[English] 日本語
Yorodumi
- PDB-7ai4: Crystal structure of the KLC1-TPR domain truncated from its nonTP... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ai4
TitleCrystal structure of the KLC1-TPR domain truncated from its nonTPR region ([A1-B6]-Delta-nonTPR fragment)
ComponentsIsoform C of Kinesin light chain 1,Isoform C of Kinesin light chain 1
KeywordsMOTOR PROTEIN / Kinesin Light Chain / kinesin1 / TPR domain / Kif5 / accesosry protein
Function / homology
Function and homology information


Kinesins / RHO GTPases activate KTN1 / stress granule disassembly / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule-based movement / cytoskeletal motor activity / kinesin binding / MHC class II antigen presentation / Signaling by ALK fusions and activated point mutants ...Kinesins / RHO GTPases activate KTN1 / stress granule disassembly / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule-based movement / cytoskeletal motor activity / kinesin binding / MHC class II antigen presentation / Signaling by ALK fusions and activated point mutants / growth cone / cytoplasmic vesicle / microtubule / cell adhesion / membrane / cytoplasm / cytosol
Similarity search - Function
Kinesin light chain / Kinesin light chain repeat / Kinesin light chain repeat. / Tetratricopeptide repeat / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Kinesin light chain 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.795 Å
AuthorsMenetrey, J. / Llinas, P.
CitationJournal: To Be Published
Title: Structural investigations of the dynamics of the TPR domain of kinesin light chain
Authors: Menetrey, J. / Llinas, P.
History
DepositionSep 26, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Isoform C of Kinesin light chain 1,Isoform C of Kinesin light chain 1
B: Isoform C of Kinesin light chain 1,Isoform C of Kinesin light chain 1


Theoretical massNumber of molelcules
Total (without water)66,5512
Polymers66,5512
Non-polymers00
Water00
1
A: Isoform C of Kinesin light chain 1,Isoform C of Kinesin light chain 1


Theoretical massNumber of molelcules
Total (without water)33,2761
Polymers33,2761
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoform C of Kinesin light chain 1,Isoform C of Kinesin light chain 1


Theoretical massNumber of molelcules
Total (without water)33,2761
Polymers33,2761
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)123.220, 55.820, 103.570
Angle α, β, γ (deg.)90.000, 108.510, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Isoform C of Kinesin light chain 1,Isoform C of Kinesin light chain 1 / KLC 1


Mass: 33275.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KLC1, KLC, KNS2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q07866

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 1.1 M sodium formate and 0.1 M Hepes pH 7.9

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.795→49.11 Å / Num. obs: 16666 / % possible obs: 99 % / Redundancy: 3.3 % / CC1/2: 0.998 / Net I/σ(I): 10.17
Reflection shellResolution: 2.795→2.96 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 0.92 / Num. unique obs: 2608 / CC1/2: 0.538 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
BUSTER2.10.3 (6-FEB-2020)refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OJ8

5oj8


Resolution: 2.795→49.11 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / SU R Cruickshank DPI: 0.696 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.619 / SU Rfree Blow DPI: 0.311 / SU Rfree Cruickshank DPI: 0.323
RfactorNum. reflection% reflectionSelection details
Rfree0.2515 834 5 %RANDOM
Rwork0.217 ---
obs0.2187 16666 99.2 %-
Displacement parametersBiso max: 176.07 Å2 / Biso mean: 111.69 Å2 / Biso min: 69.73 Å2
Baniso -1Baniso -2Baniso -3
1--13.4816 Å20 Å214.2202 Å2
2--13.4599 Å20 Å2
3---0.0217 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: final / Resolution: 2.795→49.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3501 0 0 0 3501
Num. residues----478
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1168SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes622HARMONIC5
X-RAY DIFFRACTIONt_it3555HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion494SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2781SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3555HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg4848HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion2.49
X-RAY DIFFRACTIONt_other_torsion22.46
LS refinement shellResolution: 2.795→2.82 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3215 21 5.16 %
Rwork0.3194 386 -
obs--82.06 %
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)
15.19780.432.02661.0067-0.14821.7960.1646-0.192-0.0278-0.0377-0.0011-0.088-0.08810.0348-0.1635-0.88690.02290.0616-1.0233-0.0426-0.8325-15.79-5.19263.2868
22.6694-0.41523.58680.9981-0.55087.18390.00590.1257-0.1827-0.27670.2340.1610.1773-0.0644-0.2399-0.52680.01120.0452-0.87640.065-0.9988-27.1699-7.2987-48.8087
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A208 - 495
2X-RAY DIFFRACTION2{ B|* }B209 - 495

+
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