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- PDB-5o8w: CRYSTAL STRUCTURE ANALYSIS OF THE YEAST ELONGATION FACTOR COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 5o8w
TitleCRYSTAL STRUCTURE ANALYSIS OF THE YEAST ELONGATION FACTOR COMPLEX EEF1A:EEF1BA
Components
  • Elongation factor 1-alpha
  • Elongation factor 1-beta
KeywordsTRANSLATION / PROTEIN-PROTEIN COMPLEX / COVALENT MODIFICATION
Function / homology
Function and homology information


Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / negative regulation of actin filament bundle assembly / melatonin binding / HSF1 activation / regulation of translational termination / tRNA export from nucleus / Protein methylation / fungal-type vacuole membrane / translational elongation ...Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / negative regulation of actin filament bundle assembly / melatonin binding / HSF1 activation / regulation of translational termination / tRNA export from nucleus / Protein methylation / fungal-type vacuole membrane / translational elongation / actin filament bundle assembly / translation elongation factor activity / cellular response to amino acid starvation / Neutrophil degranulation / guanyl-nucleotide exchange factor activity / negative regulation of protein phosphorylation / maintenance of translational fidelity / negative regulation of protein kinase activity / GDP binding / actin filament binding / ribosome binding / cytoskeleton / ribosome / translation / GTPase activity / GTP binding / protein kinase binding / mitochondrion / cytosol / cytoplasm
Similarity search - Function
: / Translation elongation factor EF1B, beta/delta chains, conserved site / Elongation factor 1 beta central acidic region, eukaryote / Eukaryotic elongation factor 1 beta central acidic region / Elongation factor 1 beta/beta'/delta chain signature 1. / Elongation factor 1 beta/beta'/delta chain signature 2. / Eukaryotic elongation factor 1 beta central acidic region / Translation elongation factor EF1B, beta/delta subunit, guanine nucleotide exchange domain / Translation elongation factor eEF-1beta-like superfamily / EF-1 guanine nucleotide exchange domain ...: / Translation elongation factor EF1B, beta/delta chains, conserved site / Elongation factor 1 beta central acidic region, eukaryote / Eukaryotic elongation factor 1 beta central acidic region / Elongation factor 1 beta/beta'/delta chain signature 1. / Elongation factor 1 beta/beta'/delta chain signature 2. / Eukaryotic elongation factor 1 beta central acidic region / Translation elongation factor EF1B, beta/delta subunit, guanine nucleotide exchange domain / Translation elongation factor eEF-1beta-like superfamily / EF-1 guanine nucleotide exchange domain / EF-1 guanine nucleotide exchange domain / Translation elongation factor EF1A, eukaryotic/archaeal / Translation elongation factor EFTu/EF1A, C-terminal / Elongation factor Tu C-terminal domain / Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal / Translation factors / Tr-type G domain, conserved site / Translational (tr)-type guanine nucleotide-binding (G) domain signature. / Translation elongation factor EFTu-like, domain 2 / Glutathione S-transferase, C-terminal domain superfamily / Elongation factor Tu domain 2 / Translational (tr)-type GTP-binding domain / Elongation factor Tu GTP binding domain / Translational (tr)-type guanine nucleotide-binding (G) domain profile. / Elongation Factor Tu (Ef-tu); domain 3 / Translation elongation factor EF1B/ribosomal protein S6 / 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
GLUTAMINE / TRIETHYLENE GLYCOL / Elongation factor 1-alpha / Elongation factor 1-beta
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.67 Å
AuthorsWirth, C. / Andersen, G.R. / Hunte, C.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationCRC746 Germany
German Federal and State GovernmentsEXC 294 BIOSS Germany
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Protein glutaminylation is a yeast-specific posttranslational modification of elongation factor 1A.
Authors: Jank, T. / Belyi, Y. / Wirth, C. / Rospert, S. / Hu, Z. / Dengjel, J. / Tzivelekidis, T. / Andersen, G.R. / Hunte, C. / Schlosser, A. / Aktories, K.
History
DepositionJun 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3May 8, 2019Group: Advisory / Data collection / Derived calculations
Category: diffrn_source / pdbx_seq_map_depositor_info ...diffrn_source / pdbx_seq_map_depositor_info / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4Jul 10, 2019Group: Data collection / Category: diffrn_source / pdbx_seq_map_depositor_info
Item: _diffrn_source.pdbx_synchrotron_site / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.5Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Elongation factor 1-alpha
B: Elongation factor 1-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0576
Polymers61,4602
Non-polymers5974
Water13,061725
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint1 kcal/mol
Surface area24090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.850, 91.810, 92.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Elongation factor 1-alpha / EF-1-alpha / Eukaryotic elongation factor 1A / eEF1A / Translation elongation factor 1A


