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

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Basic information

Entry
Database: PDB / ID: 4ncn
TitleCrystal structure of eukaryotic translation initiation factor eIF5B (517-858) from Chaetomium thermophilum in complex with GTP
ComponentsEukaryotic translation initiation factor 5B-like protein
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
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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / GUANOSINE-5'-TRIPHOSPHATE / Eukaryotic translation initiation factor 5B
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 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 1.2Oct 11, 2017Group: Data collection / Category: reflns_shell / Item: _reflns_shell.percent_possible_all
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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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 / _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-like protein
B: Eukaryotic translation initiation factor 5B-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,79116
Polymers101,9452
Non-polymers1,84614
Water9,152508
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A: Eukaryotic translation initiation factor 5B-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8197
Polymers50,9731
Non-polymers8476
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Eukaryotic translation initiation factor 5B-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9719
Polymers50,9731
Non-polymers9998
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.410, 114.840, 65.880
Angle α, β, γ (deg.)90.00, 102.41, 90.00
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
1ASNASNGLNGLNchain AAA517 - 8604 - 347
2HISHISLEULEUchain BBB515 - 8592 - 346

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Eukaryotic translation initiation factor 5B-like protein


Mass: 50972.512 Da / Num. of mol.: 2 / Fragment: unp residues 516-946
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum (fungus)
Strain: DSM 1495 / Gene: CTHT_0029840 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G0S8G9

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Non-polymers , 6 types, 522 molecules

#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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE MISMATCH RESIDUES 576-599 IS A WRONGLY ASSIGNED INTRON IN THE CHAETOMIUM THERMOPHILUM SEQUENCE. ...THE MISMATCH RESIDUES 576-599 IS A WRONGLY ASSIGNED INTRON IN THE CHAETOMIUM THERMOPHILUM SEQUENCE. MULTIPLE SEQUENCE ALIGNMENTS WITH HOMOLOGUES FROM OTHER SPECIES SHOWED THAT THIS INTRON CORRESPONDS TO A PROTEIN SEQUENCE, WHICH IS PRESENT AND HIGHLY CONSERVED IN ALL OTHER SPECIES. IN ADDITION, ISOLATION OF THE GENE FROM A CHAETOMIUM THERMOPHILUM CDNA LIBRARY WITH APPROPRIATE PRIMERS AMPLIFIED THE GENE INCLUDING THE WRONGLY ASSIGNED INTRON.

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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: 2.01 Å3/Da / Density % sol: 38.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM Hepes, 13 % PEG 4000, 100 mM NaOAc, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.87→46.645 Å / Num. obs: 66297 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 28.97 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 20.53
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.87-1.970.622.38199.8
1.97-2.070.373.84199.8
2.07-2.270.2146.27199.9
2.27-3.170.0717.3199.8
3.17-3.620.02545.27199.7
3.62-4.070.0254.88199.6
4.07-4.520.01667.581100
4.52-140.01474.43199.5
14-170.0199.661100
17-500.01194.71192.7
501

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.65 Å
Translation2.5 Å46.65 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 4N3N

