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- PDB-2qjz: Structural Basis of Microtubule Plus End Tracking by XMAP215, CLI... -

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Basic information

Entry
Database: PDB / ID: 2qjz
TitleStructural Basis of Microtubule Plus End Tracking by XMAP215, CLIP-170 and EB1
ComponentsMicrotubule-associated protein RP/EB family member 1
KeywordsPROTEIN BINDING / EB1 / calponin homology domain / microtubule plus end / +TIP
Function / homology
Function and homology information


protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / protein localization to microtubule / microtubule plus-end / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / non-motile cilium assembly / microtubule bundle formation ...protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / protein localization to microtubule / microtubule plus-end / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / non-motile cilium assembly / microtubule bundle formation / protein localization to centrosome / microtubule organizing center / negative regulation of microtubule polymerization / mitotic spindle pole / microtubule polymerization / establishment of mitotic spindle orientation / regulation of microtubule polymerization or depolymerization / spindle midzone / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule / Mitotic Prometaphase / spindle assembly / 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 / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / positive regulation of microtubule polymerization / AURKA Activation by TPX2 / ciliary basal body / RHO GTPases Activate Formins / protein localization / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / cell migration / microtubule / molecular adaptor activity / cadherin binding / cell division / focal adhesion / centrosome / protein kinase binding / Golgi apparatus / RNA binding / identical protein binding / cytosol
Similarity search - Function
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 / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily ...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 / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.25 Å
AuthorsSlep, K.C. / Vale, R.D.
CitationJournal: Mol.Cell / Year: 2007
Title: Structural Basis of Microtubule Plus End Tracking by XMAP215, CLIP-170, and EB1.
Authors: Slep, K.C. / Vale, R.D.
History
DepositionJul 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _struct_conn.pdbx_leaving_atom_flag

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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


Theoretical massNumber of molelcules
Total (without water)28,9102
Polymers28,9102
Non-polymers00
Water5,441302
1
A: Microtubule-associated protein RP/EB family member 1


Theoretical massNumber of molelcules
Total (without water)14,4551
Polymers14,4551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Microtubule-associated protein RP/EB family member 1


Theoretical massNumber of molelcules
Total (without water)14,4551
Polymers14,4551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.334, 65.220, 63.091
Angle α, β, γ (deg.)90.000, 96.240, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer formed by a conserved C-terminal coiled-coil / four helix bundle dimerization domain not included in this construct.

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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: 14455.015 Da / Num. of mol.: 2 / Fragment: Calponin Homology Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPRE1 / Plasmid: pGEX-6P2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 pLysS / References: UniProt: Q15691
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.07 Å3/Da / Density % sol: 40.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 11.5% 2-propanol, 190 mM Sodium citrate, 100 mM Hepes, Protein concentration 20 mg/ml, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9798, 1.1271, 0.7999
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 10, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
21.12711
30.79991
Reflection

Χ2: 0.99 / D res low: 50 Å

IDAv σ(I) over netINumberRmerge(I) obsD res high (Å)Num. obs% possible obs
116.41950100.0491.56967294.1
229.11384980.0351.65170384.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squared
3.75091.610.0260.985
2.943.795.110.030.957
2.562.9496.710.0350.964
2.332.5697.610.0411.013
2.162.3398.910.0481.014
2.042.1699.310.0570.996
1.932.0499.410.0721.02
1.851.9399.710.0960.973
1.781.8599.510.1210.986
1.721.7899.410.1530.974
1.661.7298.910.1750.975
1.621.6697.410.2060.987
1.571.628910.2280.961
1.531.578110.2580.976
1.51.5368.710.3150.938
3.955095.920.0240.998
3.133.9598.120.0260.973
2.743.1398.920.030.985
2.492.7499.220.0340.969
2.312.4999.520.0390.99
2.172.3199.720.0450.986
2.062.1799.920.0521.018
1.972.0699.920.0610.991
1.91.9799.920.0740.958
1.831.995.120.0791.019
1.771.8384.520.081.052
1.721.7770.320.0881.009
1.681.7257.320.0991.036
1.641.6843.720.1261.027
1.61.6431.920.1431.036
ReflectionResolution: 1.25→50 Å / Num. obs: 63420 / % possible obs: 97.4 % / Rmerge(I) obs: 0.054 / Rsym value: 5.4 / Χ2: 0.97 / Net I/σ(I): 13.8
Reflection shellResolution: 1.25→1.29 Å / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5181 / Rsym value: 32.1 / Χ2: 0.941 / % possible all: 95.7

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Phasing

PhasingMethod: MAD
Phasing dm shellResolution: 1.6→500.01 Å / Delta phi final: 0.123 / FOM : 0.126 / Reflection: 51131

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
SCALEPACKdata scaling
CNSphasing
CNSrefinement
DENZOdata reduction
PDB_EXTRACT2data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MAD / Resolution: 1.25→45.22 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.382 / SU ML: 0.028 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.057 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.198 6318 9.9 %RANDOM
Rwork0.174 ---
obs0.177 63420 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.271 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.25→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1974 0 0 302 2276
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222020
X-RAY DIFFRACTIONr_angle_refined_deg1.0331.9452708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4345238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.23525.192104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.16415380
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.908156
X-RAY DIFFRACTIONr_chiral_restr0.0760.2276
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021536
X-RAY DIFFRACTIONr_nbd_refined0.1960.21000
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21425
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.2192
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0850.236
X-RAY DIFFRACTIONr_mcbond_it0.9991.51222
X-RAY DIFFRACTIONr_mcangle_it1.5521904
X-RAY DIFFRACTIONr_scbond_it2.2693905
X-RAY DIFFRACTIONr_scangle_it3.2094.5804
X-RAY DIFFRACTIONr_rigid_bond_restr1.46132127
X-RAY DIFFRACTIONr_sphericity_free2.7793302
X-RAY DIFFRACTIONr_sphericity_bonded2.47431974
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 486 -
Rwork0.19 4140 -
obs-4626 95.44 %

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