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- PDB-2ful: Crystal Structure of the C-terminal Domain of S. cerevisiae eIF5 -

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Basic information

Entry
Database: PDB / ID: 2ful
TitleCrystal Structure of the C-terminal Domain of S. cerevisiae eIF5
ComponentsEukaryotic translation initiation factor 5
KeywordsTRANSLATION / atypical HEAT motif
Function / homology
Function and homology information


eukaryotic initiation factor eIF2 binding / multi-eIF complex / formation of cytoplasmic translation initiation complex / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / GDP-dissociation inhibitor activity / regulation of translational initiation / Ribosomal scanning and start codon recognition / translation initiation factor binding / negative regulation of translational initiation ...eukaryotic initiation factor eIF2 binding / multi-eIF complex / formation of cytoplasmic translation initiation complex / formation of translation preinitiation complex / eukaryotic 48S preinitiation complex / GDP-dissociation inhibitor activity / regulation of translational initiation / Ribosomal scanning and start codon recognition / translation initiation factor binding / negative regulation of translational initiation / translation initiation factor activity / GTPase activator activity / cytosolic ribosome assembly / GTP binding / cytosol
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / Translation initiation factor IF2/IF5 / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain ...Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #180 / Translation initiation factor IF2/IF5 / Translation initiation factor IF2/IF5 domain / Translation initiation factor IF2/IF5, N-terminal / Translation initiation factor IF2/IF5, zinc-binding / Domain found in IF2B/IF5 / domain present in translation initiation factor eIF2B and eIF5 / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Eukaryotic translation initiation factor 5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsWei, Z. / Xue, Y. / Xu, H. / Gong, W.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of the C-terminal Domain of S.cerevisiae eIF5
Authors: Wei, Z. / Xue, Y. / Xu, H. / Gong, W.
History
DepositionJan 27, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Eukaryotic translation initiation factor 5
B: Eukaryotic translation initiation factor 5
C: Eukaryotic translation initiation factor 5
D: Eukaryotic translation initiation factor 5
E: Eukaryotic translation initiation factor 5
F: Eukaryotic translation initiation factor 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,39926
Polymers122,4776
Non-polymers1,92120
Water16,502916
1
A: Eukaryotic translation initiation factor 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7014
Polymers20,4131
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic translation initiation factor 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6053
Polymers20,4131
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Eukaryotic translation initiation factor 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6053
Polymers20,4131
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Eukaryotic translation initiation factor 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8936
Polymers20,4131
Non-polymers4805
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Eukaryotic translation initiation factor 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7975
Polymers20,4131
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Eukaryotic translation initiation factor 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7975
Polymers20,4131
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.849, 64.536, 108.916
Angle α, β, γ (deg.)88.60, 86.57, 74.93
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Eukaryotic translation initiation factor 5 / eIF-5


Mass: 20412.895 Da / Num. of mol.: 6 / Fragment: residues 236-412
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pGEX4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38431
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 916 / 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: 2.48 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: 2.8M (NH4)2SO4, 0.1M MES pH6.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9794 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionRedundancy: 4 % / Av σ(I) over netI: 23.4 / Number: 261803 / Rmerge(I) obs: 0.061 / Χ2: 2.56 / D res high: 2.1 Å / D res low: 50 Å / Num. obs: 65439 / % possible obs: 94.7
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsChi squaredRedundancy
4.5250669396.80.0656.3463.9
3.594.52659595.50.0472.6473.9
3.143.59666496.40.0512.4154
2.853.14660495.90.062.2834
2.652.85660795.60.0692.3674
2.492.65653894.50.0762.4114
2.372.49650094.30.0862.1174
2.262.37645393.10.1011.874
2.182.266421930.1131.6484
2.12.186364920.1291.4584
ReflectionResolution: 1.5→50 Å / Num. obs: 173580 / % possible obs: 92.8 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.044 / Χ2: 1.045 / Net I/σ(I): 25
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID
1.5-1.5568.92.50.245128951.0641
1.55-1.6289.12.90.205166521.0021
1.62-1.6992.93.10.175173390.991
1.69-1.7894.13.30.141176540.9851
1.78-1.8995.13.50.112177981.0351
1.89-2.0496.13.60.08179671.1321
2.04-2.2497.13.70.054182041.0741
2.24-2.5697.83.80.042182381.0471
2.56-3.2398.53.90.035184851.0841
3.23-5098.13.80.034183481.0071

