[English] 日本語
Yorodumi
- PDB-6ign: The crystal structure of Kif5b stalk 1 coiled-coil region -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ign
TitleThe crystal structure of Kif5b stalk 1 coiled-coil region
ComponentsKinesin-1 heavy chainKinesin
KeywordsMOTOR PROTEIN / coiled-coil
Function / homology
Function and homology information


RHO GTPases activate KTN1 / membrane-bounded organelle / cytoplasm organization / plus-end-directed vesicle transport along microtubule / anterograde dendritic transport of neurotransmitter receptor complex / positive regulation of voltage-gated sodium channel activity / retrograde neuronal dense core vesicle transport / Kinesins / positive regulation of vesicle fusion / anterograde axonal protein transport ...RHO GTPases activate KTN1 / membrane-bounded organelle / cytoplasm organization / plus-end-directed vesicle transport along microtubule / anterograde dendritic transport of neurotransmitter receptor complex / positive regulation of voltage-gated sodium channel activity / retrograde neuronal dense core vesicle transport / Kinesins / positive regulation of vesicle fusion / anterograde axonal protein transport / COPI-dependent Golgi-to-ER retrograde traffic / cytoskeleton-dependent intracellular transport / vesicle transport along microtubule / lysosome localization / positive regulation of intracellular protein transport / positive regulation of potassium ion transport / natural killer cell mediated cytotoxicity / MHC class II antigen presentation / JUN kinase binding / plus-end-directed microtubule motor activity / stress granule disassembly / microtubule lateral binding / ciliary rootlet / centrosome localization / kinesin complex / synaptic vesicle transport / microtubule motor activity / mitochondrial transport / microtubule-based movement / positive regulation of insulin secretion involved in cellular response to glucose stimulus / endocytic vesicle / centriolar satellite / microtubule-based process / phagocytic vesicle / axonal growth cone / axon cytoplasm / dendrite cytoplasm / regulation of membrane potential / axon guidance / positive regulation of synaptic transmission, GABAergic / hippocampus development / positive regulation of protein localization to plasma membrane / cellular response to type II interferon / microtubule cytoskeleton / microtubule binding / vesicle / microtubule / neuron projection / lysosomal membrane / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding / identical protein binding / cytosol / 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-1 heavy chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.451 Å
AuthorsZhang, S.J. / Sun, W.P. / Kong, B.
CitationJournal: To Be Published
Title: The crystal structure of Kif5b stalk 1 coiled-coil region
Authors: Zhang, S.J. / Sun, W.P. / Kong, B.
History
DepositionSep 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kinesin-1 heavy chain


Theoretical massNumber of molelcules
Total (without water)14,1261
Polymers14,1261
Non-polymers00
Water0
1
A: Kinesin-1 heavy chain

A: Kinesin-1 heavy chain


Theoretical massNumber of molelcules
Total (without water)28,2522
Polymers28,2522
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Buried area4460 Å2
ΔGint-32 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.559, 50.559, 162.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222

-
Components

#1: Protein Kinesin-1 heavy chain / Kinesin / C


Mass: 14125.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kif5b, Khcs, Kns1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q61768

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 66.6 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I_PLUS/MINUS COLUMNS.
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.05 M magnesium chloride,5% PEG 8000, 40% MPD, 0.1M sodium cacodylate pH6.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.45→50 Å / Num. obs: 3101 / % possible obs: 86.9 % / Redundancy: 19.2 % / CC1/2: 0.961 / Rmerge(I) obs: 0.063 / Net I/σ(I): 46.389
Reflection shellResolution: 3.45→3.51 Å / Redundancy: 17.2 % / Rmerge(I) obs: 0.583 / CC1/2: 0.985

-
Processing

Software
NameVersionClassification
PHENIX(1.14_3228: ???)refinement
HKL-2000vdata reduction
HKL-2000data scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 3.451→36.971 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.16
RfactorNum. reflection% reflection
Rfree0.3175 436 10.07 %
Rwork0.2744 --
obs0.2787 2743 81.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.451→36.971 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms983 0 0 0 983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001985
X-RAY DIFFRACTIONf_angle_d0.4251317
X-RAY DIFFRACTIONf_dihedral_angle_d2.425643
X-RAY DIFFRACTIONf_chiral_restr0.027153
X-RAY DIFFRACTIONf_plane_restr0.001175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4515-3.95040.3965890.3091841X-RAY DIFFRACTION52
3.9504-4.97520.28691650.24561487X-RAY DIFFRACTION94
4.9752-36.97330.31081820.29091566X-RAY DIFFRACTION98

+
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