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- PDB-3jar: Cryo-EM structure of GDP-microtubule co-polymerized with EB3 -

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Entry
Database: PDB / ID: 3jar
TitleCryo-EM structure of GDP-microtubule co-polymerized with EB3
Components
  • Microtubule-associated protein RP/EB family member 3
  • Tubulin alpha-1B chain
  • Tubulin beta chain
KeywordsSTRUCTURAL PROTEIN / microtubule / EB3 / GDP
Function / homology
Function and homology information


mitotic spindle astral microtubule end / positive regulation of microtubule plus-end binding / protein localization to microtubule plus-end / protein localization to microtubule / microtubule plus-end / microtubule plus-end binding / regulation of microtubule polymerization / regulation of microtubule polymerization or depolymerization / spindle assembly / cytoplasmic microtubule ...mitotic spindle astral microtubule end / positive regulation of microtubule plus-end binding / protein localization to microtubule plus-end / protein localization to microtubule / microtubule plus-end / microtubule plus-end binding / regulation of microtubule polymerization / regulation of microtubule polymerization or depolymerization / spindle assembly / cytoplasmic microtubule / microtubule-based process / spindle midzone / positive regulation of protein kinase activity / positive regulation of cyclin-dependent protein serine/threonine kinase activity / cellular response to interleukin-4 / microtubule organizing center / protein localization / structural constituent of cytoskeleton / neuron migration / microtubule cytoskeleton / microtubule cytoskeleton organization / midbody / double-stranded RNA binding / mitotic cell cycle / microtubule binding / microtubule / protein C-terminus binding / GTPase activity / cell division / GTP binding / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / positive regulation of transcription, DNA-templated / identical protein binding / cytoplasm
Tubulin / Microtubule-associated protein RP/EB / Calponin homology domain / Alpha tubulin / Beta tubulin / Tubulin/FtsZ, GTPase domain / EB1, C-terminal / Tubulin/FtsZ, C-terminal / Beta tubulin, autoregulation binding site / Tubulin, conserved site ...Tubulin / Microtubule-associated protein RP/EB / Calponin homology domain / Alpha tubulin / Beta tubulin / Tubulin/FtsZ, GTPase domain / EB1, C-terminal / Tubulin/FtsZ, C-terminal / Beta tubulin, autoregulation binding site / Tubulin, conserved site / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin, C-terminal / EB3 / EB1, C-terminal domain superfamily / Tubulin/FtsZ, GTPase domain superfamily / CH domain superfamily / Tubulin/FtsZ, C-terminal domain superfamily / Intermediate filament, rod domain, coil 1B / Tubulin/FtsZ family, GTPase domain / Tubulin C-terminal domain / Calponin homology (CH) domain / Calponin-like domain / Actin-binding Protein, T-fimbrin; domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Tubulin beta chain / Microtubule-associated protein RP/EB family member 3 / Tubulin alpha-1B chain
Biological speciesHomo sapiens (human)
Sus scrofa (pig)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZhang, R. / Nogales, E.
CitationJournal: Cell / Year: 2015
Title: Mechanistic Origin of Microtubule Dynamic Instability and Its Modulation by EB Proteins.
Authors: Rui Zhang / Gregory M Alushin / Alan Brown / Eva Nogales /
Abstract: Microtubule (MT) dynamic instability is driven by GTP hydrolysis and regulated by microtubule-associated proteins, including the plus-end tracking end-binding protein (EB) family. We report six cryo- ...Microtubule (MT) dynamic instability is driven by GTP hydrolysis and regulated by microtubule-associated proteins, including the plus-end tracking end-binding protein (EB) family. We report six cryo-electron microscopy (cryo-EM) structures of MTs, at 3.5 Å or better resolution, bound to GMPCPP, GTPγS, or GDP, either decorated with kinesin motor domain after polymerization or copolymerized with EB3. Subtle changes around the E-site nucleotide during hydrolysis trigger conformational changes in α-tubulin around an "anchor point," leading to global lattice rearrangements and strain generation. Unlike the extended lattice of the GMPCPP-MT, the EB3-bound GTPγS-MT has a compacted lattice that differs in lattice twist from that of the also compacted GDP-MT. These results and the observation that EB3 promotes rapid hydrolysis of GMPCPP suggest that EB proteins modulate structural transitions at growing MT ends by recognizing and promoting an intermediate state generated during GTP hydrolysis. Our findings explain both EBs end-tracking behavior and their effect on microtubule dynamics.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 19, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Jul 18, 2018Group: Author supporting evidence / Data collection / Category: em_single_particle_entity / em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Dec 18, 2019Group: Database references / Other / Category: atom_sites / struct_ref_seq_dif
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _struct_ref_seq_dif.details

