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- EMDB-47948: Tubulin cofactors D,E,G,C bound to tubulin dimer -- TBCC N termin... -

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Basic information

Entry
Database: EMDB / ID: EMD-47948
TitleTubulin cofactors D,E,G,C bound to tubulin dimer -- TBCC N terminus unbound
Map data
Sample
  • Complex: Tubulin Cofactors D,E,G,C and Tubulin complex
    • Protein or peptide: Chromosome instability protein 1
    • Protein or peptide: Protein PAC2
    • Protein or peptide: GTP-binding protein CIN4
    • Protein or peptide: Tubulin alpha-1A chain
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: Tubulin-specific chaperone C
    • Protein or peptide: iih5 Alpha Repeating
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
KeywordsTubulin / Cofactors / Tubulin biogeneis / Tubulin degradation / microtubules / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


post-chaperonin tubulin folding pathway / tubulin complex assembly / motile cilium / small molecule binding / alpha-tubulin binding / beta-tubulin binding / GTPase activator activity / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration ...post-chaperonin tubulin folding pathway / tubulin complex assembly / motile cilium / small molecule binding / alpha-tubulin binding / beta-tubulin binding / GTPase activator activity / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / protein folding / mitotic cell cycle / microtubule cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / molecular adaptor activity / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
: / Tubulin-specific chaperone D-like, ARM repeats / Tubulin-specific chaperone C / Tubulin-folding cofactor D / Tubulin-specific chaperone D-like, ARM repeat / C-CAP/cofactor C-like domain / C-CAP/cofactor C-like domain profile. / Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal / ADP-ribosylation factor-like protein 2/3 / : ...: / Tubulin-specific chaperone D-like, ARM repeats / Tubulin-specific chaperone C / Tubulin-folding cofactor D / Tubulin-specific chaperone D-like, ARM repeat / C-CAP/cofactor C-like domain / C-CAP/cofactor C-like domain profile. / Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal / ADP-ribosylation factor-like protein 2/3 / : / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Leucine Rich repeat / 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 / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Small GTP-binding protein domain / Ubiquitin-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Tubulin alpha-1A chain / Tubulin beta chain / GTP-binding protein CIN4 / Protein PAC2 / Chromosome instability protein 1 / Tubulin-specific chaperone C
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Sus scrofa (pig) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsTaheri A / Al-bassam J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM structures of the tubulin cofactors reveal the molecular basis of alpha/beta-tubulin biogenesis.
Authors: Aryan Taheri / Zhoaqian Wang / Bharti Singal / Fei Guo / Jawdat Al-Bassam /
Abstract: Microtubule polarity and dynamic polymerization arise from the self-association properties of the αβ-tubulin heterodimer. For decades, it has remained unclear how the tubulin cofactors TBCD, TBCE, ...Microtubule polarity and dynamic polymerization arise from the self-association properties of the αβ-tubulin heterodimer. For decades, it has remained unclear how the tubulin cofactors TBCD, TBCE, TBCC, and the Arl2 GTPase mediate the biogenesis of αβ-tubulin from individual α- and β-tubulins. Here, we use cryo-electron microscopy to determine structures of tubulin cofactors bound to αβ-tubulin. TBCD, TBCE, and Arl2 form a heterotrimeric cage-like assembly, we term TBC-DEG, around the αβ-tubulin heterodimer. The TBC-DEG-αβ-tubulin structures show that TBC-DEG wraps around β-tubulin while TBCE extends along α-tubulin. The TBC-DEG/TBCC-αβ-tubulin structures reveal that TBCC forms multi-domain interactions with Arl2 and TBCD to engage the αβ-tubulin intradimer-interface, promoting TBCE rotation while TBCD holds β-tubulin. TBCC engages the GTP-bound Arl2, multiple sites of TBCD, and the native αβ-tubulin intradimer interface near the α-tubulin N-site GTP. Together, these structures uncover transition states for αβ-tubulin biogenesis and degradation, suggesting a vise-like, GTP-hydrolysis-dependent mechanism in which TBCC binding to TBC-DEG modulates αβ-tubulin interfaces. Our studies provide structural evidence that tubulin cofactors act as enzymatic regulators that assemble the invariant αβ-tubulin architecture. By catalyzing α- and β-tubulin biogenesis and degradation, the TBC-DEG and TBCC assemblies regulate the polymerization competency of αβ-tubulin for microtubule formation.
History
DepositionNov 18, 2024-
Header (metadata) releaseFeb 4, 2026-
Map releaseFeb 4, 2026-
UpdateFeb 4, 2026-
Current statusFeb 4, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47948.png

