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- EMDB-8266: Near-atomic cryo-EM structure of PRC1 bound to the microtubule -

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Entry
Database: EMDB / ID: 8266
TitleNear-atomic cryo-EM structure of PRC1 bound to the microtubule
Map dataNear-atomic cryo-EM structure of PRC1 bound to the microtubule
SampleTernary complex of PRC1 fragment (PRC1-SC), alpha-tubulin, and beta-tubulin.:
Tubulin alpha-1B chain / Tubulin beta chain / Protein regulator of cytokinesis 1 / (ligand) x 4
Function / homologyProtein regulator of cytokinesis 1 / Tubulin, conserved site / Tubulin / Alpha tubulin / Beta tubulin / Tubulin/FtsZ, GTPase domain / Microtubule-associated protein, MAP65/Ase1/PRC1 / Tubulin/FtsZ, C-terminal / Beta tubulin, autoregulation binding site / Tubulin/FtsZ, 2-layer sandwich domain ...Protein regulator of cytokinesis 1 / Tubulin, conserved site / Tubulin / Alpha tubulin / Beta tubulin / Tubulin/FtsZ, GTPase domain / Microtubule-associated protein, MAP65/Ase1/PRC1 / Tubulin/FtsZ, C-terminal / Beta tubulin, autoregulation binding site / Tubulin/FtsZ, 2-layer sandwich domain / Regulation of PLK1 Activity at G2/M Transition / Tubulin, C-terminal / Separation of Sister Chromatids / Tubulin/FtsZ, GTPase domain superfamily / Tubulin/FtsZ, C-terminal domain superfamily / Tubulin/FtsZ family, GTPase domain / Tubulin C-terminal domain / Tubulin subunits alpha, beta, and gamma signature. / Tubulin-beta mRNA autoregulation signal. / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / RHO GTPases Activate Formins / Kinesins / Carboxyterminal post-translational modifications of tubulin / AURKA Activation by TPX2 / The role of GTSE1 in G2/M progression after G2 checkpoint / Mitotic Prometaphase / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / RHO GTPases activate IQGAPs / Loss of Nlp from mitotic centrosomes / Intraflagellar transport / Anchoring of the basal body to the plasma membrane / Cilium Assembly / Hedgehog 'off' state / Recycling pathway of L1 / Recruitment of NuMA to mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / RHO GTPases activate CIT / contractile ring / mitotic spindle elongation / microtubule bundle formation / kinesin binding / microtubule-based process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / regulation of cytokinesis / neuron migration / spindle microtubule / spindle / spindle pole / midbody / mitotic cell cycle / microtubule / microtubule binding / GTPase activity / cell division / GTP binding / positive regulation of cell population proliferation / protein kinase binding / identical protein binding / nucleus / cytosol / cytoplasm / Protein regulator of cytokinesis 1 / Tubulin beta chain / Tubulin alpha-1B chain
Function and homology information
SourcePig (pig) / Homo sapiens (human)
Methodhelical reconstruction / cryo EM / 3.5 Å resolution
AuthorsKellogg EH / Howes S / Ti S-C / Ramirez-Aportela E / Kapoor TM / Chacon P / Nogales E
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Near-atomic cryo-EM structure of PRC1 bound to the microtubule.
Authors: Elizabeth H Kellogg / Stuart Howes / Shih-Chieh Ti / Erney Ramírez-Aportela / Tarun M Kapoor / Pablo Chacón / Eva Nogales
Validation ReportPDB-ID: 5kmg

SummaryFull reportAbout validation report
DateDeposition: Jul 21, 2016 / Header (metadata) release: Aug 3, 2016 / Map release: Aug 3, 2016 / Last update: Sep 27, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.27
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4.27
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5kmg
  • Surface level: 4.27
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5kmg
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_8266.map.gz (map file in CCP4 format, 536871 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.32 Å/pix.
= 675.84 Å
512 pix
1.32 Å/pix.
= 675.84 Å
512 pix
1.32 Å/pix.
= 675.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density
Contour Level:4.27 (by author), 4.27 (movie #1):
Minimum - Maximum-16.888908000000001 - 31.584765999999998
Average (Standard dev.)0.0872013 (1.2133477)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions512512512
Origin0.00.00.0
Limit511.0511.0511.0
Spacing512512512
CellA=B=C: 675.84 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z675.840675.840675.840
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-16.88931.5850.087

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Supplemental data

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Sample components

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Entire Ternary complex of PRC1 fragment (PRC1-SC), alpha-tubulin, and be...

EntireName: Ternary complex of PRC1 fragment (PRC1-SC), alpha-tubulin, and beta-tubulin.
Details: The PRC1 fragment referred to as PRC1-SC contains the spectrin domain and the unstructured C-terminal domain, spanning (337-620)
Number of components: 8

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Component #1: protein, Ternary complex of PRC1 fragment (PRC1-SC), alpha-tubuli...

ProteinName: Ternary complex of PRC1 fragment (PRC1-SC), alpha-tubulin, and beta-tubulin.
Details: The PRC1 fragment referred to as PRC1-SC contains the spectrin domain and the unstructured C-terminal domain, spanning (337-620)
Recombinant expression: No

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Component #2: protein, Tubulin alpha-1B chain

ProteinName: Tubulin alpha-1B chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.095438 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: brain

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Component #3: protein, Tubulin beta chain

ProteinName: Tubulin beta chain / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.299293 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: brain

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Component #4: protein, Protein regulator of cytokinesis 1

ProteinName: Protein regulator of cytokinesis 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 15.69394 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

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Component #6: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #7: ligand, GUANOSINE-5'-DIPHOSPHATE

LigandName: GUANOSINE-5'-DIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.443201 kDa

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Component #8: ligand, Peloruside A

LigandName: Peloruside A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.548663 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 8.67 Å / Delta phi: -25.76 deg.
Sample solutionSpecimen conc.: 0.4 mg/ml / pH: 6.8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 100 % / Details: blot for 4 seconds, blot force 10.

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 8 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 27500.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000.0 - 2500.0 nm
Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: K ( 93.0 - 93.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 312 / Sampling size: 5 microns

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: FOURIER SPACE / Software: FREALIGN / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Target criteria: correlation coefficient / Refinement space: REAL
Input PDB model: 3NRX, 4L6Y
Chain ID: A, A
Output model

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