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- PDB-3gjo: Crystal structure of human EB1 in complex with microtubule Tip lo... -

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Basic information

Entry
Database: PDB / ID: 3gjo
TitleCrystal structure of human EB1 in complex with microtubule Tip localization signal peptide of MACF
Components
  • Dystonin
  • Microtubule-associated protein RP/EB family member 1
KeywordsSTRUCTURAL PROTEIN / EB1 STRUCTURAL MOTIF / +TIP PROTEIN COMPLEX / SXIP MOTIFF / APC/DYNACTIN BINDING PROTEIN / MICROTUBULE ACTIN CROSS-LINKING FACTOR / CELL CYCLE / CELL DIVISION / MITOSIS / PHOSPHOPROTEIN / ACTIN-BINDING CALCIUM / Microtubule / Actin-binding
Function / homology
Function and homology information


Type I hemidesmosome assembly / protein localization to astral microtubule / cortical microtubule cytoskeleton / hemidesmosome assembly / hemidesmosome / mitotic spindle astral microtubule end / H zone / protein localization to microtubule / intermediate filament cytoskeleton organization / microtubule plus-end ...Type I hemidesmosome assembly / protein localization to astral microtubule / cortical microtubule cytoskeleton / hemidesmosome assembly / hemidesmosome / mitotic spindle astral microtubule end / H zone / protein localization to microtubule / intermediate filament cytoskeleton organization / microtubule plus-end / maintenance of cell polarity / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / retrograde axonal transport / non-motile cilium assembly / microtubule bundle formation / protein localization to centrosome / intermediate filament / RND1 GTPase cycle / intermediate filament cytoskeleton / RND2 GTPase cycle / microtubule organizing center / RND3 GTPase cycle / negative regulation of microtubule polymerization / Assembly of collagen fibrils and other multimeric structures / RHOV GTPase cycle / mitotic spindle pole / microtubule polymerization / cell leading edge / establishment of mitotic spindle orientation / RHOU GTPase cycle / basement membrane / spindle assembly / regulation of microtubule polymerization or depolymerization / spindle midzone / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / stress fiber / Mitotic Prometaphase / cytoskeleton organization / EML4 and NUDC in mitotic spindle formation / axon cytoplasm / positive regulation of microtubule polymerization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / basal plasma membrane / ciliary basal body / cell motility / integrin-mediated signaling pathway / RHO GTPases Activate Formins / wound healing / protein localization / microtubule cytoskeleton organization / Z disc / response to wounding / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / cell migration / actin cytoskeleton / integrin binding / nuclear envelope / actin binding / cell cortex / cytoplasmic vesicle / microtubule binding / microtubule / molecular adaptor activity / cell adhesion / cadherin binding / cell division / axon / focal adhesion / centrosome / calcium ion binding / endoplasmic reticulum membrane / protein kinase binding / structural molecule activity / Golgi apparatus / protein homodimerization activity / RNA binding / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
GAR domain / GAR domain superfamily / Growth-Arrest-Specific Protein 2 Domain / GAR domain profile. / Growth-Arrest-Specific Protein 2 Domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / : / Spectrin-like repeat / Spectrin repeat / Spectrin-like repeat ...GAR domain / GAR domain superfamily / Growth-Arrest-Specific Protein 2 Domain / GAR domain profile. / Growth-Arrest-Specific Protein 2 Domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / : / Spectrin-like repeat / Spectrin repeat / Spectrin-like repeat / Desmoplakin, spectrin-like domain / Spectrin like domain / Plectin repeat / Plectin repeat / Plakin repeat superfamily / Desmoplakin, SH3 domain / Plakin / SH3 domain / Plectin repeat / 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 / Spectrin repeat / Spectrin repeat / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Spectrin/alpha-actinin / Spectrin repeats / Calponin homology domain / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Calponin homology (CH) domain / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / EF-hand domain pair / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Dystonin / Microtubule-associated protein RP/EB family member 1 / Fosfomycin resistance protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHonnappa, S. / Steinmetz, M.O.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: An EB1-binding motif acts as a microtubule tip localization signal
Authors: Honnappa, S. / Gouveia, S.M. / Weisbrich, A. / Damberger, F.F. / Bhavesh, N.S. / Jawhari, H. / Grigoriev, I. / van Rijssel, F.J.A. / Buey, R.M. / Lawera, A. / Jelesarov, I. / Winkler, F.K. / ...Authors: Honnappa, S. / Gouveia, S.M. / Weisbrich, A. / Damberger, F.F. / Bhavesh, N.S. / Jawhari, H. / Grigoriev, I. / van Rijssel, F.J.A. / Buey, R.M. / Lawera, A. / Jelesarov, I. / Winkler, F.K. / Wuthrich, K. / Akhmanova, A. / Steinmetz, M.O.
History
DepositionMar 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 4, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 18, 2012Group: Database references
Revision 1.3Nov 1, 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 1
C: Microtubule-associated protein RP/EB family member 1
D: Microtubule-associated protein RP/EB family member 1
E: Dystonin
F: Dystonin
G: Dystonin
H: Dystonin


