[English] 日本語
Yorodumi
- PDB-7c1m: Complex structure of tyrosinated alpha-tubulin carboxy-terminal p... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7c1m
TitleComplex structure of tyrosinated alpha-tubulin carboxy-terminal peptide and A1aY1 binder
Components
  • Carboxy-terminal peptide from tyrosinated alpha-tubulin
  • Nanobody binder from SSO7d library
KeywordsPROTEIN BINDING / Tyrosinated / Microtubule / Binder / SSO7d / yeast display
Function / homology
Function and homology information


Cargo trafficking to the periciliary membrane / Post-chaperonin tubulin folding pathway / axonemal microtubule / cytoskeleton-dependent intracellular transport / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / organelle transport along microtubule / forebrain morphogenesis / glial cell differentiation / cerebellar cortex morphogenesis ...Cargo trafficking to the periciliary membrane / Post-chaperonin tubulin folding pathway / axonemal microtubule / cytoskeleton-dependent intracellular transport / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / organelle transport along microtubule / forebrain morphogenesis / glial cell differentiation / cerebellar cortex morphogenesis / dentate gyrus development / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / neuron projection arborization / Formation of tubulin folding intermediates by CCT/TriC / Gap junction assembly / smoothened signaling pathway / pyramidal neuron differentiation / motor behavior / Kinesins / Prefoldin mediated transfer of substrate to CCT/TriC / response to L-glutamate / COPI-independent Golgi-to-ER retrograde traffic / Assembly and cell surface presentation of NMDA receptors / centrosome cycle / COPI-dependent Golgi-to-ER retrograde traffic / 'de novo' protein folding / startle response / flagellated sperm motility / regulation of synapse organization / Recycling pathway of L1 / microtubule polymerization / locomotory exploration behavior / response to tumor necrosis factor / homeostasis of number of cells within a tissue / response to mechanical stimulus / sperm flagellum / adult locomotory behavior / RHO GTPases activate IQGAPs / microtubule-based process / Hedgehog 'off' state / COPI-mediated anterograde transport / condensed chromosome / Activation of AMPK downstream of NMDARs / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / cellular response to calcium ion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / AURKA Activation by TPX2 / Resolution of Sister Chromatid Cohesion / Translocation of SLC2A4 (GLUT4) to the plasma membrane / neuromuscular junction / neuron migration / visual learning / cerebral cortex development / RHO GTPases Activate Formins / intracellular protein transport / memory / synapse organization / PKR-mediated signaling / microtubule cytoskeleton organization / recycling endosome / structural constituent of cytoskeleton / neuron differentiation / cytoplasmic ribonucleoprotein granule / HCMV Early Events / Aggrephagy / neuron apoptotic process / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / protein-folding chaperone binding / cilium / microtubule binding / microtubule / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein stabilization / protein heterodimerization activity / cell division / hydrolase activity / GTP binding / protein-containing complex binding / structural molecule activity / extracellular exosome / metal ion binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Alpha 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 ...Alpha 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
Tubulin alpha-1A chain
Similarity search - Component
Biological speciesSaccharolobus solfataricus 98/2 (archaea)
Homo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsKesarwani, S. / Reddy, P.P. / Sirajuddin, M. / Das, R.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)DBT/PR5081/INF/156/2012 India
CitationJournal: J.Cell Biol. / Year: 2020
Title: Genetically encoded live-cell sensor for tyrosinated microtubules.
Authors: Kesarwani, S. / Lama, P. / Chandra, A. / Reddy, P.P. / Jijumon, A.S. / Bodakuntla, S. / Rao, B.M. / Janke, C. / Das, R. / Sirajuddin, M.
History
DepositionMay 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nanobody binder from SSO7d library
B: Carboxy-terminal peptide from tyrosinated alpha-tubulin


Theoretical massNumber of molelcules
Total (without water)8,8422
Polymers8,8422
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1140 Å2
ΔGint-5 kcal/mol
Surface area5270 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Antibody Nanobody binder from SSO7d library


Mass: 7486.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharolobus solfataricus 98/2 (archaea)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Protein/peptide Carboxy-terminal peptide from tyrosinated alpha-tubulin


Mass: 1355.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q71U36*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HNCO
141isotropic13D HN(CA)CO
151isotropic13D HN(CA)CB
1101isotropic13D CBCA(CO)NH
191isotropic13D C(CO)NH
181isotropic13D H(CCO)NH
171isotropic13D (H)CCH-TOCSY
161isotropic22D Filtered NOESY
1111isotropic22D Filtered TOCSY
1121isotropic23D 13C-filtered, 13C-edited NOESY

-
Sample preparation

DetailsType: solution
Contents: 50 mM unlabeled sodium phosphate, 200 mM unlabeled sodium chloride, 90% H2O/10% D2O
Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
50 mMsodium phosphateunlabeled1
200 mMsodium chlorideunlabeled1
Sample conditionsIonic strength: 200 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III6001
Bruker AVANCE IIIBrukerAVANCE III8002

-
Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxchemical shift assignment
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddarddata analysis
CS-ROSETTAShen, Vernon, Baker and Baxstructure calculation
HADDOCKBonvinstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 6
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

+
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