Downloads & links

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Map

FileDownload / File: emd_47948.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 400 pix.
= 352. Å		0.88 Å/pix.
x 400 pix.
= 352. Å		0.88 Å/pix.
x 400 pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0201
Minimum - Maximum-0.015987411 - 2.234844
Average (Standard dev.)0.0017748824 (±0.030917322)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Tubulin Cofactors D,E,G,C and Tubulin complex

EntireName: Tubulin Cofactors D,E,G,C and Tubulin complex
Components
  • Complex: Tubulin Cofactors D,E,G,C and Tubulin complex
    • Protein or peptide: Chromosome instability protein 1
    • Protein or peptide: Protein PAC2
    • Protein or peptide: GTP-binding protein CIN4
    • Protein or peptide: Tubulin alpha-1A chain
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: Tubulin-specific chaperone C
    • Protein or peptide: iih5 Alpha Repeating
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: GUANOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Tubulin Cofactors D,E,G,C and Tubulin complex

SupramoleculeName: Tubulin Cofactors D,E,G,C and Tubulin complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5, #7, #6
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Chromosome instability protein 1

MacromoleculeName: Chromosome instability protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 117.739406 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MHHHHHHMNN IRALLDSIQS GVQTVSPEKH QQTIAAINKF QDDPALLDTI LPRCVPLLTK SFFCMSQRDQ KLVAELFYNL DKISHSKVL KSLDTSIFRL NEILNYLQDR ASPSSFSDVL CVYLNLSWLS VILLSPYAFK DKFNKTLQVS SRFENYPICI P PINKIKAV ...String:
MHHHHHHMNN IRALLDSIQS GVQTVSPEKH QQTIAAINKF QDDPALLDTI LPRCVPLLTK SFFCMSQRDQ KLVAELFYNL DKISHSKVL KSLDTSIFRL NEILNYLQDR ASPSSFSDVL CVYLNLSWLS VILLSPYAFK DKFNKTLQVS SRFENYPICI P PINKIKAV LYFKNFTDAF DQLPEREQAN VPFLNQFLKL FIQSSEKANY YFSNENLRHL QQVALSNDGI KLLPKLFQIS FN HGSHDIL DAIVEFFHDH LSSNSTDTRF QLAHSFAKIA KFLHQADPAS FIELIDYTIE NTVSLLQAPC DSIDSNELHT SLL IIAEVA LAKILPIDLV DRVLTLIIPK TCHFQKSHFQ IIKGHHIRDS TNFIIWSVIR SNRSNSLSPQ VLQSLLSHLL INAF FDPEL IIRYSSFAAL QELLGRSNKS LALNQNDIAL ILQANWKDLP RSFEENSGLI RRLFNPENTS KSAVCVWKVF RDWSF NWNL LENLHLTTMK LNIDYNLVPL IKSKLSSPAL LQEVLNKAGS SVTQNCQILY LYLKLFENDV NCPKISEICI DIYQKK IKF QLTTQAKRQF NDNSPELFQI FVILKYWQLT GQNDFNQELF WKFVDIVSPQ KKLNLYNEFI PIIQQIISQC VSLNYTR IV QLIKSDNELT CRSICHMPDQ EKMCSLFFSQ FPLLSPQSRS LLIGELDHHW DVRISLLPSN SYRKFRNIII NCLDDYTI T QQGDVGRLVR IQALKLMQSH PDFLSGDCDS INPKLTRLLA EPVPEIRKLS YQLLASATSQ ITVLSDSSIL NFRHKQGLS EEFWKGYAVS AGAIHFTDSQ LTSSIDSFIV YYRSLSPSQQ LELCHDLIRI IPSAKQIAES RIRDRNKDPL TGGMRFDTIK FTIHCVKFW TRIMESGLVV LHPNFNFQGV FAKFYNLHLL DCTTLRVSVI KFFPFLAISC YHTMRENADQ KNLSNIILKR L LVLVKREY AATKSKFMTD QNVALQGMFQ IFLELGVTRQ LQALQVACQK HELANILESD ITL

UniProtKB: Chromosome instability protein 1

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Macromolecule #2: Protein PAC2

