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- PDB-4cgc: Crystal structure of the trimerization domain of human EML4 -

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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


attachment of spindle microtubules to kinetochore / ALK mutants bind TKIs / microtubule organizing center / mitotic metaphase chromosome alignment / beta-tubulin binding / microtubule-based process / alpha-tubulin binding / EML4 and NUDC in mitotic spindle formation / mitotic spindle / microtubule cytoskeleton organization ...attachment of spindle microtubules to kinetochore / ALK mutants bind TKIs / microtubule organizing center / mitotic metaphase chromosome alignment / beta-tubulin binding / microtubule-based process / alpha-tubulin binding / EML4 and NUDC in mitotic spindle formation / mitotic spindle / microtubule cytoskeleton organization / microtubule cytoskeleton / Signaling by ALK fusions and activated point mutants / mitotic cell cycle / midbody / microtubule binding / microtubule / cell division / membrane / cytosol / cytoplasm
Similarity search - Function
HELP / HELP motif / : / Quinoprotein alcohol dehydrogenase-like superfamily / 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 ...HELP / HELP motif / : / Quinoprotein alcohol dehydrogenase-like superfamily / 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
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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

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