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- PDB-4tmw: Translation initiation factor eIF5B (517-858) from C. thermophilu... -

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Basic information

Entry
Database: PDB / ID: 4tmw
TitleTranslation initiation factor eIF5B (517-858) from C. thermophilum, bound to GTP and Sodium
ComponentseIF5B
KeywordsTRANSLATION / Translation factor / GTPase / 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
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-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'-TRIPHOSPHATE / Eukaryotic translation initiation factor 5B
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsKuhle, B. / Ficner, R.
CitationJournal: Embo J. / Year: 2014
Title: A monovalent cation acts as structural and catalytic cofactor in translational GTPases.
Authors: Kuhle, B. / Ficner, R.
History
DepositionJun 2, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 19, 2014Group: Database references
Revision 1.2Dec 24, 2014Group: Database references
Revision 1.3Feb 24, 2016Group: Structure summary
Revision 1.4Dec 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: eIF5B
B: eIF5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8818
Polymers76,7402
Non-polymers1,1416
Water13,349741
1
A: eIF5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9404
Polymers38,3701
Non-polymers5703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: eIF5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9404
Polymers38,3701
Non-polymers5703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.610, 116.450, 66.240
Angle α, β, γ (deg.)90.000, 101.150, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1HISHISSERSERchain AAA515 - 8572 - 344
2GLYGLYASPASPchain BBB514 - 8581 - 345
DetailsThe biological unit is a monomer. There are 2 fragments of the biological unit in the asymmetric unit (chains A & B)

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Components

#1: Protein eIF5B


Mass: 38370.016 Da / Num. of mol.: 2 / Fragment: G domain and domain II / Mutation: D533A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta2 / References: UniProt: G0S8G9*PLUS
#2: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 741 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe accession number on NCBI for the corresponding gene is XP_006693439.

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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: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.25 / Details: HEPES, PEG 4000, NaOAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0332 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 118431 / % possible obs: 98.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 17.27 Å2 / Rmerge F obs: 0.999 / Rrim(I) all: 0.047 / Χ2: 0.978 / Net I/σ(I): 15.52 / Num. measured all: 405555
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.55-1.640.7360.5052.329638886387420.63397.7
1.59-1.630.8210.4283.0629243855384860.50899.2
1.63-1.680.880.3393.828389836882900.40399.1
1.68-1.730.9140.274.7427268813780370.32198.8
1.73-1.790.9420.2035.8724734787477430.24498.3
1.79-1.850.9660.1487.8624388764375120.17798.3
1.85-1.920.9810.1210.3326194732073000.14199.7
1.92-20.9880.09612.5525216710070640.11499.5
2-2.090.9910.07416.0923904676467390.08899.6
2.09-2.190.9940.06118.9122602647264390.07299.5
2.19-2.310.9960.0522.2921294619361390.0699.1
2.31-2.450.9970.04324.7118979584357700.05198.8
2.45-2.620.9970.03726.5516812548653860.04498.2
2.62-2.830.9980.03333.818469510750880.03999.6
2.83-3.10.9990.02740.816997473747140.03199.5
3.1-3.470.9990.02149.8415035426042530.02599.8
3.47-40.9990.01954.912709377137450.02299.3
4-4.90.9990.01757.079511319331000.0297.1
4.9-6.930.9990.01859.779193247724760.021100
6.930.9990.02162.324980138613650.02598.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.55 Å46.44 Å
Translation4.55 Å46.44 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALE2.5.2data scaling
X-PLORmodel building
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.9_1690)refinement
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NCN