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Structure viewerMolecule:
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Assembly

Deposited unit
E: Tubulin alpha-1B chain
F: Tubulin beta chain
N: Microtubule-associated protein RP/EB family member 3
J: Tubulin alpha-1B chain
G: Tubulin beta chain
C: Tubulin alpha-1B chain
D: Tubulin beta chain
L: Tubulin alpha-1B chain
I: Tubulin beta chain
A: Tubulin alpha-1B chain
B: Tubulin beta chain
M: Microtubule-associated protein RP/EB family member 3
K: Tubulin alpha-1B chain
H: Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)652,34832
Polymers646,40414
Non-polymers5,94418
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 1 / Rise per n subunits: 9.42 Å / Rotation per n subunits: -27.71 °)
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11E
21J
12E
22C
13E
23L
14E
24A
15E
25K
16F
26G
17F
27D
18F
28I
19F
29B
110F
210H
111N
211M
112J
212C
113J
213L
114J
214A
115J
215K
116G
216D
117G
217I
118G
218B
119G
219H
120C
220L
121C
221A
122C
222K
123D
223I
124D
224B
125D
225H
126L
226A
127L
227K
128I
228B
129I
229H
130A
230K
131B
231H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010E1 - 441
2010J1 - 441
1020E1 - 441
2020C1 - 441
1030E1 - 441
2030L1 - 441
1040E1 - 441
2040A1 - 441
1050E1 - 441
2050K1 - 441
1060F1 - 429
2060G1 - 429
1070F1 - 429
2070D1 - 429
1080F1 - 429
2080I1 - 429
1090F1 - 429
2090B1 - 429
10100F1 - 429
20100H1 - 429
10110N1 - 131
20110M1 - 131
10120J1 - 441
20120C1 - 441
10130J1 - 441
20130L1 - 441
10140J1 - 441
20140A1 - 441
10150J1 - 441
20150K1 - 441
10160G1 - 429
20160D1 - 429
10170G1 - 429
20170I1 - 429
10180G1 - 429
20180B1 - 429
10190G1 - 429
20190H1 - 429
10200C1 - 441
20200L1 - 441
10210C1 - 441
20210A1 - 441
10220C1 - 441
20220K1 - 441
10230D1 - 429
20230I1 - 429
10240D1 - 429
20240B1 - 429
10250D1 - 429
20250H1 - 429
10260L1 - 441
20260A1 - 441
10270L1 - 441
20270K1 - 441
10280I1 - 429
20280B1 - 429
10290I1 - 429
20290H1 - 429
10300A1 - 441
20300K1 - 441
10310B1 - 429
20310H1 - 429

NCS ensembles:
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
Detailspseudo-helical symmetry

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Components

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Protein , 3 types, 14 molecules EJCLAKFGDIBHNM

#1: Protein
Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: brain / References: UniProt: Q2XVP4
#2: Protein
Tubulin beta chain / Beta-tubulin


Mass: 49907.770 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / Organ: brain / References: UniProt: P02554
#3: Protein Microtubule-associated protein RP/EB family member 3 / EB1 protein family member 3 / EBF3 / End-binding protein 3 / EB3 / RP3


Mass: 22865.203 Da / Num. of mol.: 2 / Fragment: UNP residues 1-200
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPRE3 / Plasmid: 2BT / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-CodonPlus-(DE3)-RIL / References: UniProt: Q9UPY8

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Non-polymers , 3 types, 18 molecules

#4: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

Component
IDNameTypeDetailsParent-ID
1GDP-microtubule co-polymerized with EB3COMPLEXhelical assembly0
2Alpha tubulin1
3Beta tubulin1
4EB31
Buffer solutionName: BRB80 / pH: 6.8
Details: 80 mM PIPES, 1 mM EGTA, 1 mM MgCl2, 1 mM DTT, 0.05% Nonidet P-40
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 400 mesh C-flat 1.2/1.3 EM grid, glow discharged in Ar/O2 gas (Solarus, Gatan Inc)
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Temp: 90.4 K / Humidity: 95 %
Details: Blot once for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK II).
Method: Blot once for 4 seconds before plunging/

