEQ 212:216 OR RESSEQ 219:227 OR RESSEQ...

NCS ensembles :
ID
1
2

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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: 9067.903 Da / Num. of mol.: 1 / Fragment: EB1 c-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPRE1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q15691
#2: Protein Microtubule-associated protein RP/EB family member 3 / EB1 protein family member 3 / EBF3 / End-binding protein 3 / EB3 / RP3


Mass: 9517.311 Da / Num. of mol.: 1 / Fragment: EB3 c-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPRE3 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9UPY8
#3: Protein Dynactin subunit 1 / 150 kDa dynein-associated polypeptide / DAP-150 / DP-150 / p135 / p150-glued


Mass: 7781.931 Da / Num. of mol.: 2 / Fragment: CAP-Gly domain of P150glued / Mutation: A49M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCTN1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q14203
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.75 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 15% PEG 4000, 0.1M Tris-HCl, 0.2M Magnesium chloride hexahydrate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2009 / Details: dynamically bendable mirror
RadiationMonochromator: LN2 cooled fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→44.095 Å / Num. obs: 15694 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 13.4 % / Biso Wilson estimate: 59.999 Å2 / Net I/σ(I): 27.64
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allRsym valueDiffraction-ID% possible all
2.3-2.414.25.42193842199.1
2.4-2.514.18.22162926.2199
2.5-2.813.613.31366215.6199.5
2.8-313.322.0317009.3199.7
3-412.936.8535815.5183.6
4-201357.8831303.6199.2

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1wu9

1wu9


Resolution: 2.3→44.09 Å / SU ML: 0.39 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 34.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2811 971 6.2 %random
Rwork0.2255 ---
obs0.229 15666 95.34 %-
Solvent computationShrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.324 Å2 / ksol: 0.305 e/Å3
Displacement parametersBiso mean: 69.585 Å2
Baniso -1Baniso -2Baniso -3
1--9.9429 Å2-0 Å26.9514 Å2
2---19.8847 Å20 Å2
3---29.8277 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2016 0 0 36 2052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072047
X-RAY DIFFRACTIONf_angle_d1.0272745
X-RAY DIFFRACTIONf_dihedral_angle_d14.13761
X-RAY DIFFRACTIONf_chiral_restr0.071306
X-RAY DIFFRACTIONf_plane_restr0.003352
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11P547X-RAY DIFFRACTIONPOSITIONAL
12Q547X-RAY DIFFRACTIONPOSITIONAL0.041
21A29X-RAY DIFFRACTIONPOSITIONAL
22B29X-RAY DIFFRACTIONPOSITIONAL0.13
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.42130.35251440.30242174X-RAY DIFFRACTION99
2.4213-2.5730.3071430.24732181X-RAY DIFFRACTION99
2.573-2.77160.35061450.25592188X-RAY DIFFRACTION100
2.7716-3.05050.33741430.24752166X-RAY DIFFRACTION100
3.0505-3.49170.32961290.25281946X-RAY DIFFRACTION88
3.4917-4.39830.26421200.20631819X-RAY DIFFRACTION83
4.3983-40.57370.23461470.20572221X-RAY DIFFRACTION100
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)
10.632-0.1247-0.94240.00670.29481.6081-0.5936-0.03150.14670.9870.5037-0.2663-0.4012-1.3815-0.03430.92380.1379-0.11610.5392-0.00430.148614.320624.378522.6289
22.38810.3582-1.64321.54560.83291.9408-0.1091-0.22060.8826-0.25520.27040.8001-0.1503-0.0482-0.19360.44830.0542-0.03210.36550.11810.42558.403731.7904-1.8058
35.0322-1.5259-4.95739.0471-6.28022.00630.78541.6095-0.56570.42450.28632.049-0.3372-1.19311.4130.45420.01310.23150.7743-0.56521.433.281746.42712.4173
41.4196-0.01230.92680.3503-0.54171.1853-0.50940.16240.1930.752-0.18750.73810.11270.081-0.02150.86780.06450.29780.3416-0.03070.46095.831426.812624.2107
52.5967-0.2665-1.89654.3871-0.69731.4851-0.585-0.285-0.4569-0.88180.46660.33330.34910.30610.02290.56780.0001-0.04710.43780.01370.356311.393621.0551-2.0226
63.0407-3.0551-1.23783.07491.07362.45220.55470.28270.29810.82090.5598-1.0232-0.0971-0.210.41930.78830.1633-0.28930.33040.26881.70616.73564.909311.0112
71.93011.05630.49742.3894-1.65812.33930.10210.2819-1.03970.4970.1965-0.54940.06510.1469-0.13630.34660.07170.00820.4281-0.04910.62698.58533.10914.4401
81.8155-0.31790.76821.8420.31642.5499-0.07920.28421.16820.2811-0.0958-0.1855-0.05160.15810.10480.3962-0.009-0.02210.43070.11530.732211.90248.93677.0244
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 198:219)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 220:251)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 265:268)
4X-RAY DIFFRACTION4(CHAIN B AND RESID 204:228)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 229:259)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 278:281)
7X-RAY DIFFRACTION7(CHAIN P AND RESID 27:97)
8X-RAY DIFFRACTION8(CHAIN Q AND RESID 27:97)

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