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
SHARPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.475 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.074 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.205 8647 5 %RANDOM
Rwork0.177 ---
all0.178 ---
obs-173578 92.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.323 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.03 Å20.13 Å2
2---0.15 Å20.16 Å2
3---0.07 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7829 0 100 916 8845
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228419
X-RAY DIFFRACTIONr_angle_refined_deg1.2041.99511459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.91551062
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62126.105421
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.628151608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.491531
X-RAY DIFFRACTIONr_chiral_restr0.0840.21271
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026293
X-RAY DIFFRACTIONr_nbd_refined0.2050.24229
X-RAY DIFFRACTIONr_nbtor_refined0.3110.25884
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2745
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.2150
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.247
X-RAY DIFFRACTIONr_mcbond_it0.631.55131
X-RAY DIFFRACTIONr_mcangle_it1.00928171
X-RAY DIFFRACTIONr_scbond_it1.72433629
X-RAY DIFFRACTIONr_scangle_it2.6074.53235
LS refinement shellResolution: 1.502→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 400 -
Rwork0.253 7908 -
obs-8308 59.68 %
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)
11.2375-1.77092.39914.1096-2.65865.0318-0.23090.003-0.00130.2066-0.1608-0.1509-0.37490.38680.39170.0882-0.0053-0.02980.01940.0523-0.00328.87475.633-1.67
21.6257-0.28350.25541.3144-0.00111.0527-0.04530.0886-0.0433-0.00260.0779-0.0111-0.06760.0018-0.03260.04980.0068-0.0135-0.01140.0178-0.051713.09974.552-6.49
31.05881.0630.92122.420.82431.6701-0.0171-0.0567-0.0616-0.01360.0203-0.0745-0.0123-0.0194-0.00310.05470.0083-0.0137-0.02310.014-0.000415.59671.448-6.861
41.48570.8020.39952.2999-0.09351.5717-0.0649-0.0252-0.0182-0.0450.03950.0653-0.0992-0.06610.02540.0458-0.0018-0.0158-0.01910.009-0.017610.16475.892-15.349
51.29870.16920.38253.8112-1.95181.70780.00690.0691-0.07950.02060.0211-0.09280.0272-0.0368-0.0280.04350.0017-0.0008-0.0554-0.0161-0.004812.29868.811-17.336
60.0698-0.1266-0.67863.77232.39136.97740.0947-0.07150.0366-0.09930.0543-0.20330.25780.2641-0.1490.0851-0.0001-0.0368-0.0083-0.04-0.038314.09243.6913.544
71.2223-0.5556-0.80462.52240.82912.45060.01660.08750.0468-0.129-0.0379-0.00320.0708-0.00710.02130.05210.001-0.0191-0.0403-0.0204-0.062313.92250.07924.341
81.3134-1.3090.88993.5957-0.93261.9260.00910.0708-0.02470.0196-0.0715-0.0612-0.0032-0.01410.06240.06520.0079-0.0164-0.00410.0027-0.045616.43753.21725.955
91.3915-0.79640.01912.5437-0.42752.4755-0.0131-0.0125-0.07060.1392-0.03330.1237-0.0155-0.06490.04640.0530.0028-0.0153-0.0206-0.0004-0.044711.55259.30333.504
101.1952-0.4-1.12730.7081-0.11386.81110.04540.01210.1251-0.064-0.10120.0106-0.06610.15740.05580.0394-0.0092-0.0261-0.02130.0194-0.039715.27464.92929.073
1124.922-19.28-15.471521.93814.08614.5886-0.0444-0.72850.48780.36480.2596-0.20230.1848-0.1597-0.21520.03120.01070.00520.0012-0.00830.00138.57164.8331.111
123.83762.21292.34055.70041.55113.2605-0.18630.12790.0904-0.20020.26010.0916-0.28970.1518-0.07390.06850.0185-0.0346-0.0921-0.0038-0.00349.83846.826-11.555
