[English] 日本語
Yorodumi
- PDB-4bxn: Eg5(WT) complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4bxn
TitleEg5(WT) complex
ComponentsKINESIN-LIKE PROTEIN KIF11
KeywordsMOTOR PROTEIN / MITOSIS
Function / homology
Function and homology information


spindle elongation / regulation of mitotic centrosome separation / plus-end-directed microtubule motor activity / mitotic centrosome separation / Kinesins / kinesin complex / microtubule motor activity / spindle organization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement ...spindle elongation / regulation of mitotic centrosome separation / plus-end-directed microtubule motor activity / mitotic centrosome separation / Kinesins / kinesin complex / microtubule motor activity / spindle organization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / mitotic spindle assembly / MHC class II antigen presentation / mitotic spindle organization / spindle / spindle pole / mitotic spindle / mitotic cell cycle / microtubule binding / microtubule / ciliary basal body / cell division / intracellular membrane-bounded organelle / protein kinase binding / protein-containing complex / ATP binding / nucleus / membrane / cytosol
Similarity search - Function
Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain / Kinesin / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. ...Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain / Kinesin / 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
Chem-6LX / ADENOSINE-5'-DIPHOSPHATE / : / Kinesin-like protein KIF11
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.793 Å
AuthorsTalapatra, S.K. / Anthony, N.G. / Mackay, S.P. / Kozielski, F.
CitationJournal: J.Med.Chem. / Year: 2013
Title: The Mitotic Kinesin Eg5 Overcomes Inhibition to the Phase I/II Clinical Candidate Sb743921 by an Allosteric Resistance Mechanism.
Authors: Talapatra, S.K. / Anthony, N.G. / Mackay, S.P. / Kozielski, F.
History
DepositionJul 15, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 31, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Sep 17, 2014Group: Atomic model / Derived calculations / Non-polymer description
Revision 1.3Nov 20, 2019Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _pdbx_database_status.status_code_sf
Revision 1.4Mar 8, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 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: KINESIN-LIKE PROTEIN KIF11
B: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,75636
Polymers82,1112
Non-polymers4,64534
Water1,04558
1
A: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,18917
Polymers41,0561
Non-polymers2,13316
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: KINESIN-LIKE PROTEIN KIF11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,56819
Polymers41,0561
Non-polymers2,51218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.426, 81.426, 115.202
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein KINESIN-LIKE PROTEIN KIF11 / KINESIN-LIKE PROTEIN 1 / KINESIN-LIKE SPINDLE PROTEIN HKSP / KINESIN-RELATED MOTOR PROTEIN EG5 / ...KINESIN-LIKE PROTEIN 1 / KINESIN-LIKE SPINDLE PROTEIN HKSP / KINESIN-RELATED MOTOR PROTEIN EG5 / THYROID RECEPTOR-INTERACTING PROTEIN 5 / TR-INTERACTING PROTEIN 5 / TRIP-5 / EG5


Mass: 41055.582 Da / Num. of mol.: 2 / Fragment: MOTOR DOMAIN, RESIDUES 1-368
Source method: isolated from a genetically manipulated source
Details: SB743921 AS A LIGAND / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPROEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS / References: UniProt: P52732

-
Non-polymers , 5 types, 92 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cd
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-6LX / N-(3-aminopropyl)-N-[(1R)-1-(3-benzyl-7-chloro-4-oxo-4H-chromen-2-yl)-2-methylpropyl]-4-methylbenzamide


Mass: 517.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H33ClN2O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 20

-
Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.23 % / Description: NONE
Crystal growpH: 6.8
Details: 0.02 M CACL2, 0.02 M CADMIUM CHLORIDE, 0.02 M COBALT(II) CHLORIDE, 20% W/V PEG-3350, pH 6.8

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
Reflection twinOperator: -h,-k,l / Fraction: 0.5
ReflectionResolution: 2.8→30 Å / Num. obs: 9633 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Biso Wilson estimate: 83.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.6
Reflection shellResolution: 3→30 Å / Redundancy: 6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
CCP4SUITEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AS7

4as7


Resolution: 2.793→27.935 Å / σ(F): 1.96 / Phase error: 34.63 / Stereochemistry target values: TWIN_LSQ_F
Details: DISORDERED REGION EITHER DELETED OR MODELLED STEREOCHEMICALLY
RfactorNum. reflection% reflection
Rfree0.274 1087 5.3 %
Rwork0.2302 --
obs0.2333 9633 97.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 71.9 Å2
Refinement stepCycle: LAST / Resolution: 2.793→27.935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5305 0 158 58 5521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015552
X-RAY DIFFRACTIONf_angle_d1.5877527
X-RAY DIFFRACTIONf_dihedral_angle_d22.3782065
X-RAY DIFFRACTIONf_chiral_restr0.099879
X-RAY DIFFRACTIONf_plane_restr0.006954
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7997-2.9270.41771320.38042406X-RAY DIFFRACTION91
2.927-3.08110.3511500.34642385X-RAY DIFFRACTION90
3.0811-3.27390.37091200.32362510X-RAY DIFFRACTION95
3.2739-3.52620.34261440.30052487X-RAY DIFFRACTION94
3.5262-3.88020.34891250.27742438X-RAY DIFFRACTION93
3.8802-4.43980.27581230.2232391X-RAY DIFFRACTION91
4.4398-5.58630.23831270.20072469X-RAY DIFFRACTION95
5.5863-27.93650.20761380.16482434X-RAY DIFFRACTION92

+
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