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Electron microscopy imaging

MicroscopyModel: FEI TITAN / Date: Apr 9, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 27500 X / Calibrated magnification: 27500 X / Nominal defocus max: 3500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Astigmatism: Objective lens astigmatism was corrected at 27,500 times magnification.
Specimen holderModel: GATAN LIQUID NITROGEN / Specimen holder type: Gatan 626 holder / Temperature: 90 K
Image recordingElectron dose: 27.6 e/Å2 / Film or detector model: GATAN K2 (4k x 4k)
Details: The camera was operated in counting mode with a dose rate of ~8 electrons/pixel/s on the camera. A total exposure time of 6 seconds was fractionated into 20 movie frames.
Image scansNum. digital images: 383
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0091refinement
PDB_EXTRACT3.15data extraction
EM software
IDNameVersionCategory
1EMAN13D reconstruction
2FREALIGN3D reconstruction
CTF correctionDetails: CTFFIND4, each particle
Helical symmertyAngular rotation/subunit: 27.71 ° / Axial rise/subunit: 9.42 Å / Axial symmetry: C1
3D reconstructionMethod: projection matching / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Nominal pixel size: 1.32 Å / Actual pixel size: 1.32 Å
Details: IHRSR algorithm with microtubule-specific pseudo-helical symmetry applied
Symmetry type: HELICAL
RefinementResolution: 3.5→211.2 Å / Cor.coef. Fo:Fc: 0.855 / SU B: 32.393 / SU ML: 0.495 / σ(F): 0 / ESU R: 1.841
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.3701 --
Obs0.3701 193403 100 %
Solvent computationSolvent model: NONE
Displacement parametersBiso max: 369.61 Å2 / Biso mean: 59.036 Å2 / Biso min: 15.58 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å2-1.3 Å20.54 Å2
2--3.73 Å2-0.38 Å2
3----2.88 Å2
Refinement stepCycle: LAST / Resolution: 3.5→211.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms42658 0 366 0 43024
Refine LS restraints
Refinement-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0080.01944010
ELECTRON MICROSCOPYr_bond_other_d0.0020.0240650
ELECTRON MICROSCOPYr_angle_refined_deg1.3181.95759764
ELECTRON MICROSCOPYr_angle_other_deg0.932393506
ELECTRON MICROSCOPYr_dihedral_angle_1_deg11.794.8646026
ELECTRON MICROSCOPYr_dihedral_angle_2_deg35.25524.2552094
ELECTRON MICROSCOPYr_dihedral_angle_3_deg14.638157145
ELECTRON MICROSCOPYr_dihedral_angle_4_deg11.99915261
ELECTRON MICROSCOPYr_chiral_restr0.0790.26528
ELECTRON MICROSCOPYr_gen_planes_refined0.0060.02150240
ELECTRON MICROSCOPYr_gen_planes_other0.0010.0210400
ELECTRON MICROSCOPYr_mcbond_it1.9695.80721692
ELECTRON MICROSCOPYr_mcbond_other1.9695.80721691
ELECTRON MICROSCOPYr_mcangle_it3.6328.727080
Refine LS restraints NCS

Refinement-ID: ELECTRON MICROSCOPY / Type: interatomic distance / Rms dev position: 0 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11E53160
12J53160
21E53162
22C53162
31E53156
32L53156
41E53160
42A53160
51E53158
52K53158
61F52546
62G52546
71F52542
72D52542
81F52544
82I52544
91F52548
92B52548
101F52546
102H52546
111N15798
112M15798
121J53158
122C53158
131J53158
132L53158
141J53158
142A53158
151J53160
152K53160
161G52544
162D52544
171G52552
172I52552
181G52544
182B52544
191G52550
192H52550
201C53158
202L53158
211C53156
212A53156
221C53156
222K53156
231D52546
232I52546
241D52542
242B52542
251D52546
252H52546
261L53150
262A53150
271L53158
272K53158
281I52544
282B52544
291I52550
292H52550
301A53154
302K53154
311B52548
312H52548
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.807 14402 -
Obs--100 %

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