[English] 日本語
Yorodumi
- PDB-8tt7: NMR Assignments and Structure for the Dimeric Kinesin Neck Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tt7
TitleNMR Assignments and Structure for the Dimeric Kinesin Neck Domain
ComponentsKinesin heavy chain isoform 5C
KeywordsMOTOR PROTEIN / microtubule motors / intracellular transport
Function / homology
Function and homology information


distal axon / anterograde dendritic transport of messenger ribonucleoprotein complex / anterograde axonal protein transport / apolipoprotein receptor binding / intracellular mRNA localization / motor neuron axon guidance / microtubule motor activity / ciliary rootlet / postsynaptic cytosol / GABA-ergic synapse ...distal axon / anterograde dendritic transport of messenger ribonucleoprotein complex / anterograde axonal protein transport / apolipoprotein receptor binding / intracellular mRNA localization / motor neuron axon guidance / microtubule motor activity / ciliary rootlet / postsynaptic cytosol / GABA-ergic synapse / mRNA transport / axonal growth cone / axon cytoplasm / dendrite cytoplasm / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / microtubule binding / microtubule / neuron projection / neuronal cell body / dendrite / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Kinesin heavy chain isoform 5C
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
AuthorsAlexandrescu, A.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MB 0236316 United States
CitationJournal: Biomol.Nmr Assign. / Year: 2023
Title: Solution NMR assignments and structure for the dimeric kinesin neck domain.
Authors: Seo, D. / Kammerer, R.A. / Alexandrescu, A.T.
History
DepositionAug 12, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2May 15, 2024Group: Database references / Category: database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kinesin heavy chain isoform 5C
B: Kinesin heavy chain isoform 5C


Theoretical massNumber of molelcules
Total (without water)12,6762
Polymers12,6762
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, Actually the correct answer here would be "according to the literature". This option was not given: Tripet B, Vale RD, Hodges RS (1997) Demonstration of coiled-coil ...Evidence: NMR Distance Restraints, Actually the correct answer here would be "according to the literature". This option was not given: Tripet B, Vale RD, Hodges RS (1997) Demonstration of coiled-coil interactions within the kinesin neck region using synthetic peptides. Implications for motor activity J Biol Chem 272:8946-8956 doi:10.1074/jbc.272.14.8946 Kozielski F et al. (1997) The crystal structure of dimeric kinesin and implications for microtubule-dependent motility Cell 91:985-994 doi:10.1016/s0092-8674(00)80489-4
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with the lowest energy
RepresentativeModel #1closest to the average

-
Components

#1: Protein Kinesin heavy chain isoform 5C / Kinesin heavy chain neuron-specific 2 / Kinesin-1


Mass: 6338.247 Da / Num. of mol.: 2 / Fragment: Neck domain, residues 325-376
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kif5c, Nkhc2 / Plasmid: pHisTrx2
Details (production host): The plasmid is a derivative of pET-32a (Novagen) that encodes E. coli thioredoxin with an N-terminal 6-His tag and a thrombin cleavage site, followed by a unique multiple cloning site
Production host: Escherichia coli (E. coli) / Strain (production host): JM109(DE3)
References: UniProt: P56536, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
313isotropic12D 1H-15N HSQC
121isotropic13D HN(CA)CB
131isotropic13D HNCA
141isotropic13D HN(CO)CA
353isotropic13D 1H-15N TOCSY
363isotropic13D 1H-15N NOESY
272isotropic22D 1H-13C HSQC
282isotropic33D HCACO
292isotropic23D (H)CCH-TOCSY
2102isotropic23D 1H-13C NOESY
4114isotropic1Hydrogen Exchange N-HSQC

-
Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution10.75 mM [U-13C; U-15N] Kinesin_neck, 90% H2O/10% D2OH2O sample90% H2O/10% D2O
solution20.75 mM [U-13C; U-15N] Kinesin_neck, 100% D2OD2O sample100% D2O
solution30.75 mM [U-15N] Kinesin_neck, 90% H2O/10% D2OH2O sample290% H2O/10% D2O
solution40.75 mM [U-15N] Kinesin_neck, 100% D2OD2O sample2100% D2OUsed for HX experiments at 23 C (296K)
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.75 mMKinesin_neck[U-13C; U-15N]1
0.75 mMKinesin_neck[U-13C; U-15N]2
0.75 mMKinesin_neck[U-15N]3
0.75 mMKinesin_neck[U-15N]4
Sample conditions
Conditions-IDDetailsIonic strengthLabelpHPressure (kPa)Temperature (K)
113C/15N in H2O used for backbone assignments150 mMH2O6.11 atm310 K
215N/13C used for side chain assignments and 13C-NOESY150 mMD2O6.1 pD1 atm310 K
315N-sample for TOCSY-HSQC and NOESY-HSQC150 mMH2O sample 26.11 atm310 K
415N-sample for HX experiments at 296K150 mMD2O sample 26.1 pD1 atm296 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Varian INOVAVarianINOVA6001w/ cryoprobe
Bruker AVANCE NEOBrukerAVANCE NEO6002w/ cryoprobe
Bruker AVANCEBrukerAVANCE5003room temp probe

-
Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
In-house / customiNMR from MNovaprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
FelixAccelrys Software Inc.processing
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
CcpNmr AnalysisCCPNchemical shift assignment
CcpNmr AnalysisCCPNpeak picking
VnmrJVariancollection
TopSpinBruker Biospincollection
CcpNmr AnalysisCCPNdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
Details: sa.inp script of X-Plor NIH tutorial followed by 3 cycles of refine.inp (from X-PLOR NIH). Structures with no violations selected for next round. multiple cycles of prot_sa_refine.inp from ...Details: sa.inp script of X-Plor NIH tutorial followed by 3 cycles of refine.inp (from X-PLOR NIH). Structures with no violations selected for next round. multiple cycles of prot_sa_refine.inp from this site (https://nesgwiki.chem.buffalo.edu/index.php/Structure_Refinement_Using_XPLOR-NIH) until no violations. Structures have no differences the human eye can see but have better PDB quality bars.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / 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://pdbjlvh1.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