[English] 日本語
Yorodumi
- PDB-5lxo: Coiled-coil protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5lxo
TitleCoiled-coil protein
ComponentsTransforming acidic coiled-coil-containing protein 3
KeywordsSTRUCTURAL PROTEIN / TACC3 / coiled-coil / helix / fgfr fusion / fgfr / growth factors / cancer / fusion / parallel helix
Function / homology
Function and homology information


microtubule cytoskeleton organization involved in mitosis / metaphase/anaphase transition of mitotic cell cycle / centriolar satellite / regulation of mitotic spindle organization / mitotic spindle organization / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulation of NOTCH4 signaling / cerebral cortex development / mitotic spindle / spindle pole ...microtubule cytoskeleton organization involved in mitosis / metaphase/anaphase transition of mitotic cell cycle / centriolar satellite / regulation of mitotic spindle organization / mitotic spindle organization / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulation of NOTCH4 signaling / cerebral cortex development / mitotic spindle / spindle pole / microtubule cytoskeleton organization / cell population proliferation / cell division / intracellular membrane-bounded organelle / cytoplasm / cytosol
Similarity search - Function
Transforming acidic coiled-coil-containing protein, C-terminal / TACC family / Transforming acidic coiled-coil-containing protein (TACC), C-terminal
Similarity search - Domain/homology
ACETATE ION / TRIETHYLENE GLYCOL / Transforming acidic coiled-coil-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.179 Å
AuthorsThiyagarajan, N. / Bunney, T.D. / Katan, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Cancer Research UKA16567 United Kingdom
CitationJournal: To Be Published
Title: Coiled-coil protein
Authors: Thiyagarajan, N. / Bunney, T.D. / Katan, M.
History
DepositionSep 22, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transforming acidic coiled-coil-containing protein 3
B: Transforming acidic coiled-coil-containing protein 3
C: Transforming acidic coiled-coil-containing protein 3
D: Transforming acidic coiled-coil-containing protein 3
E: Transforming acidic coiled-coil-containing protein 3
F: Transforming acidic coiled-coil-containing protein 3
G: Transforming acidic coiled-coil-containing protein 3
H: Transforming acidic coiled-coil-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,07813
Polymers75,5878
Non-polymers4915
Water6,972387
1
A: Transforming acidic coiled-coil-containing protein 3
B: Transforming acidic coiled-coil-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2025
Polymers18,8972
Non-polymers3053
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Transforming acidic coiled-coil-containing protein 3
D: Transforming acidic coiled-coil-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9323
Polymers18,8972
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Transforming acidic coiled-coil-containing protein 3
F: Transforming acidic coiled-coil-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0473
Polymers18,8972
Non-polymers1501
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Transforming acidic coiled-coil-containing protein 3
H: Transforming acidic coiled-coil-containing protein 3


Theoretical massNumber of molelcules
Total (without water)18,8972
Polymers18,8972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.250, 76.460, 86.891
Angle α, β, γ (deg.)90.00, 90.10, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Transforming acidic coiled-coil-containing protein 3 / ERIC-1


Mass: 9448.420 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: Coiled-coil 2 domain / Source: (gene. exp.) Homo sapiens (human) / Gene: TACC3, ERIC1 / Plasmid: pJ821 / Details (production host): Rhamnose induced / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: Q9Y6A5

-
Non-polymers , 5 types, 392 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.54 Å3/Da / Density % sol: 51.6 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 35 % PEG 400, 0.05 M Sodium sulphate, 0.05 M Lithium sulphate, 0.05 M Tris pH 8.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9681 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 7, 2015 / Details: Mirrors
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9681 Å / Relative weight: 1
ReflectionResolution: 2.179→28.964 Å / Num. obs: 37534 / % possible obs: 95.5 % / Redundancy: 13.1 % / Biso Wilson estimate: 19.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.094 / Net I/σ(I): 21
Reflection shellResolution: 2.18→2.24 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.838 / % possible all: 67.8

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSNov 3, 2014data reduction
Aimless0.3.11data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5LXN

5lxn


Resolution: 2.179→28.964 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.38
RfactorNum. reflection% reflectionSelection details
Rfree0.2853 1844 4.91 %Random selection
Rwork0.2333 ---
obs0.2352 37524 95.53 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 42.4 Å2
Refinement stepCycle: LAST / Resolution: 2.179→28.964 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5094 0 30 387 5511
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085266
X-RAY DIFFRACTIONf_angle_d1.0667017
X-RAY DIFFRACTIONf_dihedral_angle_d19.372197
X-RAY DIFFRACTIONf_chiral_restr0.037796
X-RAY DIFFRACTIONf_plane_restr0.005926
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1804-2.23930.39251190.33651944X-RAY DIFFRACTION66
2.2393-2.3050.39041130.31952366X-RAY DIFFRACTION78
2.305-2.37930.36541200.29772656X-RAY DIFFRACTION89
2.3793-2.46410.39981270.29962855X-RAY DIFFRACTION95
2.4641-2.56250.37561400.28912824X-RAY DIFFRACTION95
2.5625-2.67870.35731310.27992867X-RAY DIFFRACTION96
2.6787-2.81950.31781360.27152894X-RAY DIFFRACTION96
2.8195-2.99540.36111460.26592866X-RAY DIFFRACTION95
2.9954-3.22540.27691510.24032845X-RAY DIFFRACTION95
3.2254-3.54770.27451230.22662877X-RAY DIFFRACTION96
3.5477-4.05590.23661510.18492878X-RAY DIFFRACTION95
4.0559-5.09060.23381610.17672884X-RAY DIFFRACTION95
5.0906-17.94480.25251560.21782929X-RAY DIFFRACTION95

+
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://pdbjlvh1.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