[English] 日本語
Yorodumi
- PDB-4icu: Ubiquitin-like domain of human tubulin folding cofactor E - cryst... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4icu
TitleUbiquitin-like domain of human tubulin folding cofactor E - crystal from A
ComponentsTubulin-specific chaperone E
KeywordsCHAPERONE / Ubiquitin-like domain / tubulin folding cofactor / alpha tubulin / tubulin folding cofactor B
Function / homology
Function and homology information


peripheral nervous system neuron axonogenesis / post-chaperonin tubulin folding pathway / muscle atrophy / Post-chaperonin tubulin folding pathway / tubulin complex assembly / alpha-tubulin binding / developmental growth / adult locomotory behavior / post-embryonic development / mitotic spindle organization ...peripheral nervous system neuron axonogenesis / post-chaperonin tubulin folding pathway / muscle atrophy / Post-chaperonin tubulin folding pathway / tubulin complex assembly / alpha-tubulin binding / developmental growth / adult locomotory behavior / post-embryonic development / mitotic spindle organization / microtubule cytoskeleton organization / protein folding / protein-folding chaperone binding / microtubule / cytoplasm
Similarity search - Function
Tubulin-specific chaperone E / TBCE, ubiquitin-like (Ubl) domain / Ubiquitin-like domain / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...Tubulin-specific chaperone E / TBCE, ubiquitin-like (Ubl) domain / Ubiquitin-like domain / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Leucine-rich repeat domain superfamily / Ubiquitin-like (UB roll) / Ubiquitin-like domain / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Tubulin-specific chaperone E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJanowski, R. / Boutin, M. / Zabala, J.C. / Coll, M.
CitationJournal: J Cell Sci / Year: 2015
Title: The structure of the complex between α-tubulin, TBCE and TBCB reveals a tubulin dimer dissociation mechanism.
Authors: Marina Serna / Gerardo Carranza / Jaime Martín-Benito / Robert Janowski / Albert Canals / Miquel Coll / Juan Carlos Zabala / José María Valpuesta /
Abstract: Tubulin proteostasis is regulated by a group of molecular chaperones termed tubulin cofactors (TBC). Whereas tubulin heterodimer formation is well-characterized biochemically, its dissociation ...Tubulin proteostasis is regulated by a group of molecular chaperones termed tubulin cofactors (TBC). Whereas tubulin heterodimer formation is well-characterized biochemically, its dissociation pathway is not clearly understood. Here, we carried out biochemical assays to dissect the role of the human TBCE and TBCB chaperones in α-tubulin-β-tubulin dissociation. We used electron microscopy and image processing to determine the three-dimensional structure of the human TBCE, TBCB and α-tubulin (αEB) complex, which is formed upon α-tubulin-β-tubulin heterodimer dissociation by the two chaperones. Docking the atomic structures of domains of these proteins, including the TBCE UBL domain, as we determined by X-ray crystallography, allowed description of the molecular architecture of the αEB complex. We found that heterodimer dissociation is an energy-independent process that takes place through a disruption of the α-tubulin-β-tubulin interface that is caused by a steric interaction between β-tubulin and the TBCE cytoskeleton-associated protein glycine-rich (CAP-Gly) and leucine-rich repeat (LRR) domains. The protruding arrangement of chaperone ubiquitin-like (UBL) domains in the αEB complex suggests that there is a direct interaction of this complex with the proteasome, thus mediating α-tubulin degradation.
History
DepositionDec 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 18, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tubulin-specific chaperone E
B: Tubulin-specific chaperone E
C: Tubulin-specific chaperone E
D: Tubulin-specific chaperone E


Theoretical massNumber of molelcules
Total (without water)39,2784
Polymers39,2784
Non-polymers00
Water1,38777
1
A: Tubulin-specific chaperone E


Theoretical massNumber of molelcules
Total (without water)9,8201
Polymers9,8201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tubulin-specific chaperone E


Theoretical massNumber of molelcules
Total (without water)9,8201
Polymers9,8201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tubulin-specific chaperone E


Theoretical massNumber of molelcules
Total (without water)9,8201
Polymers9,8201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tubulin-specific chaperone E


Theoretical massNumber of molelcules
Total (without water)9,8201
Polymers9,8201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.200, 60.110, 130.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: 2 / Auth seq-ID: 444 - 527 / Label seq-ID: 2 - 85

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

-
Components

#1: Protein
Tubulin-specific chaperone E / Tubulin-folding cofactor E


Mass: 9819.529 Da / Num. of mol.: 4 / Fragment: Ubiquitin-like domain, UNP residues 443-527
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBCE / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q15813
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.95 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris pH 8.5, 200 mM sodium acetate and 26% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 13724 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 23.53 Å2 / Rmerge(I) obs: 0.143 / Net I/σ(I): 11.2
Reflection shellResolution: 2.4→2.46 Å / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 2.3 / % possible all: 87.5

-
Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ICV

4icv


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.908 / SU B: 20.031 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.649 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26349 684 5 %RANDOM
Rwork0.20417 ---
all0.20698 13039 --
obs0.20698 13039 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.579 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--3 Å20 Å2
3----2.83 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2728 0 0 77 2805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222809
X-RAY DIFFRACTIONr_angle_refined_deg1.112.0333791
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3895340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43625.268112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.9615593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1491514
X-RAY DIFFRACTIONr_chiral_restr0.070.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212000
X-RAY DIFFRACTIONr_mcbond_it0.3571.51699
X-RAY DIFFRACTIONr_mcangle_it0.742.52769
X-RAY DIFFRACTIONr_scbond_it2.04251110
X-RAY DIFFRACTIONr_scangle_it3.327101019
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A329tight positional0.220.05
B329tight positional0.230.05
C329tight positional0.190.05
D329tight positional0.20.05
A321medium positional0.570.5
B321medium positional0.560.5
C321medium positional0.420.5
D321medium positional0.520.5
A329tight thermal0.71.5
B329tight thermal0.391.5
C329tight thermal0.371.5
D329tight thermal0.431.5
A321medium thermal0.862.5
B321medium thermal0.672.5
C321medium thermal0.562.5
D321medium thermal0.682.5
LS refinement shellResolution: 2.4→2.529 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.298 94 -
Rwork0.233 1721 -
obs--92.37 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8930.3001-0.10792.1871-0.34572.53290.02550.1630.0704-0.0976-0.06540.04560.0033-0.06140.03990.02170.0096-0.01110.0152-0.00120.009-2.558815.8594-6.9764
24.3511-0.16890.15572.0190.50613.73570.05840.06630.0526-0.1239-0.05890.1047-0.1323-0.06840.00050.1338-0.0124-0.01680.0547-0.05250.0647-19.78166.7107-24.5067
33.1933-0.0473-0.40132.4376-0.96023.5664-0.0351-0.0256-0.04450.00590.0521-0.04110.05760.066-0.0170.132-0.0061-0.05220.08870.07020.078-1.469327.3232-31.029
45.35581.5051-0.81934.14140.23571.6932-0.03180.3720.0052-0.23940.1015-0.0015-0.0028-0.0772-0.06970.10690.0005-0.01040.02770.01730.1794-14.170439.2756-3.4641
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A444 - 527
2X-RAY DIFFRACTION2B444 - 527
3X-RAY DIFFRACTION3C444 - 527
4X-RAY DIFFRACTION4D444 - 527

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more