[English] 日本語
Yorodumi
- PDB-5lt4: nucleotide-free kinesin-1 motor domain T92V mutant, P1 crystal form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lt4
Titlenucleotide-free kinesin-1 motor domain T92V mutant, P1 crystal form
ComponentsKinesin-1 heavy chain
KeywordsMOTOR PROTEIN / Kinesin motor domain / ADP dissociation / nucleotide-free
Function / homology
Function and homology information


regulation of modification of synapse structure, modulating synaptic transmission / plus-end-directed vesicle transport along microtubule / cytoplasm organization / cytolytic granule membrane / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / mitocytosis / retrograde neuronal dense core vesicle transport / anterograde axonal protein transport / ciliary rootlet ...regulation of modification of synapse structure, modulating synaptic transmission / plus-end-directed vesicle transport along microtubule / cytoplasm organization / cytolytic granule membrane / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / mitocytosis / retrograde neuronal dense core vesicle transport / anterograde axonal protein transport / ciliary rootlet / lysosome localization / positive regulation of potassium ion transport / vesicle transport along microtubule / plus-end-directed microtubule motor activity / RHO GTPases activate KTN1 / Kinesins / kinesin complex / microtubule motor activity / centrosome localization / mitochondrion transport along microtubule / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / stress granule disassembly / natural killer cell mediated cytotoxicity / Insulin processing / synaptic vesicle transport / postsynaptic cytosol / phagocytic vesicle / axon cytoplasm / MHC class II antigen presentation / dendrite cytoplasm / axon guidance / positive regulation of synaptic transmission, GABAergic / regulation of membrane potential / positive regulation of protein localization to plasma membrane / cellular response to type II interferon / centriolar satellite / Signaling by ALK fusions and activated point mutants / nuclear membrane / microtubule binding / vesicle / microtubule / cadherin binding / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Kinesin motor domain / Kinesin / 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 ...Kinesin motor domain / Kinesin / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Kinesin-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.881 Å
AuthorsCao, L. / Gigant, B.
Funding support France, 3items
OrganizationGrant numberCountry
French National Research AgencyANR-12-BSV8-0002-01 France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-05-01 France
ARC France
CitationJournal: Sci Rep / Year: 2017
Title: The structural switch of nucleotide-free kinesin.
Authors: Cao, L. / Cantos-Fernandes, S. / Gigant, B.
History
DepositionSep 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2024Group: 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
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
B: Kinesin-1 heavy chain
C: Kinesin-1 heavy chain
D: Kinesin-1 heavy chain
E: Kinesin-1 heavy chain
K: Kinesin-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,80118
Polymers217,6496
Non-polymers1,15312
Water4,540252
1
A: Kinesin-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4673
Polymers36,2751
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kinesin-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3712
Polymers36,2751
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kinesin-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4673
Polymers36,2751
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Kinesin-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6595
Polymers36,2751
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Kinesin-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3712
Polymers36,2751
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Kinesin-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4673
Polymers36,2751
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.145, 102.108, 102.137
Angle α, β, γ (deg.)119.49, 91.95, 91.85
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
Kinesin-1 heavy chain / Conventional kinesin heavy chain / Ubiquitous kinesin heavy chain / UKHC


Mass: 36274.773 Da / Num. of mol.: 6 / Mutation: C7S, C65A, T92V, C168A, C174S, C294A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF5B, KNS, KNS1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P33176
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.38 Å3/Da / Density % sol: 48.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM Mes pH 6.5 0.16 M ammonium sulfate 30% mPEG 5000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.87→49.3 Å / Num. obs: 43981 / % possible obs: 96.5 % / Redundancy: 3.4 % / CC1/2: 0.964 / Rrim(I) all: 0.32 / Net I/σ(I): 4.5
Reflection shellRrim(I) all: 1.68

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4lnu

4lnu


Resolution: 2.881→49.277 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 30.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2799 2015 4.58 %
Rwork0.2051 --
obs0.2085 43981 97.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.881→49.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13824 0 60 252 14136
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01114091
X-RAY DIFFRACTIONf_angle_d1.4819097
X-RAY DIFFRACTIONf_dihedral_angle_d14.1354974
X-RAY DIFFRACTIONf_chiral_restr0.0592210
X-RAY DIFFRACTIONf_plane_restr0.0072481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8812-2.95330.38641430.30432429X-RAY DIFFRACTION80
2.9533-3.03310.32251230.27673057X-RAY DIFFRACTION98
3.0331-3.12230.32411450.26483026X-RAY DIFFRACTION98
3.1223-3.22310.33721540.26563007X-RAY DIFFRACTION98
3.2231-3.33830.36141550.27653038X-RAY DIFFRACTION98
3.3383-3.47190.311290.26823014X-RAY DIFFRACTION98
3.4719-3.62990.33851450.23983042X-RAY DIFFRACTION99
3.6299-3.82120.27841630.19343079X-RAY DIFFRACTION99
3.8212-4.06050.26131390.17493029X-RAY DIFFRACTION99
4.0605-4.37380.2351500.16563055X-RAY DIFFRACTION99
4.3738-4.81360.21591470.1563049X-RAY DIFFRACTION99
4.8136-5.50940.27011280.17943038X-RAY DIFFRACTION99
5.5094-6.93810.27591420.21473059X-RAY DIFFRACTION99
6.9381-49.28440.24871520.17783044X-RAY DIFFRACTION98
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)
13.08620.51380.19241.34440.35021.53480.004-0.316-0.34090.2286-0.02520.00220.0327-0.10750.02110.39780.0624-0.06870.24060.10230.436312.676311.865511.2217
23.4041-0.9235-0.10512.5708-0.72661.95370.2710.68910.8604-0.0841-0.2203-0.1681-0.10530.1417-0.06530.41910.0426-0.01540.43640.19190.544324.01027.123951.392
32.57090.0217-0.67442.0678-0.19121.99690.11650.18850.905-0.0828-0.00470.2904-0.1711-0.1365-0.02520.33180.0258-0.00880.28120.05150.617828.750252.449.0121
43.5498-0.68050.3352.1603-0.14071.46090.03530.2758-0.2046-0.08410.01150.04490.0329-0.0619-0.04340.33360.0024-0.04140.29380.01090.228-2.716129.4087-25.7232
53.3628-0.1123-1.07421.69540.03192.46020.31-0.67590.2340.1731-0.1259-0.1969-0.01340.2808-0.13240.3601-0.0325-0.04680.4222-0.06960.40011.210747.937238.7967
62.25030.70560.33032.613-0.11651.23480.11690.2259-0.94830.0582-0.0275-0.27320.16450.0867-0.06030.4320.0207-0.00410.2577-0.02520.8011-14.737-12.032-7.2288
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 4 through 324)
2X-RAY DIFFRACTION2(chain 'B' and resid 6 through 324)
3X-RAY DIFFRACTION3(chain 'C' and resid 4 through 324)
4X-RAY DIFFRACTION4(chain 'D' and resid 6 through 325)
5X-RAY DIFFRACTION5(chain 'E' and resid 7 through 324)
6X-RAY DIFFRACTION6(chain 'K' and resid 5 through 324)

+
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