[English] 日本語
Yorodumi
- PDB-8v11: Structure of a Saccharomyces cerevisiae Ipl1 peptide Bound to dwa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8v11
TitleStructure of a Saccharomyces cerevisiae Ipl1 peptide Bound to dwarf Ndc80 complex
Components
  • Ipl1/Nuf2 chimera protein
  • Kinetochore protein NDC80
  • Kinetochore protein SPC24
  • Kinetochore protein SPC25
KeywordsCELL CYCLE / Stu2 / tension sensing / Ndc80 / kinetochore
Function / homology
Function and homology information


centromere clustering / Ndc80 complex / mitotic sister chromatid biorientation / kinetochore organization / sister chromatid biorientation / meiotic chromosome segregation / outer kinetochore / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / protein localization to kinetochore ...centromere clustering / Ndc80 complex / mitotic sister chromatid biorientation / kinetochore organization / sister chromatid biorientation / meiotic chromosome segregation / outer kinetochore / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / protein localization to kinetochore / spindle pole body / mitotic spindle organization / spindle microtubule / chromosome segregation / kinetochore / cell division / protein-containing complex binding / identical protein binding / nucleus
Similarity search - Function
Spc24, Fungi, globular domain superfamily / Kinetochore protein Nuf2, N-terminal / Nuf2, N-terminal domain superfamily / Nuf2 family / Kinetochore protein Ndc80 / Ndc80 domain superfamily / Domain of unknown function DUF5595 / : / HEC/Ndc80p family / Domain of unknown function (DUF5595) ...Spc24, Fungi, globular domain superfamily / Kinetochore protein Nuf2, N-terminal / Nuf2, N-terminal domain superfamily / Nuf2 family / Kinetochore protein Ndc80 / Ndc80 domain superfamily / Domain of unknown function DUF5595 / : / HEC/Ndc80p family / Domain of unknown function (DUF5595) / Kinetochore-Ndc80 subunit Spc24 / Spc24 subunit of Ndc80
Similarity search - Domain/homology
Kinetochore protein NUF2 / Kinetochore protein SPC25 / Kinetochore protein NDC80 / Kinetochore protein SPC24
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.95 Å
AuthorsZahm, J.A. / Harrison, S.C.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Curr.Biol. / Year: 2024
Title: A communication hub for phosphoregulation of kinetochore-microtubule attachment.
Authors: Zahm, J.A. / Harrison, S.C.
History
DepositionNov 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jun 12, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kinetochore protein NDC80
B: Ipl1/Nuf2 chimera protein
C: Kinetochore protein SPC24
D: Kinetochore protein SPC25
E: Kinetochore protein NDC80
F: Ipl1/Nuf2 chimera protein
G: Kinetochore protein SPC24
H: Kinetochore protein SPC25


Theoretical massNumber of molelcules
Total (without water)166,9408
Polymers166,9408
Non-polymers00
Water00
1
A: Kinetochore protein NDC80
B: Ipl1/Nuf2 chimera protein
C: Kinetochore protein SPC24
D: Kinetochore protein SPC25


Theoretical massNumber of molelcules
Total (without water)83,4704
Polymers83,4704
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13390 Å2
ΔGint-119 kcal/mol
Surface area41170 Å2
MethodPISA
2
E: Kinetochore protein NDC80
F: Ipl1/Nuf2 chimera protein
G: Kinetochore protein SPC24
H: Kinetochore protein SPC25