4ncn


Resolution: 1.55→43.367 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / Phase error: 18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1837 5920 5 %
Rwork0.1571 112461 -
obs0.1584 118431 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 110.52 Å2 / Biso mean: 25.3067 Å2 / Biso min: 10 Å2
Refinement stepCycle: final / Resolution: 1.55→43.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5361 0 68 758 6187
Biso mean--14.33 36.58 -
Num. residues----688
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0195950
X-RAY DIFFRACTIONf_angle_d1.7578109
X-RAY DIFFRACTIONf_chiral_restr0.102910
X-RAY DIFFRACTIONf_plane_restr0.011077
X-RAY DIFFRACTIONf_dihedral_angle_d17.2812315
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3186X-RAY DIFFRACTION7.259TORSIONAL
12B3186X-RAY DIFFRACTION7.259TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5501-1.56770.30391920.25963650384298
1.5677-1.58620.28571990.2413771397099
1.5862-1.60550.24941960.23013738393499
1.6055-1.62580.26651990.2153774397399
1.6258-1.64720.22781980.2133751394999
1.6472-1.66980.24751950.20313722391799
1.6698-1.69360.22921980.19243755395399
1.6936-1.71890.19891960.18273716391299
1.7189-1.74580.21171970.18143741393899
1.7458-1.77440.2191930.17873676386998
1.7744-1.8050.24251930.18553673386697
1.805-1.83780.22821970.17413745394299
1.8378-1.87320.20321980.1637473945100
1.8732-1.91140.20911980.159237583956100
1.9114-1.9530.19771980.157837743972100
1.953-1.99840.18772000.15823791399199
1.9984-2.04840.18511980.150137623960100
2.0484-2.10380.18281960.15283732392899
2.1038-2.16570.18141970.15123746394399
2.1657-2.23560.17982000.14943798399899
2.2356-2.31550.17121970.14643736393399
2.3155-2.40820.16261970.1473751394899
2.4082-2.51770.18151950.14783709390498
2.5177-2.65050.20811970.15323744394199
2.6505-2.81650.19091990.159537763975100
2.8165-3.03390.16681990.156437823981100
3.0339-3.33910.18612000.151338014001100
3.3391-3.82210.14911990.146837723971100
3.8221-4.81440.15731960.12733730392698
4.8144-43.38360.15882030.15623840404399
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)
10.9322-0.2127-0.15021.3119-0.16290.9008-0.0391-0.00320.0123-0.02250.0278-0.1446-0.02020.0862-0.0080.1309-0.00910.01140.1318-0.01040.118459.116319.174315.2048
20.9709-0.1122-0.10221.1860.11780.7242-0.0153-0.09230.06370.11550.02350.0643-0.0008-0.0373-0.00370.1274-0.01330.01120.1338-0.00920.100149.464621.991923.3274
30.8539-0.0077-0.08121.9232-0.12640.75060.03830.1045-0.0896-0.2037-0.0166-0.10810.0374-0.0177-0.00070.17380.01770.01330.2341-0.03270.207867.24351.134510.9141
42.7369-0.81221.06260.9285-0.14910.70770.1431-0.6784-0.36860.42090.0873-0.15680.49940.0067-0.20120.365-0.0165-0.03630.37240.030.300369.5035-9.357721.5241
50.9004-0.06330.32870.90120.07950.7240.0243-0.0291-0.01470.0569-0.0473-0.0577-0.02130.04630.03850.1320.0006-0.00510.1285-0.00540.138141.7246-14.46721.8396
60.7564-0.15830.03951.30220.16690.9636-0.00460.00730.0222-0.0219-0.03160.0628-0.0648-0.00120.03290.11560.00160.00080.1338-0.00850.144936.1861-8.7598-2.0733
72.91372.546-0.42523.9098-0.58121.3826-0.07190.26070.4044-0.3475-0.0260.433-0.2955-0.19070.0810.27680.0561-0.06340.25080.02070.209928.94780.3675-15.9987
81.249-0.61360.60352.50070.83212.22040.01690.0836-0.0298-0.0266-0.10390.46-0.1097-0.36230.07540.15580.0198-0.01840.1792-0.00310.204128.5518-3.151-5.0516
90.7875-0.2613-0.07361.1296-0.33540.9369-0.0206-0.1224-0.0680.14060.03890.2761-0.0333-0.1169-0.05320.1523-0.00230.00690.1829-0.00660.180530.8483-14.4119.6123
103.6354-1.7388-0.56432.09310.56092.28960.11470.02750.0871-0.0877-0.0489-0.42910.1220.5167-0.01250.20420.02670.01050.26180.02130.279849.6198-28.72298.3693
111.32470.7306-0.16681.4861-0.55451.95440.0523-0.0575-0.15920.0154-0.0753-0.19990.26860.10480.04750.19030.0065-0.02640.17910.03180.170547.2681-27.20213.4411
120.2796-0.10540.41030.54930.51672.94150.0472-0.0722-0.3344-0.006-0.10550.03010.7848-0.67730.12540.4369-0.0946-0.00870.30840.00580.286738.6985-39.788512.8077
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 515 through 588 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 589 through 753 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 754 through 826 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 827 through 857 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid 514 through 560 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 561 through 672 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 673 through 692 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 693 through 722 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 723 through 753 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 754 through 771 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 772 through 826 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 827 through 858 )B0

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