4n3n


Resolution: 1.87→46.645 Å / Occupancy max: 1 / Occupancy min: 0.32 / SU ML: 0.23 / σ(F): 1.35 / Phase error: 21.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2038 3311 5 %
Rwork0.1635 --
obs0.1656 66261 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.8536 Å2
Refinement stepCycle: LAST / Resolution: 1.87→46.645 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5378 0 114 508 6000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0195641
X-RAY DIFFRACTIONf_angle_d1.7737623
X-RAY DIFFRACTIONf_dihedral_angle_d18.0732172
X-RAY DIFFRACTIONf_chiral_restr0.096865
X-RAY DIFFRACTIONf_plane_restr0.009986
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3262X-RAY DIFFRACTION7.205TORSIONAL
12B3262X-RAY DIFFRACTION7.205TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.89680.30841390.26232633X-RAY DIFFRACTION100
1.8968-1.92510.31591380.24872614X-RAY DIFFRACTION100
1.9251-1.95520.25941370.23942605X-RAY DIFFRACTION100
1.9552-1.98720.29671380.23372626X-RAY DIFFRACTION100
1.9872-2.02150.2491370.21512590X-RAY DIFFRACTION100
2.0215-2.05820.27751400.20572668X-RAY DIFFRACTION100
2.0582-2.09780.22431360.20262571X-RAY DIFFRACTION100
2.0978-2.14060.2491370.19482611X-RAY DIFFRACTION100
2.1406-2.18720.24181380.19042620X-RAY DIFFRACTION100
2.1872-2.23810.21621380.18152616X-RAY DIFFRACTION100
2.2381-2.2940.20021360.17212617X-RAY DIFFRACTION100
2.294-2.35610.20321390.16922625X-RAY DIFFRACTION100
2.3561-2.42540.24641380.16762629X-RAY DIFFRACTION100
2.4254-2.50370.22811370.16842610X-RAY DIFFRACTION100
2.5037-2.59310.20241370.16692611X-RAY DIFFRACTION100
2.5931-2.6970.24851370.17282612X-RAY DIFFRACTION100
2.697-2.81970.19841390.16462644X-RAY DIFFRACTION100
2.8197-2.96830.23231390.172622X-RAY DIFFRACTION100
2.9683-3.15430.21361380.15672621X-RAY DIFFRACTION100
3.1543-3.39770.17951370.15012620X-RAY DIFFRACTION100
3.3977-3.73950.19651370.14232637X-RAY DIFFRACTION100
3.7395-4.28030.16491400.12792645X-RAY DIFFRACTION100
4.2803-5.39150.14951380.13372620X-RAY DIFFRACTION100
5.3915-46.65980.19571410.17192683X-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)
10.0183-0.17460.04072.37140.38651.69040.0168-0.16790.02880.20650.0141-0.57410.15780.13980.04410.2108-0.0105-0.03350.19380.01410.29353.635914.579321.291
22.17540.4440.29032.47690.65051.747-0.01320.3403-0.107-0.5799-0.0534-0.14720.0581-0.0370.04290.2286-0.00460.02050.2074-0.00680.1637-5.050915.50248.1379
31.9873-0.8788-0.20143.0697-1.19560.8106-0.0601-0.08880.21190.21230.0569-0.8956-0.19520.1378-0.00250.2005-0.0309-0.01820.2551-0.00110.33219.860526.464518.8247
41.09750.39390.10252.80310.55681.32480.0917-0.2138-0.14770.4082-0.13040.08060.2406-0.15680.03460.2393-0.05330.0290.21350.020.1712-8.30513.342922.8021
52.98170.4427-1.72643.80050.12162.11220.21180.32690.7836-0.3321-0.10250.1371-0.3837-0.1403-0.11040.29050.0163-0.03140.21690.02480.3181-9.196537.51315.3416
61.818-0.38180.91352.5375-2.49954.1148-0.2044-0.43870.21510.37170.34990.5336-0.0516-0.8424-0.06480.21240.02080.07820.3505-0.07470.2601-17.628229.88326.8956
71.11160.4394-0.02471.91680.30971.70680.1347-0.24060.12050.4424-0.0588-0.06470.2390.039-0.08440.2796-0.01640.00960.2265-0.02240.1577-6.173527.345827.8023
