[English] 日本語
Yorodumi
- PDB-4cgc: Crystal structure of the trimerization domain of human EML4 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4cgc
TitleCrystal structure of the trimerization domain of human EML4
ComponentsECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 4
KeywordsCELL CYCLE / EML4-ALK / NSCLC / COILED-COIL
Function / homology
Function and homology information


microtubule-based process / EML4 and NUDC in mitotic spindle formation / microtubule cytoskeleton organization / mitotic cell cycle / microtubule binding / microtubule / membrane / cytoplasm
Similarity search - Function
HELP / HELP motif / : / Quinoprotein alcohol dehydrogenase-like superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats ...HELP / HELP motif / : / Quinoprotein alcohol dehydrogenase-like superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Echinoderm microtubule-associated protein-like 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.901 Å
AuthorsRichards, M.W. / Bayliss, R.
CitationJournal: Biochem.J. / Year: 2015
Title: Microtubule Association of Eml Proteins and the Eml4-Alk Variant 3 Oncoprotein Require an N-Terminal Trimerization Domain.
Authors: Richards, M.W. / O'Regan, L. / Roth, D. / Montgomery, J.M. / Straube, A. / Fry, A.M. / Bayliss, R.
History
DepositionNov 21, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references
Revision 1.2Apr 29, 2015Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 4
B: ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 4
C: ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 4


Theoretical massNumber of molelcules
Total (without water)19,2303
Polymers19,2303
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-15 kcal/mol
Surface area5130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.491, 67.491, 50.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 4 / EMAP-4 / RESTRICTEDLY OVEREXPRESSED PROLIFERATION-ASSOCIATED PROTEIN / ROPP 120 / ECHINODERM ...EMAP-4 / RESTRICTEDLY OVEREXPRESSED PROLIFERATION-ASSOCIATED PROTEIN / ROPP 120 / ECHINODERM MICROTUBULE ASSOCIATED PROTEIN-LIKE PROTEIN 4


Mass: 6409.938 Da / Num. of mol.: 3 / Fragment: TRIMERIZATION DOMAIN, RESIDUES 6-64 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET30TEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q9HC35

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.51 Å3/Da / Density % sol: 18.61 % / Description: NONE
Crystal growpH: 8.5 / Details: 100 MM TRIS/HCL PH 8.5, 30% PEG 4000, 200 MM MGCL2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Apr 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.9→67.49 Å / Num. obs: 2864 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 13.4 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 13.3
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 14.4 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 3.1 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
SCALAphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.901→47.723 Å / SU ML: 0.41 / σ(F): 1.38 / Phase error: 37.35 / Stereochemistry target values: ML
Details: ONLY RESIDUES 16-44 ARE VISIBLE IN THE ELECTION DENSITY. RESIDUES 6-15 AND 45-64 WERE NOT MODELLED.
RfactorNum. reflection% reflection
Rfree0.2915 228 4.6 %
Rwork0.2675 --
obs0.2687 4949 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.901→47.723 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms641 0 0 0 641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006651
X-RAY DIFFRACTIONf_angle_d1.02875
X-RAY DIFFRACTIONf_dihedral_angle_d23.604259
X-RAY DIFFRACTIONf_chiral_restr0.052106
X-RAY DIFFRACTIONf_plane_restr0.005119
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9014-3.65520.38611080.30122366X-RAY DIFFRACTION100
3.6552-47.72990.26131200.25582355X-RAY DIFFRACTION100

+
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