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

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Basic information

Entry
Database: PDB / ID: 4tmv
TitleTranslation initiation factor eIF5B (517-858) from C. thermophilum, bound to GTPgammaS and Sodium
ComponentseIF5B
KeywordsTRANSLATION / Ribosome / Initiation factor / GTPase
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 (Ef-tu); domain 3 / Translational (tr)-type GTP-binding domain / Elongation factor Tu 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 (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
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Eukaryotic translation initiation factor 5B
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.53 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 1.2Feb 24, 2016Group: Structure summary
Revision 1.3Mar 7, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
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 / diffrn_radiation_wavelength / 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
B: eIF5B
A: eIF5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,55815
Polymers76,7402
Non-polymers1,81813
Water11,494638
1
B: eIF5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3258
Polymers38,3701
Non-polymers9557
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: eIF5B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2337
Polymers38,3701
Non-polymers8636
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.640, 115.850, 66.090
Angle α, β, γ (deg.)90.000, 101.350, 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
1LYSLYSGLUGLUchain AAB518 - 8565 - 343
2GLYGLYASPASPchain BBA514 - 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

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Protein , 1 types, 2 molecules BA

#1: Protein eIF5B


Mass: 38370.016 Da / Num. of mol.: 2 / Fragment: G domain and domain II
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: G0S8G9*PLUS

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Non-polymers , 5 types, 651 molecules

#2: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 638 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.72 Å3/Da / Density % sol: 54.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: HEPES, PEG 4000, NaOAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.92 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 121606 / % possible obs: 98.5 % / Redundancy: 4.2 % / Biso Wilson estimate: 20.75 Å2 / Rmerge F obs: 0.999 / Rrim(I) all: 0.042 / Χ2: 0.98 / Net I/σ(I): 18.76 / Num. measured all: 510862
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
1.53-1.630.8220.4962.798673821284209420.56998.4
1.63-1.730.9170.3184.367016416651164990.36499.1
1.73-1.930.9770.1578.069633723845233990.1898.1
1.93-2.950.9980.04823.3418678144271436830.05598.7
2.95-3.460.9990.02445.4525564655063900.02897.6
3.46-3.970.9990.0257.9915673363536090.02399.3
3.97-4.480.9990.01964.359364216921600.02199.6
4.48-140.9990.01961.6619639485147620.02298.2
14-170.9990.0268.631475740.02398.7
17-500.9990.01956.8328896880.02391.7
506

