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- PDB-4n3n: Crystal structure of eukaryotic translation initiation factor eIF... -

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Basic information

Entry
Database: PDB / ID: 4n3n
TitleCrystal structure of eukaryotic translation initiation factor eIF5B (517-1116) from Chaetomium thermophilum, apo form
ComponentsEukaryotic translation initiation factor 5B-like protein, eIF5B(517-C)
KeywordsTRANSLATION / Translation initiation / GTPase / eIF5B/IF2 / Subunit joining / Ribosome
Function / homology
Function and homology information


protein-synthesizing GTPase / translation initiation factor activity / GTPase activity / GTP binding / mitochondrion / metal ion binding
Similarity search - Function
Translation initiation factor IF- 2, domain 3 / Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / Translation factors / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 ...Translation initiation factor IF- 2, domain 3 / Elongation factor Tu-type domain / Elongation factor Tu domain 4 / Translation initiation factor IF- 2, domain 3 / Translation-initiation factor 2 / Translation initiation factor IF- 2 / Translation initiation factor IF-2, domain 3 superfamily / Translation factors / Elongation factor Tu domain 2 / Elongation Factor Tu (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Small GTP-binding protein domain / Translation protein, beta-barrel domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
LACTIC ACID / Eukaryotic translation initiation factor 5B
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.752 Å
AuthorsKuhle, B. / Ficner, R.
CitationJournal: Embo J. / Year: 2014
Title: eIF5B employs a novel domain release mechanism to catalyze ribosomal subunit joining.
Authors: Kuhle, B. / Ficner, R.
History
DepositionOct 7, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Structure summary
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 5B-like protein, eIF5B(517-C)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3302
Polymers67,2401
Non-polymers901
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Eukaryotic translation initiation factor 5B-like protein, eIF5B(517-C)
hetero molecules

A: Eukaryotic translation initiation factor 5B-like protein, eIF5B(517-C)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,6594
Polymers134,4792
Non-polymers1802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-1/31
Buried area4560 Å2
ΔGint-12 kcal/mol
Surface area53240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.470, 111.470, 115.210
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Eukaryotic translation initiation factor 5B-like protein, eIF5B(517-C)


Mass: 67239.531 Da / Num. of mol.: 1 / Fragment: unp residues 517-1092
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0029840 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0S8G9
#2: Chemical ChemComp-LAC / LACTIC ACID


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 3.07 Å3/Da / Density % sol: 59.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 12% PEG 20000, 10 mM Na-lactate, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.82658 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82658 Å / Relative weight: 1
ReflectionResolution: 2.75→35.68 Å / Num. obs: 21910 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 77.16 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 33
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.75-2.850.5153.76159602198100
2.85-2.950.415.15153791898100
2.95-3.150.2348.54245263105100
3.15-3.750.08520.65460565904100
3.75-4.050.04238.2413320176599.7
4.05-4.350.03150.04101591330100
4.35-4.650.02759.937923101799.6
4.65-140.01875.5333264450199.9
14-170.01114.854928198.8
17-500.013110.6660911195.7
50

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å48.27 Å
Translation3 Å48.27 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1G7R

1g7r


Resolution: 2.752→35.683 Å / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.7751 / SU ML: 0.41 / σ(F): 1.36 / Phase error: 28.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2382 1094 5 %
Rwork0.1927 --
obs0.195 21879 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 156.58 Å2 / Biso mean: 64.6618 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 2.752→35.683 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4573 0 6 27 4606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044670
X-RAY DIFFRACTIONf_angle_d0.8256304
X-RAY DIFFRACTIONf_chiral_restr0.056729
X-RAY DIFFRACTIONf_plane_restr0.003815
X-RAY DIFFRACTIONf_dihedral_angle_d14.7331775
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.7521-2.87730.38911360.308725672703
2.8773-3.02890.33171360.275425712707
3.0289-3.21860.34251340.255925562690
3.2186-3.46690.31841360.249525712707
3.4669-3.81540.25071360.204125832719
3.8154-4.36670.2621350.170325752710
4.3667-5.49830.17931390.161826372776
5.4983-35.68640.19821420.171127252867
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)
10.2883-0.0872-0.14860.23280.01830.1874-0.0490.2164-0.18710.23820.0030.15360.1059-0.1321-00.446-0.10970.07050.3852-0.03850.3992-53.3677-2.7948-4.6928
20.2223-0.0702-0.0280.27490.08230.15810.06280.16140.1870.1208-0.03820.0658-0.1287-0.263100.27990.0280.01660.54490.0140.4117-59.690518.2299-19.369
30.0584-0.00910.1088-0.03660.21410.12490.0910.216-0.28280.02940.1815-0.062-0.1046-0.09440.07210.281-0.00850.02950.4825-0.04170.4552-18.022115.6811-32.2565
40.2620.4639-0.46650.8987-0.94031.23920.44360.4087-0.20550.4290.28750.1941-0.1217-0.12290.72990.3102-0.0349-0.18710.4656-0.42930.51888.956617.4529-33.5542
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 514 through 722 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 723 through 879 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 880 through 1026 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 1027 through 1116 )A0

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