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- EMDB-51768: Cryo-EM structure of taxol-microtubules in complex with the C1 do... -

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Basic information

Entry
Database: EMDB / ID: EMD-51768
TitleCryo-EM structure of taxol-microtubules in complex with the C1 domain of GEFH1
Map dataCryo-EM reconstruction of the C1 domain of GEFH1 in complex with taxol-stabilized 13 protofilament microtubule
Sample
  • Complex: The C1 domain of GEFH1 in complex with microtubule
    • Organelle or cellular component: C1 domain of GEFH1
      • Protein or peptide: Rho guanine nucleotide exchange factor 2
    • Organelle or cellular component: Tubulin alpha 1B
      • Protein or peptide: Tubulin alpha-1B chain
    • Organelle or cellular component: Tubulin beta 2B
      • Protein or peptide: Tubulin beta-2B chain
  • Ligand: ZINC ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOL
KeywordsRhoGEF / C1 / Cytoskeleton / Complex / SIGNALING PROTEIN
Function / homology
Function and homology information


asymmetric neuroblast division / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / cellular response to muramyl dipeptide / positive regulation of neuron migration / negative regulation of microtubule depolymerization / regulation of Rho protein signal transduction / negative regulation of necroptotic process / cellular hyperosmotic response / positive regulation of axon guidance / regulation of small GTPase mediated signal transduction ...asymmetric neuroblast division / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / cellular response to muramyl dipeptide / positive regulation of neuron migration / negative regulation of microtubule depolymerization / regulation of Rho protein signal transduction / negative regulation of necroptotic process / cellular hyperosmotic response / positive regulation of axon guidance / regulation of small GTPase mediated signal transduction / positive regulation of peptidyl-tyrosine phosphorylation / RHOB GTPase cycle / NRAGE signals death through JNK / RHOA GTPase cycle / bicellular tight junction / microtubule-based process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cytoplasmic microtubule / positive regulation of neuron differentiation / cellular response to interleukin-4 / guanyl-nucleotide exchange factor activity / actin filament organization / intracellular protein transport / positive regulation of NF-kappaB transcription factor activity / structural constituent of cytoskeleton / positive regulation of interleukin-6 production / small GTPase binding / microtubule cytoskeleton organization / ruffle membrane / spindle / neuron migration / cell morphogenesis / positive regulation of tumor necrosis factor production / cellular response to tumor necrosis factor / G alpha (12/13) signalling events / mitotic cell cycle / double-stranded RNA binding / regulation of cell population proliferation / microtubule cytoskeleton / cytoplasmic vesicle / microtubule binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / vesicle / microtubule / cytoskeleton / cilium / protein heterodimerization activity / innate immune response / focal adhesion / GTPase activity / ubiquitin protein ligase binding / GTP binding / Golgi apparatus / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
ARHGEF2, PH domain / : / ARHGEF1-like, PH domain / PH domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Zinc finger phorbol-ester/DAG-type signature. ...ARHGEF2, PH domain / : / ARHGEF1-like, PH domain / PH domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / 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 / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
Tubulin alpha-1B chain / Tubulin beta-2B chain / Rho guanine nucleotide exchange factor 2
Similarity search - Component
Biological speciesHomo sapiens (human) / Bos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsChoi SR / Blum T / Steinmetz MO
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_166608 Switzerland
CitationJournal: To Be Published
Title: Structural Basis of Microtubule-Controlled Signaling
Authors: Choi SR / Blum T / Steinmetz MO
History
DepositionOct 9, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51768.png

Downloads & links

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Map

FileDownload / File: emd_51768.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of the C1 domain of GEFH1 in complex with taxol-stabilized 13 protofilament microtubule
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 160 pix.
= 169.28 Å		1.06 Å/pix.
x 160 pix.
= 169.28 Å		1.06 Å/pix.
x 160 pix.
= 169.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.058 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.256
Minimum - Maximum-0.0003189909 - 1.6447606
Average (Standard dev.)0.025862684 (±0.103441164)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 169.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map 1: Cryo-EM reconstruction of the C1...

