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

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Basic information

Entry
Database: PDB / ID: 4ncf
TitleCrystal structure of eukaryotic translation initiation factor eIF5B (399-852) from Saccharomyces cerevisiae in complex with GDP
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 / ribosome assembly / cytosolic 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 / ribosome assembly / cytosolic ribosome assembly / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / translational initiation / cytoplasmic stress granule / ribosome binding / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / 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 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Eukaryotic translation initiation factor 5B
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.015 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 24, 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_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)102,9326
Polymers101,9972
Non-polymers9354
Water00
1
A: Eukaryotic translation initiation factor 5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4663
Polymers50,9991
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Eukaryotic translation initiation factor 5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4663
Polymers50,9991
Non-polymers4682
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.560, 119.460, 120.730
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-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: GLU / End label comp-ID: GLU

Dom-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASPASPchain AAA402 - 8527 - 457
2LYSLYSchain BBB401 - 8486 - 453

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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: S288c / Gene: FUN12, NM_001178180, YAL035W / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P39730
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop
Details: 8 % PEG 8000 0.37 M Li2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 283K

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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: 3.02→46.664 Å / Num. obs: 21521 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 77.83 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 23.32
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.02-3.120.6063.52199.5
3.12-3.210.434.61199.5
3.21-3.410.2936.45199.4
3.41-3.930.13512.38199
3.93-4.20.06821.3199.2
4.2-4.450.04728.05199.5
4.45-4.720.03532.85198.3
4.72-140.02149.55199.5
14-170.01290.811100
17-500.01384.45197.3
501

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.02 Å46.66 Å
Translation3.02 Å46.66 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 4N3S

