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- PDB-5izm: The crystal structure of human eEFSec in complex with GDPNP -

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Basic information

Entry
Database: PDB / ID: 5izm
TitleThe crystal structure of human eEFSec in complex with GDPNP
ComponentsSelenocysteine-specific elongation factor
KeywordsTRANSLATION / elongation factor / selenocysteine / selenocysteine tRNA / GTPase / GDPNP / GTP
Function / homology
Function and homology information


selenocysteine incorporation / selenocysteine insertion sequence binding / Selenocysteine synthesis / translation elongation factor activity / ribonucleoprotein complex binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / tRNA binding / ribonucleoprotein complex / GTPase activity / GTP binding ...selenocysteine incorporation / selenocysteine insertion sequence binding / Selenocysteine synthesis / translation elongation factor activity / ribonucleoprotein complex binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / tRNA binding / ribonucleoprotein complex / GTPase activity / GTP binding / nucleus / cytoplasm
Similarity search - Function
: / : / eEFSec C-terminal RIFT domain / Selenocysteine-specific elongation factor, eukaryotes, 3rd domain / : / Translation elongation factor EFTu-like, domain 2 / 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. ...: / : / eEFSec C-terminal RIFT domain / Selenocysteine-specific elongation factor, eukaryotes, 3rd domain / : / Translation elongation factor EFTu-like, domain 2 / 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. / Translation protein, beta-barrel domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / Selenocysteine-specific elongation factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.4 Å
AuthorsDobosz-Bartoszek, M. / Otwinowski, Z. / Simonovic, M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097042 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM070773 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM22854 United States
CitationJournal: Nat Commun / Year: 2016
Title: Crystal structures of the human elongation factor eEFSec suggest a non-canonical mechanism for selenocysteine incorporation.
Authors: Dobosz-Bartoszek, M. / Pinkerton, M.H. / Otwinowski, Z. / Chakravarthy, S. / Soll, D. / Copeland, P.R. / Simonovic, M.
History
DepositionMar 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Selenocysteine-specific elongation factor
B: Selenocysteine-specific elongation factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,8776
Polymers136,7222
Non-polymers1,1544
Water00
1
A: Selenocysteine-specific elongation factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9383
Polymers68,3611
Non-polymers5772
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Selenocysteine-specific elongation factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9383
Polymers68,3611
Non-polymers5772
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.316, 112.398, 327.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Selenocysteine-specific elongation factor / Elongation factor sec / Eukaryotic elongation factor / selenocysteine-tRNA-specific


Mass: 68361.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EEFSEC, SELB / Production host: Escherichia coli (E. coli) / References: UniProt: P57772
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
Has protein modificationY

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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: 3.25 Å3/Da / Density % sol: 62.15 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES pH 7.6, 0.3 M ammonium sulfate, 16% (w/v) PEG 3,350, 0.02 M glycine, 4% dextran sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3.38→46.158 Å / Num. obs: 24257 / % possible obs: 98.5 % / Redundancy: 9.5 % / CC1/2: 0.51 / Net I/σ(I): 19.7
Reflection shellResolution: 3.38→3.46 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 3.4→46.158 Å / SU ML: 0.43 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.75 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2848 1114 5.16 %
Rwork0.2353 --
obs0.2379 19648 78.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.4→46.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6559 0 66 0 6625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086755
X-RAY DIFFRACTIONf_angle_d1.7559237
X-RAY DIFFRACTIONf_dihedral_angle_d15.2632218
X-RAY DIFFRACTIONf_chiral_restr0.0891156
X-RAY DIFFRACTIONf_plane_restr0.0071165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4004-3.49230.4445240.3472548X-RAY DIFFRACTION16
3.4923-3.59510.3347630.31521218X-RAY DIFFRACTION37
3.5951-3.71110.4106900.30421753X-RAY DIFFRACTION53
3.7111-3.84360.25951130.25912026X-RAY DIFFRACTION61
3.8436-3.99740.31621430.24312372X-RAY DIFFRACTION73
3.9974-4.17930.23141620.22532838X-RAY DIFFRACTION86
4.1793-4.39940.26351630.20543125X-RAY DIFFRACTION95
4.3994-4.67480.26421840.19543258X-RAY DIFFRACTION98
4.6748-5.03540.28421880.18973262X-RAY DIFFRACTION100
5.0354-5.54140.23911750.21593344X-RAY DIFFRACTION100
5.5414-6.34140.31611830.26283253X-RAY DIFFRACTION100
6.3414-7.98280.28521780.26913333X-RAY DIFFRACTION100
7.9828-46.16220.29531640.24343314X-RAY DIFFRACTION100

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