Mass: 50846.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P02994
#2: Protein Elongation factor 1-beta / EF-1-beta / Eukaryotic elongation factor 1Balpha / eEF1Balpha / Translation elongation factor 1B alpha


Mass: 10613.515 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: EEF1BA, CATALYTICAL C-TERMINAL DOMAIN
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: EFB1, TEF5, YAL003W / Production host: Escherichia coli (E. coli) / References: UniProt: P32471
#3: Chemical ChemComp-GLN / GLUTAMINE / Glutamine


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H10N2O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 725 / 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: 1.87 Å3/Da / Density % sol: 34.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: mmE 2000, Tris, Hepes, KCl, DTT, NaAzid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9184 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.67→20 Å / Num. obs: 63533 / % possible obs: 99.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 36.1
Reflection shellResolution: 1.67→1.73 Å / Redundancy: 3 % / Rmerge(I) obs: 0.155 / % possible all: 93.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.67→19.724 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.88 / Phase error: 18.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1844 3217 5.06 %
Rwork0.1558 --
obs0.1573 63528 99.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→19.724 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4122 0 80 725 4927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094381
X-RAY DIFFRACTIONf_angle_d0.975930
X-RAY DIFFRACTIONf_dihedral_angle_d12.6682687
X-RAY DIFFRACTIONf_chiral_restr0.064665
X-RAY DIFFRACTIONf_plane_restr0.006766
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.69490.26441130.20512206X-RAY DIFFRACTION85
1.6949-1.72140.231250.17172627X-RAY DIFFRACTION100
1.7214-1.74960.23021390.16712580X-RAY DIFFRACTION100
1.7496-1.77980.22881100.16052652X-RAY DIFFRACTION100
1.7798-1.81210.18381370.16262599X-RAY DIFFRACTION100
1.8121-1.84690.21571290.17342623X-RAY DIFFRACTION100
1.8469-1.88460.22411300.16592639X-RAY DIFFRACTION100
1.8846-1.92560.22161330.16192615X-RAY DIFFRACTION100
1.9256-1.97030.20241380.15972594X-RAY DIFFRACTION100
1.9703-2.01950.20531450.15842629X-RAY DIFFRACTION100
2.0195-2.07410.17821420.15422628X-RAY DIFFRACTION100
2.0741-2.1350.19181520.15792624X-RAY DIFFRACTION100
2.135-2.20390.18041610.15142605X-RAY DIFFRACTION100
2.2039-2.28250.17741410.15522625X-RAY DIFFRACTION100
2.2825-2.37380.18031520.15532600X-RAY DIFFRACTION100
2.3738-2.48160.20151260.16622655X-RAY DIFFRACTION100
2.4816-2.61220.18381490.1592629X-RAY DIFFRACTION100
2.6122-2.77540.19711250.16322677X-RAY DIFFRACTION100
2.7754-2.9890.17741590.16822632X-RAY DIFFRACTION100
2.989-3.28860.19151760.15462640X-RAY DIFFRACTION100
3.2886-3.76160.1731520.14782682X-RAY DIFFRACTION100
3.7616-4.72840.16391420.13262718X-RAY DIFFRACTION100
4.7284-19.7250.14161410.15052832X-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)
11.82460.0413-0.4330.6784-0.01080.8589-0.030.0334-0.136-0.0373-0.0057-0.0880.07140.08140.02110.07990.0076-0.00250.08040.01440.099838.880730.649531.7926
21.1947-1.0644-0.08613.0985-1.41351.46330.11540.0728-0.1254-0.3218-0.02130.2250.1041-0.1575-0.09060.07720.0064-0.00790.1084-0.00280.108222.669135.445632.2816
