[English] 日本語
Yorodumi
- PDB-6l7r: Crystal structure of Chaetomium GCP3 N-terminus and Mozart1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6l7r
TitleCrystal structure of Chaetomium GCP3 N-terminus and Mozart1
Components
  • Mozart1
  • Putative spindle pole body component alp6 protein
KeywordsTRANSLATION / gamma tubulin complex / microprotien / microtubule
Function / homology
Function and homology information


gamma-tubulin complex localization / gamma-tubulin ring complex / microtubule nucleation / spindle pole body / gamma-tubulin binding / microtubule organizing center / spindle pole / microtubule / cytoplasm
Similarity search - Function
Mitotic-spindle organizing protein 1 / Mitotic-spindle organizing gamma-tubulin ring associated / Gamma tubulin complex component, C-terminal / Gamma-tubulin complex component, C-terminal domain superfamily / Gamma tubulin complex component C-terminal / Gamma-tubulin complex component protein / Gamma tubulin complex component protein, N-terminal / Gamma tubulin complex component N-terminal
Similarity search - Domain/homology
Mitotic-spindle organizing protein 1 / Putative spindle pole body component alp6 protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.84813131157 Å
AuthorsHuang, T.L. / Wang, H.J. / Hsia, K.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Cell Rep / Year: 2020
Title: Promiscuous Binding of Microprotein Mozart1 to gamma-Tubulin Complex Mediates Specific Subcellular Targeting to Control Microtubule Array Formation.
Authors: Huang, T.L. / Wang, H.J. / Chang, Y.C. / Wang, S.W. / Hsia, K.C.
History
DepositionNov 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative spindle pole body component alp6 protein
B: Mozart1


Theoretical massNumber of molelcules
Total (without water)21,3142
Polymers21,3142
Non-polymers00
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-48 kcal/mol
Surface area10050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.515, 61.989, 52.244
Angle α, β, γ (deg.)90.000, 119.205, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-240-

HOH

-
Components

#1: Protein Putative spindle pole body component alp6 protein / / GCP3


Mass: 11821.466 Da / Num. of mol.: 1 / Fragment: N-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0063320 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SED1
#2: Protein Mozart1


Mass: 9492.858 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0002490 / Production host: Escherichia coli (E. coli) / References: UniProt: G0RZC6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M lithium sulfate monohydrate, 0.1 M Tris hydrochloride pH 8.5, 30% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.9784 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9784 Å / Relative weight: 1
ReflectionResolution: 1.84→20 Å / Num. obs: 101437 / % possible obs: 99.5 % / Redundancy: 6 % / Biso Wilson estimate: 29.5273447895 Å2 / CC1/2: 0.995 / Net I/σ(I): 26.1
Reflection shellResolution: 1.84→1.92 Å / Num. unique obs: 1621 / CC1/2: 0.973

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.84813131157→19.9518531996 Å / SU ML: 0.193769979505 / Cross valid method: FREE R-VALUE / σ(F): 1.40459111588 / Phase error: 24.0380271756
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.225817314747 3232 9.99628850674 %
Rwork0.18805688641 29100 -
obs0.191834798649 32332 99.1718299491 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.1126660995 Å2
Refinement stepCycle: LAST / Resolution: 1.84813131157→19.9518531996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1420 0 0 97 1517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005524950160081439
X-RAY DIFFRACTIONf_angle_d0.7929049003591955
X-RAY DIFFRACTIONf_chiral_restr0.0437190048533234
X-RAY DIFFRACTIONf_plane_restr0.0056060696866258
X-RAY DIFFRACTIONf_dihedral_angle_d11.7966019429897
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.87570.3008921614481260.234374006661133X-RAY DIFFRACTION86.2919808088
1.8757-1.9050.2712087771981360.2285184648471215X-RAY DIFFRACTION100
1.905-1.93620.2735708954021470.2126618247841340X-RAY DIFFRACTION99.9327956989
1.9362-1.96950.2451923503371350.2086981819811201X-RAY DIFFRACTION100
1.9695-2.00530.2706290706091490.2177993075651330X-RAY DIFFRACTION100
2.0053-2.04390.2870754470961380.2016611429811238X-RAY DIFFRACTION100
2.0439-2.08550.2306731469151430.1995386113361279X-RAY DIFFRACTION100
2.0855-2.13080.2530887721671400.1907394512421298X-RAY DIFFRACTION100
2.1308-2.18030.2224604494811430.1895276088551270X-RAY DIFFRACTION100
2.1803-2.23480.2121592840041380.1923330634411275X-RAY DIFFRACTION100
2.2348-2.29510.23513225491390.1733984099551262X-RAY DIFFRACTION99.9286733238
2.2951-2.36260.2252326381711440.1864756731971283X-RAY DIFFRACTION100
2.3626-2.43870.2477605439761460.2012609852721290X-RAY DIFFRACTION99.9304105776
2.4387-2.52570.2452963577881380.1992087548041265X-RAY DIFFRACTION100
2.5257-2.62660.2108177047051400.1947354180471266X-RAY DIFFRACTION99.9289267946
2.6266-2.74590.2195293276811430.1961944535191287X-RAY DIFFRACTION100
2.7459-2.89020.2151335039671440.2086910625561284X-RAY DIFFRACTION100
2.8902-3.07070.2471698191571410.2060228369921262X-RAY DIFFRACTION100
3.0707-3.30680.1992509412651430.1991298X-RAY DIFFRACTION100
3.3068-3.63780.2164146515381420.1949219760791236X-RAY DIFFRACTION99.9274836838
3.6378-4.160.1969725714761430.1621487568611281X-RAY DIFFRACTION99.9298245614
4.16-5.22560.2016413370811400.1562724086481290X-RAY DIFFRACTION99.7906489881
5.2256-100.2656199534461340.1724538154641217X-RAY DIFFRACTION95.6798866856
Refinement TLS params.Method: refined / Origin x: -19.1395126694 Å / Origin y: 8.83757201141 Å / Origin z: 9.59516055196 Å
111213212223313233
T0.207859256778 Å20.00327340202777 Å20.00846390163678 Å2-0.183554144747 Å20.0435973714383 Å2--0.19691073341 Å2
L2.08588869001 °2-1.35270822037 °2-0.779925613016 °2-2.204625572 °21.03034970824 °2--1.34700440599 °2
S0.130512860449 Å °0.27013007781 Å °0.109795250091 Å °-0.18838715285 Å °-0.146908574822 Å °-0.145689047904 Å °-0.143218081317 Å °-0.1058100671 Å °0.0270594771246 Å °
Refinement TLS groupSelection details: all

+
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