Fileemd_51768_half_map_1.map
AnnotationHalf map 1: Cryo-EM reconstruction of the C1 domain of GEFH1 in complex with taxol-stabilized 13 protofilament microtubule
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2: Cryo-EM reconstruction of the C1...

Fileemd_51768_half_map_2.map
AnnotationHalf map 2: Cryo-EM reconstruction of the C1 domain of GEFH1 in complex with taxol-stabilized 13 protofilament microtubule
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The C1 domain of GEFH1 in complex with microtubule

EntireName: The C1 domain of GEFH1 in complex with microtubule
Components
  • Complex: The C1 domain of GEFH1 in complex with microtubule
    • Organelle or cellular component: C1 domain of GEFH1
      • Protein or peptide: Rho guanine nucleotide exchange factor 2
    • Organelle or cellular component: Tubulin alpha 1B
      • Protein or peptide: Tubulin alpha-1B chain
    • Organelle or cellular component: Tubulin beta 2B
      • Protein or peptide: Tubulin beta-2B chain
  • Ligand: ZINC ION
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: TAXOL

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Supramolecule #1: The C1 domain of GEFH1 in complex with microtubule

SupramoleculeName: The C1 domain of GEFH1 in complex with microtubule / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Supramolecule #2: C1 domain of GEFH1

SupramoleculeName: C1 domain of GEFH1 / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Tubulin alpha 1B

SupramoleculeName: Tubulin alpha 1B / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Bos taurus (domestic cattle)

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Supramolecule #4: Tubulin beta 2B

SupramoleculeName: Tubulin beta 2B / type: organelle_or_cellular_component / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Bos taurus (domestic cattle)

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Macromolecule #1: Rho guanine nucleotide exchange factor 2

MacromoleculeName: Rho guanine nucleotide exchange factor 2 / type: protein_or_peptide / ID: 1 / Details: C1 domain of GEFH1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.250749 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GPMKEAKDAR YTNGHLFTTI SVSGMTMCYA CNKSITAKEA LICPTCNVTI HNRCKDTLAN CTKVKQKQQK AALLK

UniProtKB: Rho guanine nucleotide exchange factor 2

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Macromolecule #2: Tubulin alpha-1B chain

MacromoleculeName: Tubulin alpha-1B chain / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 50.204445 KDa
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLISQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRIHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRSIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY

UniProtKB: Tubulin alpha-1B chain

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Macromolecule #3: Tubulin beta-2B chain

MacromoleculeName: Tubulin beta-2B chain / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 49.983824 KDa
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEATGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEATGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VMPSPKVSDT VVEPYNATLS VHQLVENTDE TYSIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDSK NMMAACDPRH GRYLTVAAIF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATADEQGE FEEEEGEDEA

UniProtKB: Tubulin beta-2B chain

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 2 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 4 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Macromolecule #8: TAXOL

MacromoleculeName: TAXOL / type: ligand / ID: 8 / Number of copies: 4 / Formula: TA1
Molecular weightTheoretical: 853.906 Da
Chemical component information

ChemComp-TA1:
TAXOL / medication*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 6.9
Component:
ConcentrationFormulaName
80.0 mMC8H18N2O6S2PIPES
1.0 mMMgCl2Magnesium Chloride
1.0 mMC14H24N2O10EGTA

Details: BRB80 buffer 80mM PIPES, 1mM MgCl2, 1mM EGTA, pH 6.9
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 12 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
DetailsC1 domain of GEFH1 was in complex with microtubules

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: RELION (ver. 3.0.8) / Software - details: GCTF / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: In-house model of 13pf-microtubule
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 326559
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0.8)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9h1o:
Cryo-EM structure of taxol-microtubules in complex with the C1 domain of GEFH1

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