4n3s


Resolution: 3.015→46.664 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / σ(F): 1.34 / Phase error: 31.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2808 1074 5 %
Rwork0.2525 --
obs0.254 21468 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 107.1292 Å2
Refinement stepCycle: LAST / Resolution: 3.015→46.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6641 0 58 0 6699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036794
X-RAY DIFFRACTIONf_angle_d0.819218
X-RAY DIFFRACTIONf_dihedral_angle_d14.812500
X-RAY DIFFRACTIONf_chiral_restr0.031109
X-RAY DIFFRACTIONf_plane_restr0.0031170
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3450X-RAY DIFFRACTION11.956TORSIONAL
12B3450X-RAY DIFFRACTION11.956TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0152-3.15240.36431330.36752510X-RAY DIFFRACTION99
3.1524-3.31860.34191320.31992510X-RAY DIFFRACTION99
3.3186-3.52640.33361320.30762508X-RAY DIFFRACTION99
3.5264-3.79860.36051320.29552509X-RAY DIFFRACTION99
3.7986-4.18070.29011340.25242531X-RAY DIFFRACTION99
4.1807-4.78510.2541330.21382538X-RAY DIFFRACTION99
4.7851-6.02670.28061350.24182587X-RAY DIFFRACTION100
6.0267-46.66960.23581430.22222701X-RAY DIFFRACTION99
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)
11.589-0.82051.21977.13840.43673.84890.0470.00880.0648-0.0572-0.20831.7102-0.0907-0.66070.18260.49710.06020.02160.4825-0.05910.58725.445126.434229.7152
21.8322-0.54561.57374.12843.15889.1363-0.20170.08410.20720.0404-0.0471-0.7717-1.03350.50280.31350.517-0.07040.1560.47420.08570.697313.268427.04127.7924
34.7077-0.1005-0.67594.44130.59826.7655-0.12320.1602-0.05560.3188-0.279-0.30.30330.06640.4490.4744-0.04970.01970.31550.00850.432210.461720.314543.2472
45.9053-1.83640.14378.4519-2.00217.9975-0.2124-0.36070.07251.0449-0.0228-1.06560.14340.91590.19560.5784-0.075-0.02390.4135-0.00940.59117.325122.451943.8567
55.9816-3.0534-3.79745.1572-1.41389.9177-0.7585-2.165-0.4540.3633-0.36010.20340.21510.91981.10591.19090.04580.08570.5922-0.07210.950510.415520.484313.4908
66.4926-0.8068-0.11866.8429-0.44717.0019-0.4780.80690.2524-1.21170.03680.05230.7064-0.03220.5781.1816-0.0643-0.01770.52080.05810.685.785820.20847.3116
75.92530.75912.77543.4682-0.20996.06610.21660.1711-0.4279-0.28670.297-0.27130.02630.8072-0.48420.79330.04920.18910.51310.02890.852713.9379-3.641316.6632
87.57386.49742.42186.60814.22846.47780.57-0.7372-0.4690.2166-0.4022-0.13531.071-0.2667-0.26321.27440.12660.09610.5492-0.02171.13934.4916-11.036322.2605
94.6347-1.51321.80091.7377-1.86597.2308-0.4682-0.75382.02760.7790.3206-1.61660.29870.26940.44210.60540.1519-0.38710.5443-0.25911.076546.7668-0.07372.8743
103.45631.8421-0.2423.89693.00277.9617-0.0815-0.11490.68220.84740.3312-0.40850.29710.6175-0.27640.84180.1565-0.44060.3898-0.16570.722239.2921-1.07732.3323
117.6001-2.181-0.86258.1547-1.39345.8259-0.4169-0.4225-0.26050.78720.29430.39810.2721-0.26630.1470.4372-0.0148-0.00970.3343-0.02310.398139.9913-15.24268.3882
123.3624-0.2042-1.88115.69981.22389.30511.3316-0.9489-1.610.4315-0.74040.0069-0.2047-0.5587-0.60260.82670.1135-0.27710.6461-0.02530.761641.371415.06477.2254
135.68223.40490.56037.168-1.93028.17540.7778-0.88980.5020.7351-0.28930.6373-1.5108-0.4581-0.21380.96760.05320.24480.61-0.04150.718344.100522.74057.757
145.3161-1.03272.18864.9923-1.42421.0978-1.1898-2.4795-1.03660.14150.54010.62744.8056-0.75620.29563.3410.38160.71272.66290.46891.311142.657815.377132.8717
157.6937-4.3747-1.38124.59152.21921.23220.6645-1.4740.6943.14192.0307-0.22081.1657-1.0848-2.07562.08370.1090.17921.70160.28130.760848.145923.154139.0679
163.3106-1.3178-1.22412.6354-1.5774.06960.8885-3.1301-0.79460.7981-1.3014-1.1395-0.6923.19730.17051.1288-0.1905-0.1782.2312-0.08711.778255.465617.059837.601
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 402 through 443 )
2X-RAY DIFFRACTION2chain 'A' and (resid 444 through 495 )
3X-RAY DIFFRACTION3chain 'A' and (resid 496 through 554 )
4X-RAY DIFFRACTION4chain 'A' and (resid 555 through 619 )
5X-RAY DIFFRACTION5chain 'A' and (resid 620 through 645 )
6X-RAY DIFFRACTION6chain 'A' and (resid 646 through 738 )
7X-RAY DIFFRACTION7chain 'A' and (resid 739 through 788 )
8X-RAY DIFFRACTION8chain 'A' and (resid 789 through 852 )
9X-RAY DIFFRACTION9chain 'B' and (resid 401 through 455 )
10X-RAY DIFFRACTION10chain 'B' and (resid 456 through 495 )
11X-RAY DIFFRACTION11chain 'B' and (resid 496 through 618 )
12X-RAY DIFFRACTION12chain 'B' and (resid 619 through 653 )
13X-RAY DIFFRACTION13chain 'B' and (resid 654 through 746 )
14X-RAY DIFFRACTION14chain 'B' and (resid 747 through 775 )
15X-RAY DIFFRACTION15chain 'B' and (resid 776 through 811 )
16X-RAY DIFFRACTION16chain 'B' and (resid 812 through 848 )

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