81.21920.1444-0.26451.98850.86020.42570.096-0.315-0.14370.70570.0027-0.55930.2340.1719-0.07880.3128-0.0142-0.12880.28960.03210.32127.441916.216626.0047
91.3141.0689-0.09991.7470.5422.43540.23180.5227-0.6851-0.49720.2641-1.75550.43260.0147-0.34150.320.1293-0.06810.397-0.07020.879811.6898-4.025712.6077
103.1808-1.022-0.74932.2439-0.34072.03940.25250.4962-0.4339-0.4341-0.058-0.68980.04990.1555-0.26260.30280.0480.08890.3395-0.02860.5510.84759.42798.215
113.09431.2932-0.43622.5423-0.62590.16980.44990.2523-0.5999-0.0383-0.1359-1.2520.206-0.0046-0.17410.3660.0760.01290.3075-0.0190.5388.0798-4.162513.2911
120.6770.0157-0.34433.28961.51944.10350.0525-1.263-0.38920.9004-0.1041-0.83850.77890.1825-0.75870.68080.0292-0.4940.58220.16781.252113.2685-10.06825.8145
131.6364-0.26780.63162.16760.28522.54010.02240.03720.0099-0.1344-0.06530.1066-0.0474-0.03470.03850.1333-0.0112-0.00730.14960.01650.192513.318743.4417-0.2991
141.65020.06890.29061.8261-0.40442.1846-0.00310.0031-0.054-0.0459-0.0545-0.17880.05410.13380.06250.1267-0.00160.00840.16120.02720.207920.362545.42861.9279
151.18630.00581.45582.2776-0.55892.1793-0.2313-0.03070.48420.0861-0.16520.0529-0.6618-0.35420.2520.37020.027-0.0390.199-0.00690.391815.51366.08727.4548
163.1264-3.48480.53235.6877-0.14820.9529-0.3463-0.49390.67140.89540.0493-0.8795-0.35370.16570.29760.3671-0.0593-0.08650.3302-0.04280.360526.458858.894516.5665
171.70050.1691.23752.7819-0.47082.2152-0.10830.11770.4312-0.0829-0.018-0.6295-0.20160.46940.09980.2327-0.0525-0.01980.25770.0320.335127.679254.77065.2911
180.9258-0.11410.65832.74461.16571.84260.01650.29140.0716-0.05750.0464-0.8580.04250.4159-0.01370.2290.01380.01940.2920.060.307524.313543.3375-8.3021
193.06751.48030.39953.05660.18632.11620.341-0.05130.44370.4494-0.00650.68430.4613-0.7848-0.34050.4604-0.09170.04440.42970.03570.28345.873928.8907-7.3082
201.760.1162-0.00082.23560.58843.5788-0.0214-0.0366-0.28060.21040.0005-0.19221.02470.2320.00260.53980.0459-0.02660.276-0.00250.206211.442725.5598-11.8855
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 517 through 535 )
2X-RAY DIFFRACTION2chain 'A' and (resid 536 through 560 )
3X-RAY DIFFRACTION3chain 'A' and (resid 561 through 588 )
4X-RAY DIFFRACTION4chain 'A' and (resid 589 through 652 )
5X-RAY DIFFRACTION5chain 'A' and (resid 653 through 672 )
6X-RAY DIFFRACTION6chain 'A' and (resid 673 through 693 )
7X-RAY DIFFRACTION7chain 'A' and (resid 694 through 722 )
8X-RAY DIFFRACTION8chain 'A' and (resid 723 through 753 )
9X-RAY DIFFRACTION9chain 'A' and (resid 754 through 797 )
10X-RAY DIFFRACTION10chain 'A' and (resid 798 through 820 )
11X-RAY DIFFRACTION11chain 'A' and (resid 821 through 838 )
12X-RAY DIFFRACTION12chain 'A' and (resid 839 through 860 )
13X-RAY DIFFRACTION13chain 'B' and (resid 515 through 560 )
14X-RAY DIFFRACTION14chain 'B' and (resid 561 through 652 )
15X-RAY DIFFRACTION15chain 'B' and (resid 653 through 672 )
16X-RAY DIFFRACTION16chain 'B' and (resid 673 through 692 )
17X-RAY DIFFRACTION17chain 'B' and (resid 693 through 722 )
18X-RAY DIFFRACTION18chain 'B' and (resid 723 through 753 )
19X-RAY DIFFRACTION19chain 'B' and (resid 754 through 771 )
20X-RAY DIFFRACTION20chain 'B' and (resid 772 through 859 )

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