[English] 日本語
Yorodumi
- PDB-8hfh: CENP-E motor domain in complex with AMPPNP and Mg2+ -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8hfh
TitleCENP-E motor domain in complex with AMPPNP and Mg2+
ComponentsCentromere-associated protein E
KeywordsCELL CYCLE / kinesin / motor domain / AMPPNP / CENP-E / centromere-associated protein
Function / homology
Function and homology information


lateral attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end directed mitotic chromosome migration / mitotic chromosome movement towards spindle pole / metaphase chromosome alignment / mitotic spindle midzone / kinetochore microtubule / kinetochore binding / attachment of mitotic spindle microtubules to kinetochore / kinetochore assembly / condensed chromosome, centromeric region ...lateral attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end directed mitotic chromosome migration / mitotic chromosome movement towards spindle pole / metaphase chromosome alignment / mitotic spindle midzone / kinetochore microtubule / kinetochore binding / attachment of mitotic spindle microtubules to kinetochore / kinetochore assembly / condensed chromosome, centromeric region / Kinesins / regulation of mitotic metaphase/anaphase transition / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / mitotic metaphase chromosome alignment / intercellular bridge / microtubule-based movement / chromosome, centromeric region / positive regulation of protein kinase activity / spindle midzone / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / mitotic spindle organization / chromosome segregation / RHO GTPases Activate Formins / mitotic spindle / kinetochore / Separation of Sister Chromatids / microtubule cytoskeleton / mitotic cell cycle / chromosome / midbody / microtubule binding / microtubule / cell division / intracellular membrane-bounded organelle / ATP binding / membrane / nucleus / cytosol
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / IMIDAZOLE / Centromere-associated protein E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsShibuya, A. / Yokoyama, H.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Febs Lett. / Year: 2023
Title: Crystal structure of the motor domain of centromere-associated protein E in complex with a non-hydrolysable ATP analogue.
Authors: Shibuya, A. / Suzuki, A. / Ogo, N. / Sawada, J.I. / Asai, A. / Yokoyama, H.
History
DepositionNov 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: 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: Centromere-associated protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4687
Polymers39,7991
Non-polymers6696
Water5,441302
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Gel filtration data suggests that CENP-E motor domain is monomeric.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.576, 46.215, 73.718
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-602-

NA

21A-605-

IMD

31A-710-

HOH

41A-735-

HOH

51A-976-

HOH

61A-986-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Centromere-associated protein E / Centromere protein E / CENP-E / Kinesin-7 / Kinesin-related protein CENPE


Mass: 39799.082 Da / Num. of mol.: 1 / Mutation: A300P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPE / Production host: Escherichia coli (E. coli) / References: UniProt: Q02224

-
Non-polymers , 5 types, 308 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MES, PEG3350, PIPES-NaOH, NaCl, MgCl2, EGTA, TCEP, sucrose, CENP-E, AMPPNP

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→73.718 Å / Num. obs: 31976 / % possible obs: 99.9 % / Redundancy: 6.3 % / Biso Wilson estimate: 12.6 Å2 / Rpim(I) all: 0.047 / Rrim(I) all: 0.119 / Rsym value: 0.11 / Net I/av σ(I): 6.1 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRpim(I) allRrim(I) allRsym value% possible all
1.8-1.94.20.5011.545880.2730.5730.50199.8
1.9-2.016.60.374243630.1560.4060.374100
2.01-2.156.90.2772.640920.1130.30.277100
2.15-2.326.70.2043.538300.0840.2210.204100
2.32-2.556.50.1574.535400.0670.1710.157100
2.55-2.856.90.1225.832230.050.1320.122100
2.85-3.296.60.085828650.0360.0920.085100
3.29-4.026.40.05611.924260.0240.0610.056100
4.02-5.696.70.04813.119460.020.0520.048100
5.69-105.80.04314.311030.0190.0470.04397.6

-
Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.572
Highest resolutionLowest resolution
Rotation19.86 Å1.88 Å

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALA3.3.22data scaling
MOLREPphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6M4I

6m4i


Resolution: 1.8→19.87 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.452 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2058 3149 9.9 %RANDOM
Rwork0.1611 ---
obs0.1654 28790 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.84 Å2 / Biso mean: 18.794 Å2 / Biso min: 3.77 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.8→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2545 0 40 302 2887
Biso mean--17.05 29.67 -
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132647
X-RAY DIFFRACTIONr_bond_other_d0.0020.0152532
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.6523575
X-RAY DIFFRACTIONr_angle_other_deg1.4441.5835820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8215321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.25821.972142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.05815481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.71520
X-RAY DIFFRACTIONr_chiral_restr0.0870.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022977
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02626
LS refinement shellResolution: 1.8→1.846 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 242 -
Rwork0.243 2079 -
all-2321 -
obs--99.66 %

+
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