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- PDB-5cqr: Dimerization of Elp1 is essential for Elongator complex assembly -

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Basic information

Entry
Database: PDB / ID: 5cqr
TitleDimerization of Elp1 is essential for Elongator complex assembly
ComponentsElongator complex protein 1
KeywordsPROTEIN BINDING / Familial Dysautonomia / Elongator Complex / Elp1 subunit / dimerization
Function / homology
Function and homology information


elongator holoenzyme complex / tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation / tRNA wobble uridine modification / regulation of translation / HATs acetylate histones / tRNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Elongator complex protein 1 / IKI3 family / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Elongator complex protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.015 Å
AuthorsLin, Z. / Xu, H. / Li, F. / Diao, W. / Long, J. / Shen, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Dimerization of elongator protein 1 is essential for Elongator complex assembly.
Authors: Xu, H. / Lin, Z. / Li, F. / Diao, W. / Dong, C. / Zhou, H. / Xie, X. / Wang, Z. / Shen, Y. / Long, J.
History
DepositionJul 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Experimental preparation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongator complex protein 1


Theoretical massNumber of molelcules
Total (without water)71,1711
Polymers71,1711
Non-polymers00
Water905
1
A: Elongator complex protein 1

A: Elongator complex protein 1


Theoretical massNumber of molelcules
Total (without water)142,3422
Polymers142,3422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_546x,x-y-1,-z+7/61
Buried area3470 Å2
ΔGint-17 kcal/mol
Surface area46570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.020, 73.020, 479.508
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Elongator complex protein 1 / ELP1 / IkappaB kinase complex-associated protein / IKK complex-associated protein / p150


Mass: 71171.211 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 715-1332
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IKBKAP, ELP1, IKAP / Production host: Escherichia coli (E. coli) / References: UniProt: O95163
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM HEPES, pH 7.0, 20% PEG 3350, 200 mM potassium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 16272 / % possible obs: 99.9 % / Redundancy: 20 % / Net I/σ(I): 19
Reflection shellResolution: 3→3.11 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3.015→46.465 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0.17 / Phase error: 23.31 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2701 1398 9.97 %
Rwork0.2212 --
obs0.2261 14026 86.79 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.641 Å2 / ksol: 0.309 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.2137 Å2-0 Å20 Å2
2--3.2137 Å2-0 Å2
3----6.4273 Å2
Refinement stepCycle: LAST / Resolution: 3.015→46.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3595 0 0 5 3600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093664
X-RAY DIFFRACTIONf_angle_d1.2354957
X-RAY DIFFRACTIONf_dihedral_angle_d18.771341
X-RAY DIFFRACTIONf_chiral_restr0.079565
X-RAY DIFFRACTIONf_plane_restr0.005631
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0152-3.12290.4037510.3215454X-RAY DIFFRACTION33
3.1229-3.24790.3126960.2986872X-RAY DIFFRACTION62
3.2479-3.39570.34091360.27051246X-RAY DIFFRACTION88
3.3957-3.57470.33551370.241278X-RAY DIFFRACTION90
3.5747-3.79850.25431540.19991387X-RAY DIFFRACTION97
3.7985-4.09170.24721550.18091386X-RAY DIFFRACTION97
4.0917-4.50310.21541580.16081420X-RAY DIFFRACTION98
4.5031-5.1540.20241610.19111445X-RAY DIFFRACTION99
5.154-6.49070.35061660.26621486X-RAY DIFFRACTION99
6.4907-46.47060.26451840.23841654X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 61.418 Å / Origin y: 18.3401 Å / Origin z: 267.2202 Å
111213212223313233
T0.3551 Å20.0598 Å2-0.0371 Å2-0.1649 Å2-0.0436 Å2--0.2356 Å2
L0.889 °20.1204 °20.5605 °2--0.1092 °20.0137 °2--0.1766 °2
S-0.1756 Å °-0.0476 Å °0.2296 Å °0.0084 Å °0.0101 Å °0.1026 Å °0.0928 Å °0.0469 Å °-0.0032 Å °
Refinement TLS groupSelection details: all

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