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- PDB-4n3s: Crystal structure of eukaryotic translation initiation factor eIF... -

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Basic information

Entry
Database: PDB / ID: 4n3s
TitleCrystal structure of eukaryotic translation initiation factor eIF5B (399-852) from Saccharomyces cerevisiae, apo form
ComponentsEukaryotic translation initiation factor 5B
KeywordsTRANSLATION / Translation initiation / GTPase / eIF5B/IF2 / Subunit joining / Ribosome
Function / homology
Function and homology information


formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / protein-synthesizing GTPase / regulation of translational initiation / GTP hydrolysis and joining of the 60S ribosomal subunit / translation initiation factor binding / translation initiation factor activity / cytosolic ribosome assembly / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...formation of cytoplasmic translation initiation complex / eukaryotic 48S preinitiation complex / protein-synthesizing GTPase / regulation of translational initiation / GTP hydrolysis and joining of the 60S ribosomal subunit / translation initiation factor binding / translation initiation factor activity / cytosolic ribosome assembly / ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational initiation / cytoplasmic stress granule / ribosome binding / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / GTPase activity / GTP binding / mitochondrion / metal ion binding / cytosol / cytoplasm
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 (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain ...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 (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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Eukaryotic translation initiation factor 5B
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.832 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 1.1Jul 23, 2014Group: Other
Revision 1.2Aug 6, 2014Group: Structure summary
Revision 1.3Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Sep 20, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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: Eukaryotic translation initiation factor 5B
B: Eukaryotic translation initiation factor 5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3687
Polymers101,9972
Non-polymers3705
Water13,962775
1
A: Eukaryotic translation initiation factor 5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2775
Polymers50,9991
Non-polymers2784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Eukaryotic translation initiation factor 5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0912
Polymers50,9991
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.010, 118.010, 77.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 401 - 852 / Label seq-ID: 6 - 457

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Eukaryotic translation initiation factor 5B / eIF-5B / Translation initiation factor IF-2


Mass: 50998.629 Da / Num. of mol.: 2 / Fragment: unp residues 399-852
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: FUN12, YAL035W / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39730
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 775 / 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: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 5 % PEG 3350 and 20 mM MgCl2., 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
Reflection twinOperator: h,-k,-l / Fraction: 0.2
ReflectionHighest resolution: 1.83 Å / Num. obs: 93360 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.039 / Net I/σ(I): 21.05
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.83-1.930.5253.11627361367799.9
1.93-2.030.315.15494561111199.8
2.03-2.230.179.477923016774100
2.23-3.150.05722.671514543326899.8
3.15-3.610.02945.8928763618799.8
3.61-4.070.02651.5416984370999.7
4.07-4.530.02453.1510071234499.3
4.53-140.02356.1626651606199.3
14-170.02460.5445102100
17-500.03152.4646912798.4
50

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.95 Å
Translation2.5 Å46.95 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: 1.832→46.949 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8054 / σ(F): 1.36 / Phase error: 26.83 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1941 4673 5.01 %
Rwork0.1677 --
obs0.1689 93326 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.98 Å2 / Biso mean: 48.7131 Å2 / Biso min: 14.07 Å2
Refinement stepCycle: LAST / Resolution: 1.832→46.949 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6915 0 24 775 7714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087088
X-RAY DIFFRACTIONf_angle_d1.1419573
X-RAY DIFFRACTIONf_chiral_restr0.0461123
X-RAY DIFFRACTIONf_plane_restr0.0051220
X-RAY DIFFRACTIONf_dihedral_angle_d15.5082684
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4083X-RAY DIFFRACTION10.85TORSIONAL
12B4083X-RAY DIFFRACTION10.85TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.832-1.86360.35682310.30924358458995
1.8636-1.89750.2942350.30724466470195
1.8975-1.9340.28662330.29134426465995
1.934-1.97350.28722290.28244362459195
1.9735-2.01640.26322330.25984434466795
2.0164-2.06330.25232320.24564405463795
2.0633-2.11490.27172340.23814436467095
2.1149-2.17210.24732330.22914425465895
2.1721-2.2360.23422330.22234423465695
2.236-2.30810.232320.21264415464795
2.3081-2.39060.25142340.21164442467695
2.3906-2.48630.26952320.21254408464095
2.4863-2.59950.22872320.19944415464795
2.5995-2.73650.21962340.19854444467895
2.7365-2.90790.20312350.18854454468995
2.9079-3.13240.19752310.16844428465994
3.1324-3.44750.15792340.14074454468895
3.4475-3.94610.16882350.12324452468795
3.9461-4.97050.14062340.10184449468394
4.9705-43.63590.15022410.13644560480195
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)
10.3467-0.45490.03390.66350.08690.1446-0.2013-0.0942-0.1991-0.17370.20060.0298-0.13590.0239-0.01330.2752-0.01120.08820.24060.02880.257351.1509-31.78817.8608
20.8556-0.1661-0.09561.01860.06310.1082-0.08470.0136-0.143-0.1980.0269-0.0249-0.0734-0.0107-0.19780.1794-0.00880.06710.1930.02590.172750.9286-26.26799.3898
30.250.167-0.25480.23490.00620.2868-0.14560.18140.0836-0.06040.11620.310.0491-0.27660.00020.2362-0.0608-0.01230.43770.07070.368721.4903-18.215211.335
40.1195-0.007-0.10080.0491-0.03840.11050.1147-0.05690.1264-0.0923-0.15080.1423-0.07590.2342-0.00630.1849-0.01080.00570.2324-0.08540.284329.35532.7124-27.5306
51.0305-0.2440.01070.5188-0.27560.66960.1148-0.3023-0.1589-0.0853-0.02860.24380.0076-0.02580.00360.1854-0.0026-0.03450.2473-0.0110.264518.6123-8.8128-21.9293
60.555-0.0604-0.01410.44470.1890.34460.028-0.10930.00820.0436-0.0388-0.09530.0839-0.0019-0.03570.176-0.0058-0.02380.2001-0.00580.127347.3164-9.4081-26.1156
70.11060.07150.16830.103-0.03890.14620.03250.0575-0.2596-0.0270.0890.16640.02170.16230.00010.3342-0.0554-0.02450.2605-0.0110.419339.554-37.4094-29.2565
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 401 through 534 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 535 through 729 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 730 through 852 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 401 through 461 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 462 through 604 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 605 through 761 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 762 through 852 )B0

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