Theoretical massNumber of molelcules
Total (without water)45,6398
Polymers45,6398
Non-polymers00
Water34219
1
A: Microtubule-associated protein RP/EB family member 1
B: Microtubule-associated protein RP/EB family member 1
E: Dystonin
F: Dystonin


Theoretical massNumber of molelcules
Total (without water)22,8204
Polymers22,8204
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-54 kcal/mol
Surface area9520 Å2
MethodPISA
2
C: Microtubule-associated protein RP/EB family member 1
D: Microtubule-associated protein RP/EB family member 1
G: Dystonin
H: Dystonin


Theoretical massNumber of molelcules
Total (without water)22,8204
Polymers22,8204
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-49 kcal/mol
Surface area8290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.614, 44.896, 74.840
Angle α, β, γ (deg.)90.00, 98.57, 90.00
Int Tables number4
Space group name H-MP1211

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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: 8179.031 Da / Num. of mol.: 4 / Fragment: EB1 C-TERMINAL DOMAIN, UNP RESIDUES 191-260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPRE1 / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15691
#2: Protein/peptide
Dystonin /


Mass: 3230.742 Da / Num. of mol.: 4 / Fragment: MACF2 C-TERMINAL PEPTIDE, UNP RESIDUES 5428-5457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DST / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5TBT1, UniProt: Q03001*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 1.66 Å3/Da / Density % sol: 25.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.2M MAGNESIUM ACETATE, 20% PEG 3350, pH 7.40, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0009 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2008
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0009 Å / Relative weight: 1
ReflectionResolution: 2.5→48.5 Å / Num. obs: 10167 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Rsym value: 0.088 / Net I/σ(I): 9.94
Reflection shellResolution: 2.5→2.68 Å / Mean I/σ(I) obs: 3.43 / Rsym value: 0.426 / % possible all: 98

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WU9

1wu9


Resolution: 2.5→25 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / SU B: 21.747 / SU ML: 0.228 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.266 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 487 4.8 %RANDOM
Rwork0.213 ---
obs0.215 9675 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20.4 Å2
2--0.36 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.5→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 0 0 19 2309
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222316
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.13123122
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8885272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.29826.311122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.71515444
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7991513
X-RAY DIFFRACTIONr_chiral_restr0.0760.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021718
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.21087
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21627
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.272
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.24721460
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.26332292
X-RAY DIFFRACTIONr_scbond_it5.594.5948
X-RAY DIFFRACTIONr_scangle_it7.7926830
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 22 -
Rwork0.268 735 -
obs--98.7 %
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)
10.40740.6303-0.67631.5431-0.90271.5094-0.00880.00410.0150.05910.11550.1126-0.0246-0.2147-0.1066-0.07380.0109-0.02220.00020.02870.0598-14.7046-21.165433.9387
21.141.5118-1.89822.4545-1.97483.81510.04450.05250.22850.00320.18550.4111-0.1655-0.2484-0.23-0.10550.05360.00220.020.04010.056-16.6602-15.779535.4238
31.2562-1.15340.85791.3991-1.33872.4001-0.02450.0033-0.0517-0.01430.15970.07750.1053-0.4346-0.1352-0.0664-0.0671-0.03920.02780.0252-0.0095-12.2234-7.0753-0.0498
41.7457-3.09061.63465.5858-3.27292.78830.0175-0.11210.02240.06550.1242-0.0701-0.0567-0.227-0.1417-0.07690.0007-0.0220.0038-0.00420.0339-8.2358-4.42952.1098
53.384-1.4934-3.73114.74833.46264.92030.14580.8101-0.2544-0.32540.4456-0.39830.3586-0.4078-0.5914-0.1784-0.0426-0.0552-0.0282-0.10860.0258-13.4229-29.236327.3238
63.2992-6.6265-6.351927.393515.268612.6768-0.98420.7669-0.0652-0.0658-0.28880.86030.4145-1.50691.273-0.16850.1610.01450.0860.03970.0079-22.8288-11.325244.1693
724.8777-11.26115.307325.0065-0.63866.02861.27460.1594-1.6756-0.4157-0.9141.25660.5675-0.8067-0.36060.0496-0.2512-0.11930.0506-0.032-0.0808-15.266-12.1917-7.5741
810.2224-18.94161.094638.3958-13.646941.048-0.3817-1.3882-0.73961.481.5267-0.5172-0.98562.5213-1.1450.0343-0.0171-0.01110.1267-0.09190.0651-9.79316.34175.7878
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A192 - 257
2X-RAY DIFFRACTION2B191 - 256
3X-RAY DIFFRACTION3C192 - 256
4X-RAY DIFFRACTION4D192 - 249
5X-RAY DIFFRACTION5E5475 - 5485
6X-RAY DIFFRACTION6F5475 - 5483
7X-RAY DIFFRACTION7G5476 - 5483
8X-RAY DIFFRACTION8H5477 - 5481

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