[English] 日本語
Yorodumi
- PDB-8yhh: The Crystal Structure of Mitotic Kinesin Eg5 from Biortus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8yhh
TitleThe Crystal Structure of Mitotic Kinesin Eg5 from Biortus
ComponentsKinesin-like protein KIF11
KeywordsCELL CYCLE / Motor protein / Cell division / ATP-binding
Function / homology
Function and homology information


spindle elongation / Kinesins / plus-end-directed microtubule motor activity / regulation of mitotic centrosome separation / mitotic centrosome separation / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / spindle organization / microtubule-based movement ...spindle elongation / Kinesins / plus-end-directed microtubule motor activity / regulation of mitotic centrosome separation / mitotic centrosome separation / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule motor activity / spindle organization / microtubule-based movement / mitotic spindle assembly / MHC class II antigen presentation / mitotic spindle organization / mitotic spindle / spindle / spindle pole / mitotic cell cycle / microtubule binding / microtubule / cell division / protein kinase binding / protein-containing complex / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / 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-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / 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
ADENOSINE-5'-DIPHOSPHATE / NITRATE ION / Kinesin-like protein KIF11
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Qi, J. / Wu, B.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: To Be Published
Title: The Crystal Structure of Mitotic Kinesin Eg5 from Biortus
Authors: Wang, F. / Cheng, W. / Lv, Z. / Qi, J. / Wu, B.
History
DepositionFeb 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

-
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)84,08817
Polymers82,3392
Non-polymers1,74915
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-39 kcal/mol
Surface area29370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.654, 78.254, 93.467
Angle α, β, γ (deg.)90.000, 94.511, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 17 - 364 / Label seq-ID: 19 - 366

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
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


Mass: 41169.684 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF11, EG5, KNSL1, TRIP5 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52732

-
Non-polymers , 7 types, 347 molecules

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


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 19% PEG3350, 0.1M MES (pH 5.2), and 200 mM NaNO3

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 10, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.95→46.59 Å / Num. obs: 51970 / % possible obs: 96.1 % / Redundancy: 5.4 % / CC1/2: 0.999 / Net I/σ(I): 13.7
Reflection shellResolution: 1.95→2 Å / Num. unique obs: 3726 / CC1/2: 0.806

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→46.59 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.671 / SU ML: 0.13 / Cross valid method: FREE R-VALUE / ESU R: 0.191 / ESU R Free: 0.174
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2605 2409 4.637 %
Rwork0.2142 49540 -
all0.216 --
obs-51949 95.875 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.48 Å2
Baniso -1Baniso -2Baniso -3
1-3.737 Å2-0 Å2-1.029 Å2
2---1.502 Å2-0 Å2
3----2.047 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4983 0 110 332 5425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0135217
X-RAY DIFFRACTIONr_bond_other_d0.0010.0145080
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.6547031
X-RAY DIFFRACTIONr_angle_other_deg1.1361.5811716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3815644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.08621.573267
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56215955
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0111543
X-RAY DIFFRACTIONr_chiral_restr0.050.2721
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025710
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021130
X-RAY DIFFRACTIONr_nbd_refined0.1840.2931
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1650.24657
X-RAY DIFFRACTIONr_nbtor_refined0.1430.22412
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0680.22628
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2338
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1310.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2020.226
X-RAY DIFFRACTIONr_nbd_other0.1680.284
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1250.210
X-RAY DIFFRACTIONr_mcbond_it1.993.9612552
X-RAY DIFFRACTIONr_mcbond_other1.993.9592551
X-RAY DIFFRACTIONr_mcangle_it3.2115.9153180
X-RAY DIFFRACTIONr_mcangle_other3.2115.9173181
X-RAY DIFFRACTIONr_scbond_it2.1074.3742665
X-RAY DIFFRACTIONr_scbond_other2.1074.3762663
X-RAY DIFFRACTIONr_scangle_it3.496.4183843
X-RAY DIFFRACTIONr_scangle_other3.4896.4193841
X-RAY DIFFRACTIONr_lrange_it5.91246.6195591
X-RAY DIFFRACTIONr_lrange_other5.84846.4585532
X-RAY DIFFRACTIONr_ncsr_local_group_10.0940.059621
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.093880.05008
12BX-RAY DIFFRACTIONLocal ncs0.093880.05008
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.0010.3061700.3123746X-RAY DIFFRACTION97.8755
2.001-2.0550.2831690.2873649X-RAY DIFFRACTION98.3514
2.055-2.1150.2681760.2523516X-RAY DIFFRACTION98.3222
2.115-2.180.2811500.2373457X-RAY DIFFRACTION97.2237
2.18-2.2520.271400.2323269X-RAY DIFFRACTION95.8392
2.252-2.330.2771530.2313114X-RAY DIFFRACTION95.8064
2.33-2.4180.2111490.2053081X-RAY DIFFRACTION96.9388
2.418-2.5170.2721600.222907X-RAY DIFFRACTION95.754
2.517-2.6290.311440.2232776X-RAY DIFFRACTION94.8976
2.629-2.7570.281270.2122740X-RAY DIFFRACTION96.4995
2.757-2.9060.271150.2152545X-RAY DIFFRACTION96.1677
2.906-3.0820.2681460.2032395X-RAY DIFFRACTION96.1044
3.082-3.2950.2531320.2012267X-RAY DIFFRACTION95.6921
3.295-3.5580.297990.222117X-RAY DIFFRACTION95.189
3.558-3.8970.287770.2021930X-RAY DIFFRACTION93.7412
3.897-4.3570.242820.1881703X-RAY DIFFRACTION91.8682
4.357-5.0290.228840.1761506X-RAY DIFFRACTION93.3099
5.029-6.1540.227510.2121293X-RAY DIFFRACTION91.6155
6.154-8.6850.245490.206990X-RAY DIFFRACTION90.9011
8.685-46.590.194360.225539X-RAY DIFFRACTION89.5639

+
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