Theoretical massNumber of molelcules
Total (without water)83,4704
Polymers83,4704
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13700 Å2
ΔGint-117 kcal/mol
Surface area40930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.757, 114.757, 423.841
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 113 through 275 or resid 277 through 312 or resid 314 through 684))
d_2ens_1(chain "E" and (resid 113 through 275 or resid 277 through 312 or resid 314 through 684))
d_1ens_2chain "B"
d_2ens_2chain "F"
d_1ens_3chain "C"
d_2ens_3chain "G"
d_1ens_4(chain "D" and resid 3 through 220)
d_2ens_4chain "H"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1ALAALAVALVALAA113 - 2753 - 165
d_12ens_1LYSLYSVALVALAA277 - 312167 - 202
d_13ens_1ILEILEGLUGLUAA314 - 684204 - 272
d_21ens_1ALAALAVALVALEE113 - 2753 - 165
d_22ens_1LYSLYSVALVALEE277 - 312167 - 202
d_23ens_1ILEILEGLUGLUEE314 - 684204 - 272
d_11ens_2ILEILEGLNGLNBB48 - 145119 - 227
d_21ens_2ILEILEGLNGLNFF48 - 145119 - 227
d_11ens_3ASNASNGLYGLYCC6 - 2126 - 99
d_21ens_3ASNASNGLYGLYGG6 - 2126 - 99
d_11ens_4SERSERSERSERDD3 - 2203 - 114
d_21ens_4SERSERSERSERHH3 - 2203 - 114

NCS ensembles :
ID
ens_1
ens_2
ens_3
ens_4

-
Components

#1: Protein Kinetochore protein NDC80 / 80 kDa spindle component protein / Nuclear division cycle protein 80 / Two-hybrid interaction with ...80 kDa spindle component protein / Nuclear division cycle protein 80 / Two-hybrid interaction with DMC1 protein 3


Mass: 32460.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: NDC80, HEC1, TID3, YIL144W / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40460
#2: Protein Ipl1/Nuf2 chimera protein


Mass: 26548.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: IPL1, NUF2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P33895
#3: Protein Kinetochore protein SPC24


Mass: 11752.278 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SPC24, YMR117C, YM9718.16C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q04477
#4: Protein Kinetochore protein SPC25


Mass: 12709.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SPC25, YER018C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P40014

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.18 Å3/Da / Density % sol: 70.57 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% polyethylene glycol 2000 monomethyl ether,500 mM sodium chloride,50 mM Tris pH 7.5

-
Data collection

DiffractionMean temperature: 80 K / Ambient temp details: Liquid nitrogen cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 2.0.1 / Wavelength: 1.0309 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0309 Å / Relative weight: 1
ReflectionResolution: 3.95→48.53 Å / Num. obs: 10981 / % possible obs: 42.6 % / Redundancy: 17.4 % / Biso Wilson estimate: 98.15 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.556 / Rpim(I) all: 0.135 / Rrim(I) all: 0.573 / Net I/σ(I): 6.7
Reflection shellResolution: 3.95→4.448 Å / Redundancy: 19 % / Rmerge(I) obs: 3.899 / Num. unique obs: 785 / CC1/2: 0.609 / Rpim(I) all: 0.909 / Rrim(I) all: 4.006 / % possible all: 10.5

-
Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.95→48.53 Å / SU ML: 0.7326 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 45.7832
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3266 559 5.1 %
Rwork0.2666 10412 -
obs0.2696 10971 42.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 162.25 Å2
Refinement stepCycle: LAST / Resolution: 3.95→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11239 0 0 0 11239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005711461
X-RAY DIFFRACTIONf_angle_d1.125715467
X-RAY DIFFRACTIONf_chiral_restr0.05921731
X-RAY DIFFRACTIONf_plane_restr0.00542013
X-RAY DIFFRACTIONf_dihedral_angle_d15.1524385
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS2.21255604163
ens_2d_2BBX-RAY DIFFRACTIONTorsion NCS2.63049277242
ens_3d_2CCX-RAY DIFFRACTIONTorsion NCS1.81705749813
ens_4d_2DDX-RAY DIFFRACTIONTorsion NCS1.89725207791
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.95-4.350.3173320.2383522X-RAY DIFFRACTION8.84
4.35-4.980.3083910.21571501X-RAY DIFFRACTION25.15
4.98-6.270.35431100.32232155X-RAY DIFFRACTION35.25
6.28-48.530.32513260.2656234X-RAY DIFFRACTION97.26

+
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