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.54 Å49.35 Å
Translation4.54 Å49.35 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: 1.53→43.185 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1879 6079 5 %
Rwork0.1634 115479 -
obs0.1646 121558 98.57 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.15 Å2 / Biso mean: 27.8439 Å2 / Biso min: 11.21 Å2
Refinement stepCycle: final / Resolution: 1.53→43.185 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5323 0 116 653 6092
Biso mean--25.47 38.73 -
Num. residues----683
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.026002
X-RAY DIFFRACTIONf_angle_d1.8738161
X-RAY DIFFRACTIONf_chiral_restr0.107914
X-RAY DIFFRACTIONf_plane_restr0.011076
X-RAY DIFFRACTIONf_dihedral_angle_d14.9282327
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3149X-RAY DIFFRACTION6.262TORSIONAL
12B3149X-RAY DIFFRACTION6.262TORSIONAL
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 (%)
1.53-1.54740.30212000.24823777397796
1.5474-1.56560.26761990.2553777397699
1.5656-1.58470.28122050.24343903410899
1.5847-1.60470.26592020.233823402599
1.6047-1.62590.24862040.22783883408799
1.6259-1.64810.24432030.22163864406799
1.6481-1.67170.2342020.21883828403099
1.6717-1.69660.26462050.20563905411099
1.6966-1.72310.23222040.19983857406199
1.7231-1.75140.23022010.19213830403199
1.7514-1.78160.21182030.17833862406599
1.7816-1.8140.20392010.1723802400398
1.814-1.84890.1871960.15963750394696
1.8489-1.88660.20752020.16313842404499
1.8866-1.92770.20552050.1723882408799
1.9277-1.97250.22020.16793846404899
1.9725-2.02180.19572030.16153856405999
2.0218-2.07650.19382050.15913891409699
2.0765-2.13760.182050.15793893409899
2.1376-2.20660.18672010.15263824402598
2.2066-2.28540.17752020.15353834403698
2.2854-2.37690.16051960.14633721391796
2.3769-2.48510.17552050.15423893409899
2.4851-2.61610.20422040.16163879408399
2.6161-2.780.16832060.16763908411499
2.78-2.99460.21512030.16213869407299
2.9946-3.29580.18262040.15373861406598
3.2958-3.77250.16582010.1463815401697
3.7725-4.7520.14232060.138539264132100
4.752-43.20260.20142040.17753878408297
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)
11.3785-0.171-0.00761.38410.42691.4279-0.0022-0.03520.04380.04750.00690.00050.0190.0184-0.01130.09490.0012-0.00020.108-0.00990.1142-10.1657-12.6559-31.0203
23.00310.2169-0.89133.67970.14873.50410.00290.1581-0.2248-0.0578-0.14280.23140.1793-0.23870.12250.12010.0257-0.02370.1737-0.02430.1757-18.3639-13.7094-40.1639
31.9484-0.09530.96051.9261-0.63023.30680.03310.11020.7708-0.0797-0.0339-0.1989-0.65680.28590.03850.3401-0.03170.07680.14210.01210.3696-9.31998.3676-39.4373
46.01954.0814-0.18827.1987-0.44273.5212-0.11550.64420.6079-0.56420.1640.4143-0.4388-0.2643-0.07250.29340.0707-0.05120.26610.0520.21-20.3750.1265-48.599
54.8797-0.42950.89751.89721.20993.16280.00370.09690.4929-0.021-0.1250.3802-0.1682-0.59790.05470.19350.0289-0.01740.22080.00080.2332-22.6771-1.6986-36.7919
61.2799-0.7205-0.2213.4171-0.51211.7028-0.0133-0.0973-0.06870.04610.00450.01410.10180.0525-0.00120.1223-0.0211-0.02420.1595-0.03240.1067-10.7716-19.7709-24.0805
71.93950.4267-0.14133.1377-0.94393.0854-0.0019-0.0174-0.1445-0.0005-0.0224-0.21070.24390.09070.03390.160.0144-0.02750.1622-0.00980.1183-1.7046-27.0814-19.2704
82.168-0.0249-0.02023.5175-0.45914.2746-0.13070.1313-0.6989-0.30750.02080.41281.1816-0.9828-0.05120.5033-0.1286-0.01720.323-0.03420.2975-10.5478-39.9477-20.0421
91.6238-0.0766-0.03522.0406-0.07531.31350.0030.0193-0.0979-0.0072-0.0380.02580.06990.04640.02910.11920.00720.00430.11040.00460.08977.3558-41.2252-49.1357
103.32740.68810.92282.16030.25122.97720.04830.2642-0.0894-0.10910.0114-0.22270.15990.2946-0.04940.14570.03250.01010.14440.01810.154816.4469-31.1091-56.7858
111.0740.9894-0.03893.7194-0.20210.29870.0864-0.0994-0.06870.166-0.09950.18750.0564-0.0498-0.01330.1572-0.00470.00650.21590.00020.1763-4.0181-52.4219-47.6065
127.53372.10222.05923.67560.14281.00180.09081.1844-0.5396-0.54590.08930.06790.33870.2919-0.15650.3080.04690.00570.398-0.07550.332-7.8504-67.7181-53.0543
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 514 through 626 )B0
2X-RAY DIFFRACTION2chain 'B' and (resid 627 through 652 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 653 through 672 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 673 through 693 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 694 through 722 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 723 through 771 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 772 through 826 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 827 through 858 )B0
9X-RAY DIFFRACTION9chain 'A' and (resid 518 through 626 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 627 through 722 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 723 through 826 )A0
12X-RAY DIFFRACTION12chain 'A' and (resid 827 through 856 )A0

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