130.78230.35450.06471.8905-0.66160.98490.00240.00430.0252-0.05540.0176-0.0232-0.00430.0805-0.01990.0560.0119-0.0125-0.0325-0.0221-0.020314.84932.764-7.96
141.35340.81440.45745.05481.96061.90570.0081-0.0242-0.27050.0361-0.01360.19730.1404-0.05540.00550.05170.0118-0.03-0.0322-0.010.03339.54516.139-2.066
155.71872.6723-1.80273.96983.31918.04310.5334-0.51970.5972-0.076-0.19520.3643-0.9173-0.1748-0.33820.14780.04850.06210.0262-0.03940.05412.42624.6694.11
160.2723-0.8870.70782.9512-2.81225.9810.01310.02720.02180.0865-0.0616-0.0560.35020.08660.04840.110.0002-0.0333-0.00470.0587-0.042928.31729.858-44.668
172.0363-0.65021.31782.0212-1.16143.42380.0958-0.1013-0.17610.08790.0394-0.12090.12160.0184-0.13520.04370.0058-0.029-0.02570.0281-0.03327.02235.903-54.142
181.2460.7170.56952.38440.72462.31410.0902-0.1207-0.0862-0.06720.0706-0.0564-0.0932-0.0202-0.16090.0542-0.0087-0.0157-0.03570.02880.004726.02738.846-61.967
192.31590.27820.86262.4125-0.11552.89880.0432-0.0214-0.0072-0.1650.03680.0093-0.2002-0.1098-0.080.06240.0163-0.0118-0.05180.0285-0.033221.87543.318-69.801
202.0348-1.61491.43626.3038-3.26942.0765-0.0167-0.0162-0.23480.34470.0483-0.0206-0.1615-0.1538-0.03160.05580.0095-0.0252-0.06710.0138-0.027121.3636.804-69.102
212.48311.0497-1.55131.9734-0.7183.7615-0.0056-0.2254-0.51620.2003-0.2256-0.09950.35180.24280.23120.0921-0.03220.0219-0.005-0.00510.030321.3946.467-22.495
222.31650.365-0.10192.16390.0481.33980.0089-0.0398-0.1310.012-0.1140.0040.0341-0.05650.10510.031-0.0009-0.0092-0.0227-0.0129-0.041524.10215.522-25.216
231.067-0.3570.0211.7312-0.1780.96680.00110.0336-0.02720.0685-0.0811-0.0387-0.03140.00140.080.0484-0.0033-0.0204-0.00380.0135-0.036328.21822.645-23.267
240.9284-0.45931.06030.5186-0.43283.064-0.0222-0.20590.05360.05010.098-0.10360.0274-0.0618-0.07580.0408-0.0003-0.06580.0347-0.0014-0.045830.94526.317-4.896
256.7945-0.3827-0.68791.9426-3.840110.9306-0.13970.75930.27750.00860.1943-0.0754-0.016-0.2883-0.05460.0401-0.0474-0.00160.05570.0125-0.021325.22736.508-22.031
2612.7773-8.1338-4.886512.78821.476822.9663-0.0421-0.04880.8246-0.21860.2521-0.92990.291.3721-0.210.0454-0.0323-0.0481-0.02950.00570.026327.0929.039-59.138
273.26483.73972.01555.12912.24883.526-0.09730.24510.0735-0.05250.15330.0061-0.42070.4305-0.0560.1015-0.0495-0.0674-0.08750.01240.045826.70218.743-64.72
282.43890.5853-0.1491.91960.10571.3611-0.01750.0570.0626-0.0067-0.0352-0.0343-0.06050.17970.05270.0542-0.0166-0.0151-0.0315-0.0006-0.016827.93.711-66.841
291.23710.45860.15062.82361.10082.53340.01850.0946-0.0293-0.0657-0.03890.08870.1632-0.0080.02040.0745-0.01620.0028-0.0453-0.019-0.053820.691-8.679-66.793
308.31232.1127-1.058212.01085.46212.71760.23850.05740.23290.1548-0.28040.3639-0.5296-0.45050.04190.0664-0.0293-0.009-0.04270.0208-0.034518.14-14.449-57.494
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA237 - 2582 - 23
22AA259 - 31324 - 78
33AA314 - 33479 - 99
44AA335 - 367100 - 132
55AA368 - 395133 - 160
66BB236 - 2671 - 32
77BB268 - 31133 - 76
88BB312 - 33577 - 100
99BB336 - 367101 - 132
1010BB368 - 394133 - 159
1111CC238 - 2423 - 7
1212CC243 - 2758 - 40
1313CC276 - 36241 - 127
1414CC363 - 390128 - 155
1515CC391 - 395156 - 160
1616DD238 - 2693 - 34
1717DD270 - 31335 - 78
1818DD314 - 33579 - 100
1919DD336 - 368101 - 133
2020DD369 - 394134 - 159
2121EE238 - 2733 - 38
2222EE274 - 31139 - 76
2323EE312 - 35877 - 123
2424EE359 - 386124 - 151
2525EE387 - 396152 - 161
2626FF238 - 2423 - 7
2727FF243 - 2808 - 45
2828FF281 - 32446 - 89
2929FF325 - 38590 - 150
3030FF386 - 395151 - 160

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