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- PDB-4a8j: Crystal Structure of the Elongator subcomplex Elp456 -

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Basic information

Entry
Database: PDB / ID: 4a8j
TitleCrystal Structure of the Elongator subcomplex Elp456
Components
  • Elongator complex protein 4
  • Elongator complex protein 5
  • Elongator complex protein 6
KeywordsTRANSCRIPTION
Function / homology
Function and homology information


elongator holoenzyme complex / protein urmylation / tRNA wobble uridine modification / tRNA modification / transcription elongation factor complex / peroxisome / regulation of translation / regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding ...elongator holoenzyme complex / protein urmylation / tRNA wobble uridine modification / tRNA modification / transcription elongation factor complex / peroxisome / regulation of translation / regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Elongator complex protein 4 / Elongator complex protein 6 / Elongator complex protein 5 / PAXNEB protein / Elongator subunit Iki1 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Elongator complex protein 5 / Elongator complex protein 4 / Elongator complex protein 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.1 Å
AuthorsGlatt, S. / Mueller, C.W.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: The Elongator Subcomplex Elp456 is a Hexameric Reca-Like ATPase.
Authors: Glatt, S. / Letoquart, J. / Faux, C. / Taylor, N.M.I. / Seraphin, B. / Muller, C.W.
History
DepositionNov 21, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Other
Revision 1.2May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Sep 11, 2024Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_struct_mod_residue / struct_conn / struct_ref / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_name_com.name ..._entity.pdbx_description / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_struct_mod_residue.details / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq_dif.details
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Elongator complex protein 4
B: Elongator complex protein 5
C: Elongator complex protein 6
D: Elongator complex protein 4
E: Elongator complex protein 5
F: Elongator complex protein 6


Theoretical massNumber of molelcules
Total (without water)208,3446
Polymers208,3446
Non-polymers00
Water15,529862
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15680 Å2
ΔGint-81.1 kcal/mol
Surface area59520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.730, 124.890, 146.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND (RESSEQ 67:136 OR RESSEQ 145:168 OR RESSEQ 234:416 )
211CHAIN D AND (RESSEQ 67:136 OR RESSEQ 145:168 OR RESSEQ 234:416 )
112CHAIN C AND (RESSEQ 5:62 OR RESSEQ 68:115 OR RESSEQ 120:226 OR RESSEQ 229:273 )
212CHAIN F AND (RESSEQ 5:62 OR RESSEQ 68:115 OR RESSEQ 120:226 OR RESSEQ 229:273 )
113CHAIN B AND (RESSEQ 2:92 OR RESSEQ 98:142 OR RESSEQ 149:232 )
213CHAIN E AND (RESSEQ 2:92 OR RESSEQ 98:142 OR RESSEQ 149:232 )

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1, 0.001, -0.0003), (0.001, -1, -0.0009), (-0.0004, 0.0009, -1)-0.2149, 227.1894, -0.0251
2given(0.9999, 0.0067, 0.0084), (0.0067, -1, 0.0003), (0.0084, -0.0002, -1)-0.7109, 226.8946, -0.4218
3given(1, 0.0029, 0.0023), (0.0029, -1, 0.0011), (0.0023, -0.001, -1)-0.3776, 227.1323, 0.0561

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Components

#1: Protein Elongator complex protein 4 / Gamma-toxin target 7 / HAT-associated protein 1


Mass: 41329.605 Da / Num. of mol.: 2 / Fragment: RESIDUES 66-426
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288C / Gene: ELP4, HAP1, TOT7, YPL101W / Plasmid: PET24D / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q02884
#2: Protein Elongator complex protein 5 / Gamma-toxin target 5 / HAT-associated protein 2 / Protein IKI1


Mass: 31045.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288C / Gene: IKI1, ELP5, HAP2, TOT5, YHR187W / Plasmid: PET24D / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P38874
#3: Protein Elongator complex protein 6 / Gamma-toxin target 6 / HAT-associated protein 3


Mass: 31797.154 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Strain: S288C / Gene: ELP6, HAP3, TOT6, YMR312W, YM9924.04 / Plasmid: PET24D / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q04868
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 862 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence details6XHIS TAG AT THE N-TERMINUS (MHHHHHHH)

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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: 2.38 Å3/Da / Density % sol: 48.4 % / Description: NONE
Crystal growpH: 7.5
Details: 200 MM MGCL2, 100 MM TRISHCL PH 7.5, AND 25% PEG 2K MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9782
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 2.1→46.2 Å / Num. obs: 112115 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 30.48 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 7.3
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.56 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS
Starting model: NONE