MacromoleculeName: Protein PAC2 / type: protein_or_peptide / ID: 2
Details: Chain E contains a well-resolved C-terminal region that was modeled with full side-chain identities. Density for the LRR and CAP-Gly domains is weaker and discontinuous, consistent with ...Details: Chain E contains a well-resolved C-terminal region that was modeled with full side-chain identities. Density for the LRR and CAP-Gly domains is weaker and discontinuous, consistent with flexibility of this portion of the protein in the complex. Therefore, residues in these regions are modeled as poly-alanine to represent the backbone trace and overall topology only (listed as UNK in the entry). Side-chain identities are not asserted in these low-density regions. The sequence register is anchored by the well-resolved C-terminal domain and supported by the AlphaFold prediction.,Chain E contains a well-resolved C-terminal region that was modeled with full side-chain identities. Density for the LRR and CAP-Gly domains is weaker and discontinuous, consistent with flexibility of this portion of the protein in the complex. Therefore, residues in these regions are modeled as poly-alanine to represent the backbone trace and overall topology only (listed as UNK in the entry). Side-chain identities are not asserted in these low-density regions. The sequence register is anchored by the well-resolved C-terminal domain and supported by the AlphaFold prediction.
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 42.767723 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)QSLVL KIKIRAGKKP SSDLDYWVLP SFTVRYVKSV ICRKLNFDIL NVKLFHENSE GMINE IKYN FRPISDFNVV NGDIIHVSSP VNNKSIQKVN SPS

UniProtKB: Protein PAC2

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Macromolecule #3: GTP-binding protein CIN4

MacromoleculeName: GTP-binding protein CIN4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 22.081746 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGLLSIIRKQ KLRDKEIRCL ILGLDNSGKS TIVNKLLPKD EQNNDGIMPT VGFQIHSLMI KDVTISLWDI GGLRTLRPFW DNYFDKTQA MIWCIDVSLS MRFDETLQEL KELINRDENR IGYECAVIVV LNKIDLVEDK SELHRRCLLV ESELKCLFKP D IRIELVKC SGVTGEGIDN LRDRLVESCH FTQ

UniProtKB: GTP-binding protein CIN4

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Macromolecule #4: Tubulin alpha-1A chain

MacromoleculeName: Tubulin alpha-1A chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 50.121266 KDa
SequenceString: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFSVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...String:
MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFSVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLIGQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRAHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRTIQFVDW CPTGFKVGIN YEPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY

UniProtKB: Tubulin alpha-1A chain

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Macromolecule #5: Tubulin beta chain

MacromoleculeName: Tubulin beta chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 49.90777 KDa
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPTGSYHGDS DLQLERINVY YNEAAGNKYV PRAILVDLEP GTMDSVRSGP FGQIFRPDN FVFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKESESCDC LQGFQLTHSL GGGTGSGMGT LLISKIREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS VHQLVENTDE TYCIDNEALY DICFRTLKLT TPTYGDLNHL VSATMSGVTT CL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTSRG SQQYRALTVP ELTQQMFDAK NMMAACDPRH GRYLTVAAVF RGR MSMKEV DEQMLNVQNK NSSYFVEWIP NNVKTAVCDI PPRGLKMSAT FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATADEQGE FEEEGEEDEA

UniProtKB: Tubulin beta chain

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Macromolecule #6: iih5 Alpha Repeating

MacromoleculeName: iih5 Alpha Repeating / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 18.866582 KDa
SequenceString:
MRGSHHHHHH TDPEKVEMYI KNLQDDSPPV RFNAAVALGK IGDERAVEPL IKALKDEDWQ VRKTAAYALG KIGDERAVEP LIKALKDED RYVRSRAALA LGKIGDERAV EPLIKALKDE DEYVRLSAAS ALGKIGGERV RAAMEKLAET GTGFARKVAV N YLETHKSL IS

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Macromolecule #7: Tubulin-specific chaperone C

MacromoleculeName: Tubulin-specific chaperone C / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 30.750805 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDFTAKIKEL ERELSETSDY KTLQKKTISL RSELNTLSHS LTSYEKEHFS NDIENVLKSI NAKLSESKGK KRLFSFKQKN SSSAVHKNV ERTELANAPA YTTTLKKHYV LEKGDSAFEN LEFCTVTSTT DYSGNSALSG SLCFRNITKC VINLQRIFFQ T GSIFITDC ...String:
MDFTAKIKEL ERELSETSDY KTLQKKTISL RSELNTLSHS LTSYEKEHFS NDIENVLKSI NAKLSESKGK KRLFSFKQKN SSSAVHKNV ERTELANAPA YTTTLKKHYV LEKGDSAFEN LEFCTVTSTT DYSGNSALSG SLCFRNITKC VINLQRIFFQ T GSIFITDC TDSIIFLRSP SDKDFQIRLR DLKNCKILIE KLSPSIDCKQ VVIIENCHKC IFNASTRDHL IIQDFSNPFQ SE ETEDNSA FAFEDFDICN KDTMQLFRAY L

UniProtKB: Tubulin-specific chaperone C

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Macromolecule #8: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 8 / 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 #9: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 9 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

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

BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm

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Image processing #1

Image processing ID1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 370000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Image processing #2

Image processing ID2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 370000
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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