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- PDB-4ci8: Crystal structure of the tandem atypical beta-propeller domain of EML1 -

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Basic information

Entry
Database: PDB / ID: 4ci8
TitleCrystal structure of the tandem atypical beta-propeller domain of EML1
ComponentsECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 1
KeywordsSTRUCTURAL PROTEIN / EML1 / EML4-ALK / HSP90 INHIBITORS / TUBULIN-BINDING / BETA PROPELLER
Function / homology
Function and homology information


mitotic spindle midzone / microtubule associated complex / mitotic spindle pole / neuroblast proliferation / hematopoietic progenitor cell differentiation / tubulin binding / mitotic spindle organization / brain development / microtubule cytoskeleton organization / microtubule binding ...mitotic spindle midzone / microtubule associated complex / mitotic spindle pole / neuroblast proliferation / hematopoietic progenitor cell differentiation / tubulin binding / mitotic spindle organization / brain development / microtubule cytoskeleton organization / microtubule binding / microtubule / calcium ion binding / perinuclear region of cytoplasm / cytosol
Similarity search - Function
HELP / HELP motif / : / Quinoprotein alcohol dehydrogenase-like superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat ...HELP / HELP motif / : / Quinoprotein alcohol dehydrogenase-like superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / 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 / Mainly Beta
Similarity search - Domain/homology
Echinoderm microtubule-associated protein-like 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsRichards, M.W. / Bayliss, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Crystal Structure of Eml1 Reveals the Basis for Hsp90 Dependence of Oncogenic Eml4-Alk by Disruption of an Atypical Beta-Propeller Domain.
Authors: Richards, M.W. / Law, E.W.P. / Rennalls, L.P. / Busacca, S. / O'Regan, L. / Fry, A.M. / Fennell, D.A. / Bayliss, R.
History
DepositionDec 6, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 1
B: ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,77927
Polymers145,3772
Non-polymers2,40225
Water3,747208
1
A: ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,93714
Polymers72,6891
Non-polymers1,24913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,84113
Polymers72,6891
Non-polymers1,15312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-280.7 kcal/mol
Surface area46970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.980, 83.980, 115.520
Angle α, β, γ (deg.)90.00, 96.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 1 / EMAP-1 / HUEMAP-1 PROTEIN 1


Mass: 72688.656 Da / Num. of mol.: 2 / Fragment: RESIDUES 167-815
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC-FSSP / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O00423
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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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: 3.05 Å3/Da / Density % sol: 59.7 % / Description: NONE
Crystal growpH: 5.6
Details: 100 MM TRI-SODIUM CITRATE PH 5.6, 2.0 M AMMONIUM SULPHATE, 200 MM POTASSIUM/SODIUM TARTRATE, 2 MM DTT.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.979
DetectorType: DECTRIS PIXEL / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→47.4 Å / Num. obs: 53683 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 42.06 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.1
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.7 / % possible all: 99.6

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Processing

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

Resolution: 2.6→47.375 Å / SU ML: 0.39 / σ(F): 1.34 / Phase error: 28.83 / Stereochemistry target values: ML
Details: RESIDUES 176-815 ARE ORDERED. THE PROTEIN CRYSTALLISED WAS SELENOMETHIONINE DERIVATIVE BUT SINCE SELENOMETHIONINE OCCUPANCY WAS PARTIAL ALL METHIONINE RESIDUES HAVE BEEN ASSIGNED AS MET RATHER THAN MSE.
RfactorNum. reflection% reflection
Rfree0.2508 2726 5.1 %
Rwork0.1995 --
obs0.2022 53587 99.19 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.676 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso mean: 48.78 Å2
Baniso -1Baniso -2Baniso -3
1--2.3728 Å2-0 Å214.5069 Å2
2--11.9981 Å20 Å2
3----9.6253 Å2
Refinement stepCycle: LAST / Resolution: 2.6→47.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9860 0 125 208 10193
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00410216
X-RAY DIFFRACTIONf_angle_d0.88513921
X-RAY DIFFRACTIONf_dihedral_angle_d13.7723491
X-RAY DIFFRACTIONf_chiral_restr0.061528
X-RAY DIFFRACTIONf_plane_restr0.0031765
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.64730.34161380.29012658X-RAY DIFFRACTION99
2.6473-2.69820.39221420.30242681X-RAY DIFFRACTION99
2.6982-2.75330.361360.30062628X-RAY DIFFRACTION99
2.7533-2.81310.37361530.28122663X-RAY DIFFRACTION99
2.8131-2.87850.30941120.25412701X-RAY DIFFRACTION99
2.8785-2.95050.37941260.26282670X-RAY DIFFRACTION99
2.9505-3.03030.3241460.26172670X-RAY DIFFRACTION99
3.0303-3.11940.31541660.26982644X-RAY DIFFRACTION99
3.1194-3.22010.31821420.23742669X-RAY DIFFRACTION100
3.2201-3.33520.27631350.21732663X-RAY DIFFRACTION99
3.3352-3.46870.23441490.19372716X-RAY DIFFRACTION99
3.4687-3.62650.26191550.19872641X-RAY DIFFRACTION99
3.6265-3.81760.25131620.1852666X-RAY DIFFRACTION100
3.8176-4.05660.18721700.16262650X-RAY DIFFRACTION100
4.0566-4.36970.17681510.14092673X-RAY DIFFRACTION99
4.3697-4.8090.1911360.13252681X-RAY DIFFRACTION98
4.809-5.5040.20271360.15562676X-RAY DIFFRACTION98
5.504-6.9310.24641290.20762742X-RAY DIFFRACTION100
6.931-47.38280.22141420.19352769X-RAY DIFFRACTION99

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