32.236-0.67521.58411.5181-0.63883.148-0.0682-0.06620.13810.05390.0421-0.017-0.25740.05680.02740.08030.00410.03440.1059-0.00860.07724.268240.548644.6255
41.2567-0.3153-0.04481.57580.01351.2847-0.0153-0.17740.02350.06040.0336-0.0541-0.02110.0488-0.0180.06580.00220.00020.09860.00580.059326.274732.09851.4755
50.0293-0.25470.37240.2488-0.50030.63450.06680.0139-0.1682-0.0925-0.00330.10710.2338-0.1649-0.08510.1172-0.0237-0.00580.1530.00110.153620.030720.809838.7059
61.08440.0836-0.84761.25720.55041.6766-0.26930.3532-0.3699-0.06960.0359-0.03540.3739-0.23590.15090.2083-0.07850.03780.2094-0.0950.24589.530124.911.845
71.424-0.1745-0.620.94470.2962.22260.05870.10430.0403-0.046-0.0178-0.0666-0.0609-0.1587-0.04250.06320.0049-0.00240.0980.01150.10252.90843.414128.0825
88.69065.44192.34147.72525.65884.71270.2682-1.54731.34941.6025-0.4774-0.7983-0.73950.85020.00520.5733-0.0737-0.21430.3882-0.0890.435938.489952.511332.2208
93.42082.03075.2992.3334.39769.83290.1253-0.0506-0.05460.0236-0.08180.03440.1386-0.1682-0.03010.0854-0.01210.0110.09780.0070.093428.497538.341518.0266
104.23574.51590.13016.3499-2.48044.4958-0.17740.9902-0.6532-0.5497-0.06720.0990.4406-0.72970.21370.1727-0.0079-0.00770.2768-0.09060.165823.729432.4698-0.6985
112.66791.06661.9130.90922.16577.17560.05490.10110.0493-0.0573-0.03930.0025-0.30260.1747-0.0220.10230.00250.01740.09540.0310.103133.092343.55549.6492
126.4145.45865.2384.66514.63996.19530.11050.0608-0.38050.3255-0.18350.04710.4098-0.14020.02220.14830.01660.00670.1041-0.04450.202428.488627.21328.1083
132.96461.49081.40734.92294.15125.9890.07780.1056-0.03810.17610.0823-0.18830.11310.0339-0.13960.0678-0.00370.01530.0630.04680.05929.821440.562217.0944
143.35040.00880.98165.55932.47625.8038-0.0330.0730.0491-0.0622-0.13120.2695-0.2488-0.29820.14260.07220.0352-0.00070.1030.01440.106622.482644.048.3647
155.5727-0.05166.66670.21270.38849.6158-0.2348-0.1655-0.0212-0.03150.10780.0068-0.4368-0.33410.14110.10470.0062-0.00210.10110.0190.095126.227137.914421.9179
162.2462-0.0333-0.45926.47710.00330.09520.1774-0.2431-0.31620.33060.0384-0.2830.0052-0.6938-0.2210.52070.0218-0.11880.6331-0.1190.5286-7.833732.3051-1.9294
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 84 )
2X-RAY DIFFRACTION2chain 'A' and (resid 85 through 119 )
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 161 )
4X-RAY DIFFRACTION4chain 'A' and (resid 162 through 219 )
5X-RAY DIFFRACTION5chain 'A' and (resid 220 through 244 )
6X-RAY DIFFRACTION6chain 'A' and (resid 245 through 344 )
7X-RAY DIFFRACTION7chain 'A' and (resid 345 through 442 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1114 through 1119 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1120 through 1128 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1129 through 1135 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1136 through 1155 )
12X-RAY DIFFRACTION12chain 'B' and (resid 1156 through 1164 )
13X-RAY DIFFRACTION13chain 'B' and (resid 1165 through 1180 )
14X-RAY DIFFRACTION14chain 'B' and (resid 1181 through 1196 )
15X-RAY DIFFRACTION15chain 'B' and (resid 1197 through 1206 )
16X-RAY DIFFRACTION16chain 'A' and (resid 447 through 454)

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