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- PDB-4cgb: Crystal structure of the trimerization domain of EML2 -

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Basic information

Entry
Database: PDB / ID: 4cgb
TitleCrystal structure of the trimerization domain of EML2
ComponentsECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 2
KeywordsCELL CYCLE / COILED-COIL
Function / homology
Function and homology information


regulation of microtubule nucleation / : / microtubule associated complex / negative regulation of microtubule polymerization / visual perception / tubulin binding / sensory perception of sound / spindle / microtubule cytoskeleton organization / microtubule binding ...regulation of microtubule nucleation / : / microtubule associated complex / negative regulation of microtubule polymerization / visual perception / tubulin binding / sensory perception of sound / spindle / microtubule cytoskeleton organization / microtubule binding / microtubule / signaling receptor binding / cytoplasm
Similarity search - Function
HELP / HELP motif / : / Quinoprotein alcohol dehydrogenase-like superfamily / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / Echinoderm microtubule-associated protein-like 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.154 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 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 2
B: ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 2
C: ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 2
D: ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 2
E: ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 2
F: ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7789
Polymers33,6086
Non-polymers1703
Water1,56787
1
A: ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 2
B: ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 2
C: ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8434
Polymers16,8043
Non-polymers391
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-31.4 kcal/mol
Surface area7870 Å2
MethodPISA
2
D: ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 2
E: ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 2
F: ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9355
Polymers16,8043
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-33.2 kcal/mol
Surface area7810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.871, 51.135, 101.691
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
ECHINODERM MICROTUBULE-ASSOCIATED PROTEIN-LIKE 2 / EMAP-2 / HUEMAP-2 / ECHINODERM MICROTUBULE ASSOCIATED PROTEIN-LIKE PROTEIN 2 ISOFORM 2


Mass: 5601.340 Da / Num. of mol.: 6 / Fragment: TRIMERIZATION DOMAIN, RESIDUES 11-60
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: BRAIN AND SPINAL CORD / Plasmid: PET30TEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: O95834
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE N-TERMINAL GLYCINE RESIDUE IS NOT PART OF THE NATIVE SEQUENCE AND DERIVES FROM THE TEV CLEAVAGE ...THE N-TERMINAL GLYCINE RESIDUE IS NOT PART OF THE NATIVE SEQUENCE AND DERIVES FROM THE TEV CLEAVAGE SITE. SEQUENCE USED HERE IS THE ISOFORM-2 OF O95834

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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: 1.86 Å3/Da / Density % sol: 33.7 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5
Details: CRYSTALS WERE OBTAINED BY THE HANGING DROP VAPOUR DIFFUSION METHOD USING 100 MM BIS-TRIS-PROPANE PH 6.5, 20% PEG 3350, 200 MM POTASSIUM THIOCYANATE IN THE RESERVOIR.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→50.86 Å / Num. obs: 14593 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 28.61 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.2
Reflection shellResolution: 2.15→2.32 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 3.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4CGC

4cgc


Resolution: 2.154→50.846 Å / SU ML: 0.2 / σ(F): 1.02 / Phase error: 23.5 / Stereochemistry target values: ML
Details: IN CHAIN A RESIDUES 14-57 ARE ORDERED. IN CHAIN B RESIDUES 14-58 ARE ORDERED. IN CHAIN C RESIDUES 13-53 ARE ORDERED. IN CHAIN D RESIDUES 13-57 ARE ORDERED. IN CHAIN E RESIDUES 13-52 ARE ...Details: IN CHAIN A RESIDUES 14-57 ARE ORDERED. IN CHAIN B RESIDUES 14-58 ARE ORDERED. IN CHAIN C RESIDUES 13-53 ARE ORDERED. IN CHAIN D RESIDUES 13-57 ARE ORDERED. IN CHAIN E RESIDUES 13-52 ARE ORDERED. IN CHAIN F RESIDUES 13-57 ARE ORDERED.
RfactorNum. reflection% reflection
Rfree0.2515 696 5 %
Rwork0.2055 --
obs0.2078 14027 99.67 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.888 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.143 Å20 Å20 Å2
2--10.0468 Å20 Å2
3----3.9039 Å2
Refinement stepCycle: LAST / Resolution: 2.154→50.846 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1968 0 8 87 2063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061991
X-RAY DIFFRACTIONf_angle_d0.932680
X-RAY DIFFRACTIONf_dihedral_angle_d17.187777
X-RAY DIFFRACTIONf_chiral_restr0.045329
X-RAY DIFFRACTIONf_plane_restr0.003362
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1542-2.32050.30181440.21382593X-RAY DIFFRACTION100
2.3205-2.5540.25591440.20462617X-RAY DIFFRACTION100
2.554-2.92350.27511300.21872639X-RAY DIFFRACTION99
2.9235-3.68320.24861470.19182676X-RAY DIFFRACTION100
3.6832-50.85960.23151310.20792806X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.12491.09833.76912.79351.63899.1057-0.0898-0.12180.1097-0.05750.03210.1005-0.1685-0.35330.12680.17450.01180.04390.14660.04340.2342-1.178821.668548.0306
23.9328-0.27881.64241.50380.18572.67590.15250.1127-0.0604-0.07130.0298-0.04890.3529-0.2631-0.26530.12390.01010.03520.11250.01260.22665.316617.435847.1587
36.1042-0.15034.51651.4969-0.93346.49320.03380.30690.07670.06580.12490.1543-0.38480.3033-0.12940.2794-0.03110.03860.20250.05190.31792.457225.508841.7592
45.11383.4841-2.32075.9317-3.09823.539-0.10140.73770.2314-0.22090.31290.34490.0848-0.3285-0.19430.24020.0704-0.05570.3014-0.00650.197816.549615.520337.3313
52.32123.28140.20988.637-0.90642.87840.08230.09670.0317-0.1329-0.211-0.2896-0.15410.0810.11960.16310.04540.02540.25140.01660.209523.729315.356341.5588
63.0252.7956-0.723810.0437-2.88982.7822-0.00910.29530.18210.1091-0.0121-0.0045-0.14780.0197-0.09920.12550.0105-0.01620.2625-0.01540.224516.428717.442444.4217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 4:57)
2X-RAY DIFFRACTION2CHAIN B AND (RESSEQ 13:60)
3X-RAY DIFFRACTION3CHAIN C AND (RESSEQ 13:60)
4X-RAY DIFFRACTION4CHAIN D AND (RESSEQ 13:57)
5X-RAY DIFFRACTION5CHAIN E AND (RESSEQ 13:60)
6X-RAY DIFFRACTION6CHAIN F AND (RESSEQ 13:60)

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