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- PDB-4abo: Mal3 CH domain homology model and mammalian tubulin (2XRP) docked... -

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Basic information

Entry
Database: PDB / ID: 4abo
TitleMal3 CH domain homology model and mammalian tubulin (2XRP) docked into the 8.6-Angstrom cryo-EM map of Mal3-GTPgammaS-microtubules
Components
  • MICROTUBULE INTEGRITY PROTEIN MAL3
  • TUBULIN ALPHA-1A CHAIN
  • TUBULIN BETA CHAIN
KeywordsSTRUCTURAL PROTEIN / CYTOSKELETON / GTPASE / END BINDING
Function / homology
Function and homology information


dynein-driven meiotic oscillatory nuclear movement / post-anaphase array microtubule end / nuclear migration involved in conjugation with cellular fusion / cell cortex of cell tip / cortical microtubule / mitotic spindle astral microtubule / karyogamy involved in conjugation with cellular fusion / mitotic spindle pole body / nuclear microtubule / mitotic spindle midzone ...dynein-driven meiotic oscillatory nuclear movement / post-anaphase array microtubule end / nuclear migration involved in conjugation with cellular fusion / cell cortex of cell tip / cortical microtubule / mitotic spindle astral microtubule / karyogamy involved in conjugation with cellular fusion / mitotic spindle pole body / nuclear microtubule / mitotic spindle midzone / astral microtubule / protein localization to microtubule / microtubule plus-end / cytoskeletal anchor activity / attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end binding / microtubule organizing center / microtubule lateral binding / ATPase activator activity / spindle assembly / regulation of microtubule polymerization or depolymerization / spindle midzone / cytoplasmic microtubule / molecular condensate scaffold activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / microtubule binding / microtubule / hydrolase activity / cell division / GTPase activity / GTP binding / metal ion binding / nucleus / cytoplasm
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 homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Tubulin-beta mRNA autoregulation signal. ...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 homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin alpha-1A chain / Tubulin beta chain / Microtubule integrity protein mal3
Similarity search - Component
Biological speciesSCHIZOSACCHAROMYCES POMBE (fission yeast)
SUS SCROFA (pig)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.6 Å
AuthorsMaurer, S.P. / Fourniol, F.J. / Bohner, G. / Moores, C.A. / Surrey, T.
CitationJournal: Cell / Year: 2012
Title: EBs recognize a nucleotide-dependent structural cap at growing microtubule ends.
Authors: Sebastian P Maurer / Franck J Fourniol / Gergő Bohner / Carolyn A Moores / Thomas Surrey /
Abstract: Growing microtubule ends serve as transient binding platforms for essential proteins that regulate microtubule dynamics and their interactions with cellular substructures. End-binding proteins (EBs) ...Growing microtubule ends serve as transient binding platforms for essential proteins that regulate microtubule dynamics and their interactions with cellular substructures. End-binding proteins (EBs) autonomously recognize an extended region at growing microtubule ends with unknown structural characteristics and then recruit other factors to the dynamic end structure. Using cryo-electron microscopy, subnanometer single-particle reconstruction, and fluorescence imaging, we present a pseudoatomic model of how the calponin homology (CH) domain of the fission yeast EB Mal3 binds to the end regions of growing microtubules. The Mal3 CH domain bridges protofilaments except at the microtubule seam. By binding close to the exchangeable GTP-binding site, the CH domain is ideally positioned to sense the microtubule's nucleotide state. The same microtubule-end region is also a stabilizing structural cap protecting the microtubule from depolymerization. This insight supports a common structural link between two important biological phenomena, microtubule dynamic instability and end tracking.
History
DepositionDec 9, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Other
Revision 1.2Aug 30, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_software
Item: _em_3d_fitting.target_criteria / _em_software.fitting_id ..._em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id / _em_software.name

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TUBULIN BETA CHAIN
B: TUBULIN ALPHA-1A CHAIN
C: TUBULIN BETA CHAIN
D: TUBULIN ALPHA-1A CHAIN
E: TUBULIN BETA CHAIN
F: TUBULIN ALPHA-1A CHAIN
G: TUBULIN BETA CHAIN
H: TUBULIN ALPHA-1A CHAIN
I: MICROTUBULE INTEGRITY PROTEIN MAL3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)421,06517
Polymers416,8159
Non-polymers4,2508
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
TUBULIN BETA CHAIN / BETA-TUBULIN


Mass: 49907.770 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: P02554*PLUS, EC: 3.6.5.6
#2: Protein
TUBULIN ALPHA-1A CHAIN / / ALPHA-TUBULIN 1 / TUBULIN ALPHA-1 CHAIN


Mass: 50107.238 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Organ: BRAIN / References: UniProt: P02550*PLUS, EC: 3.6.5.6
#3: Protein MICROTUBULE INTEGRITY PROTEIN MAL3 / MAL3


Mass: 16754.949 Da / Num. of mol.: 1 / Fragment: CALPONIN HOMOLOGY DOMAIN, RESIDUES 2-142
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q10113
#4: Chemical
ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#5: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
Nonpolymer details5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE (GSP): GTPGAMMAS WAS DOCKED IN THE STRUCTURE BY ...5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE (GSP): GTPGAMMAS WAS DOCKED IN THE STRUCTURE BY SUPERIMPOSING GDP-BOUND ALPHA-TUBULIN, 1JFF CHAIN A, AND GTPGAMMAS-BOUND GAMMA-TUBULIN, 1Z5V
Sequence detailsTHIS IS A CHIMERIC STRUCTURE BASED ON PDB ENTRIES 1JFF AND 3HKE (ALSO USED IN 2XRP) CLONING ...THIS IS A CHIMERIC STRUCTURE BASED ON PDB ENTRIES 1JFF AND 3HKE (ALSO USED IN 2XRP) CLONING INTRODUCED 4 AMINO-ACID RESIDUES AT THE N-TERMINUS. SOURCE OF PROTEIN IN COORDINATES IS BOS TAURUS, BUT SAMPLE CONTAINED SUS SCROFA TUBULIN (UNP REFERENCES P02554 AND P02550 FOR ALPHA AND BETA TUBULIN RESPECTIVELY).

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: GTPGAMMAS MICROTUBULES DECORATED WITH MONOMERIC MAL3 / Type: COMPLEX
Buffer solutionName: 40MM PIPES, 1MM MGCL2, 1MM EGTA / pH: 6.8 / Details: 40MM PIPES, 1MM MGCL2, 1MM EGTA
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 90, INSTRUMENT- VITROBOT (FEI), METHOD- CHAMBER AT 37 DEGREES C, BLOT 2S,

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 68000 X / Nominal defocus max: 3600 nm / Nominal defocus min: 700 nm / Cs: 2 mm
Specimen holderTemperature: 93 K
Image recordingElectron dose: 17 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 162
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2FREALIGN3D reconstruction
3SPIDER3D reconstruction
CTF correctionDetails: FREALIGN
3D reconstructionMethod: SINGLE PARTICLESingle particle analysis / Resolution: 8.6 Å / Num. of particles: 129000 / Nominal pixel size: 2.2 Å / Actual pixel size: 2.2 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2005.(DEPOSITION ID: 10422).
Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: METHOD--FLEXIBLE FITTING REFINEMENT PROTOCOL--FLEXIBLE FITTING IN CRYOEM MAP
Atomic model buildingPDB-ID: 2XRP

2xrp

RefinementHighest resolution: 8.6 Å
Refinement stepCycle: LAST / Highest resolution: 8.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27740 0 256 0 27996

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