Resolution: 2.1→46.2 Å / SU ML: 0.49 / σ(F): 2 / Phase error: 29.75 / Stereochemistry target values: ML
Details: TWO REGIONS IN ELP4 RESIDUES 137-144 AND 169-233, TWO SHORT LOOPS IN ELP5 AND ITS C--TERMINUS RESIDUES 93-98, 144-148 AND 233-270 AND TWO SHORT LOOPS AND THE N-TERMINAL 6XHIS-TAG OF ELP6 ...Details: TWO REGIONS IN ELP4 RESIDUES 137-144 AND 169-233, TWO SHORT LOOPS IN ELP5 AND ITS C--TERMINUS RESIDUES 93-98, 144-148 AND 233-270 AND TWO SHORT LOOPS AND THE N-TERMINAL 6XHIS-TAG OF ELP6 RESIDUES 64-66 AND 227-231 ARE DISORDERD.
RfactorNum. reflection% reflection
Rfree0.2305 5598 5 %
Rwork0.2007 --
obs0.2022 111986 98.8 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.7 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--19.67 Å20 Å20 Å2
2---11.72 Å20 Å2
3----7.96 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12143 0 0 862 13005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112396
X-RAY DIFFRACTIONf_angle_d1.15816815
X-RAY DIFFRACTIONf_dihedral_angle_d15.74577
X-RAY DIFFRACTIONf_chiral_restr0.0781970
X-RAY DIFFRACTIONf_plane_restr0.0052130
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2203X-RAY DIFFRACTIONPOSITIONAL
12D2203X-RAY DIFFRACTIONPOSITIONAL0.04
21C2034X-RAY DIFFRACTIONPOSITIONAL
22F2034X-RAY DIFFRACTIONPOSITIONAL0.038
31B1781X-RAY DIFFRACTIONPOSITIONAL
32E1781X-RAY DIFFRACTIONPOSITIONAL0.061
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1012-2.1250.34211690.33313213X-RAY DIFFRACTION90
2.125-2.150.30911860.30473538X-RAY DIFFRACTION100
2.15-2.17630.27411840.27743513X-RAY DIFFRACTION100
2.1763-2.20380.27781870.27333543X-RAY DIFFRACTION100
2.2038-2.23280.31251870.26463548X-RAY DIFFRACTION100
2.2328-2.26340.27751850.25713534X-RAY DIFFRACTION100
2.2634-2.29570.27371880.25533558X-RAY DIFFRACTION100
2.2957-2.330.28791860.24263530X-RAY DIFFRACTION100
2.33-2.36640.28271870.23483546X-RAY DIFFRACTION100
2.3664-2.40520.26491890.23493593X-RAY DIFFRACTION100
2.4052-2.44670.2421860.23283518X-RAY DIFFRACTION100
2.4467-2.49110.26121860.23063535X-RAY DIFFRACTION100
2.4911-2.53910.26631880.22073567X-RAY DIFFRACTION100
2.5391-2.59090.26971860.21333530X-RAY DIFFRACTION100
2.5909-2.64720.22151890.2083572X-RAY DIFFRACTION100
2.6472-2.70880.24011870.20713564X-RAY DIFFRACTION100
2.7088-2.77650.25121880.2033563X-RAY DIFFRACTION100
2.7765-2.85160.2561870.21593550X-RAY DIFFRACTION100
2.8516-2.93550.26281880.21323562X-RAY DIFFRACTION100
2.9355-3.03020.22231850.20123546X-RAY DIFFRACTION99
3.0302-3.13850.23891880.1983581X-RAY DIFFRACTION100
3.1385-3.26410.26451880.19393569X-RAY DIFFRACTION99
3.2641-3.41260.24521880.19273582X-RAY DIFFRACTION99
3.4126-3.59250.21831860.19153548X-RAY DIFFRACTION99
3.5925-3.81750.21651880.17933583X-RAY DIFFRACTION99
3.8175-4.1120.17651890.16653596X-RAY DIFFRACTION99
4.112-4.52550.1691890.15113587X-RAY DIFFRACTION99
4.5255-5.17960.17171880.14813584X-RAY DIFFRACTION98
5.1796-6.52290.22321920.19593636X-RAY DIFFRACTION98
6.5229-46.20770.22151840.20113499X-RAY DIFFRACTION91

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