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- PDB-3e1y: Crystal structure of human eRF1/eRF3 complex -

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Basic information

Entry
Database: PDB / ID: 3e1y
TitleCrystal structure of human eRF1/eRF3 complex
Components
  • Eukaryotic peptide chain release factor GTP-binding subunit ERF3A
  • Eukaryotic peptide chain release factor subunit 1
KeywordsTRANSLATION / Translation termination / eRF1 / eRF3 / peptide release / PTC / Protein biosynthesis / GTP-binding / Nucleotide-binding
Function / homology
Function and homology information


translation termination factor activity / cytoplasmic translational termination / translation release factor complex / regulation of translational termination / translation release factor activity / translation release factor activity, codon specific / protein methylation / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay ...translation termination factor activity / cytoplasmic translational termination / translation release factor complex / regulation of translational termination / translation release factor activity / translation release factor activity, codon specific / protein methylation / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Protein hydroxylation / Eukaryotic Translation Termination / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translational termination / cytosolic ribosome / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / G1/S transition of mitotic cell cycle / Regulation of expression of SLITs and ROBOs / ribosome binding / translation / GTPase activity / GTP binding / RNA binding / cytosol / cytoplasm
Similarity search - Function
Translation, Eukaryotic Peptide Chain Release Factor Subunit 1; Chain A / eRF1 domain 1 / eRF1 domain 2 / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1 / eRF1 domain 1/Pelota-like / eRF1 domain 3 ...Translation, Eukaryotic Peptide Chain Release Factor Subunit 1; Chain A / eRF1 domain 1 / eRF1 domain 2 / Peptide chain release factor eRF1/aRF1 / eRF1, domain 1 / eRF1 domain 2 / eRF1 domain 2 / eRF1 domain 1 / eRF1 domain 1/Pelota-like / eRF1 domain 3 / eRF1, domain 2 superfamily / eRF1 domain 3 / eRF1_1 / Ribosomal protein L30/S12 / 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. / 60s Ribosomal Protein L30; Chain: A; / 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. / Elongation Factor Tu (Ef-tu); domain 3 / 50S ribosomal protein L30e-like / Nucleotidyltransferase; domain 5 / Translation protein, beta-barrel domain superfamily / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Eukaryotic peptide chain release factor GTP-binding subunit ERF3A / Eukaryotic peptide chain release factor subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsCheng, Z. / Lim, M. / Kong, C. / Song, H.
CitationJournal: Genes Dev. / Year: 2009
Title: Structural insights into eRF3 and stop codon recognition by eRF1
Authors: Cheng, Z. / Saito, K. / Pisarev, A.V. / Wada, M. / Pisareva, V.P. / Pestova, T.V. / Gajda, M. / Round, A. / Kong, C. / Lim, M. / Nakamura, Y. / Svergun, D.I. / Ito, K. / Song, H.
History
DepositionAug 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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 / 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 / _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 peptide chain release factor subunit 1
B: Eukaryotic peptide chain release factor subunit 1
C: Eukaryotic peptide chain release factor subunit 1
D: Eukaryotic peptide chain release factor subunit 1
E: Eukaryotic peptide chain release factor GTP-binding subunit ERF3A
F: Eukaryotic peptide chain release factor GTP-binding subunit ERF3A
G: Eukaryotic peptide chain release factor GTP-binding subunit ERF3A
H: Eukaryotic peptide chain release factor GTP-binding subunit ERF3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,13410
Polymers293,1208
Non-polymers1,0142
Water0
1
A: Eukaryotic peptide chain release factor subunit 1
F: Eukaryotic peptide chain release factor GTP-binding subunit ERF3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7873
Polymers73,2802
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Eukaryotic peptide chain release factor subunit 1
E: Eukaryotic peptide chain release factor GTP-binding subunit ERF3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7873
Polymers73,2802
Non-polymers5071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Eukaryotic peptide chain release factor subunit 1
G: Eukaryotic peptide chain release factor GTP-binding subunit ERF3A


Theoretical massNumber of molelcules
Total (without water)73,2802
Polymers73,2802
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Eukaryotic peptide chain release factor subunit 1
H: Eukaryotic peptide chain release factor GTP-binding subunit ERF3A


Theoretical massNumber of molelcules
Total (without water)73,2802
Polymers73,2802
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.966, 173.966, 119.824
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12E
22F
13G
23H
14C
24D

NCS domain segments:

Component-ID: 1 / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAILEILEAA8 - 41222 - 426
21ALAALAILEILEBB8 - 41222 - 426
12ILEILEPROPROEE440 - 6347 - 201
22ILEILEPROPROFF440 - 6347 - 201
13ILEILEPROPROGG440 - 6347 - 201
23ILEILEPROPROHH440 - 6347 - 201
14ALAALAILEILECC8 - 41222 - 426
24ALAALAILEILEDD8 - 41222 - 426

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
Eukaryotic peptide chain release factor subunit 1 / eRF1 / Eukaryotic release factor 1 / TB3-1 / Protein Cl1


Mass: 50700.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ETF1, ERF1, RF1, SUP45L1 / Plasmid: pRC-Niv-N / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) / References: UniProt: P62495
#2: Protein
Eukaryotic peptide chain release factor GTP-binding subunit ERF3A / Eukaryotic peptide chain release factor subunit 3a / eRF3a / G1 to S phase transition protein 1 homolog


Mass: 22579.457 Da / Num. of mol.: 4 / Fragment: UNP residues 301-499
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GSPT1, ERF3A / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 (DE3) / References: UniProt: P15170
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM

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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: 3.09 Å3/Da / Density % sol: 60.23 %
Crystal growTemperature: 288 K / Method: evaporation / pH: 5.6
Details: 50mM MES, pH5.6, 20-22% ethylene glycol, 2mM DTT, 2mM ATP, EVAPORATION, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9793 Å
DetectorDetector: CCD / Date: Mar 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.8→30 Å / Num. obs: 35459 / % possible obs: 99.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2.5 / Rmerge(I) obs: 0.068 / Net I/σ(I): 11.5

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Processing

Software
NameVersionClassification
REFMAC5.4.0077refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DT9, 1R5B

1dt9

1r5b


Resolution: 3.8→30 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.895 / SU B: 112.939 / SU ML: 0.713 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.838 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30358 1777 5 %RANDOM
Rwork0.25977 ---
obs0.26193 33542 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.893 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å2-0 Å2-0 Å2
2--0.99 Å20 Å2
3----1.98 Å2
Refinement stepCycle: LAST / Resolution: 3.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17048 0 62 0 17110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02217360
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.98423364
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.45752146
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.19224.632734
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.75153304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6551598
X-RAY DIFFRACTIONr_chiral_restr0.1030.22714
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112540
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6181.510744
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.195217360
X-RAY DIFFRACTIONr_scbond_it1.01936616
X-RAY DIFFRACTIONr_scangle_it1.6544.56004
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2905TIGHT POSITIONAL0.010.05
1A2905TIGHT THERMAL0.020.5
2E1513TIGHT POSITIONAL0.030.05
2E1513TIGHT THERMAL0.020.5
3G1513TIGHT POSITIONAL0.010.05
3G1513TIGHT THERMAL0.020.5
4C2449TIGHT POSITIONAL0.010.05
4C2449TIGHT THERMAL0.010.5
LS refinement shellResolution: 3.8→3.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 129 -
Rwork0.35 2423 -
obs--100 %
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)
19.50561.7554-0.50636.9813-1.12993.2957-0.1590.61350.337-0.2374-0.0436-0.35960.5101-0.35360.20260.34540.020.08070.37250.04980.4059-25.4417106.3734-0.5756
23.572-0.62421.9673.4035-1.64428.64730.0115-0.4909-0.1749-0.0030.00010.10080.2583-0.0371-0.01170.6941-0.02890.14650.5032-0.11610.6845-24.258279.864139.416
38.496-0.27983.51326.8086-0.87219.0153-0.14350.51-0.4783-0.2341-0.11161.30420.6181-0.51420.25510.9249-0.06010.04510.5759-0.34980.2126-30.499974.6641-3.164
46.70771.717-1.14089.5014-0.10753.2451-0.072-0.2639-0.30820.555-0.13460.2781-0.29670.47260.20660.38460.02240.0610.35680.09230.3739-19.3708112.430818.9921
53.3302-0.5377-1.55293.90441.80558.85490.00830.02830.0983-0.42310.0496-0.166-0.00010.2581-0.0580.4837-0.0344-0.11010.68720.15030.68457.1189111.2391-21.0437
65.5989-0.36940.38128.5112.25457.9115-0.15-0.21131.29430.5717-0.1312-0.459-0.5170.52760.28120.5814-0.0745-0.34350.97830.04260.213712.3199117.559521.502
73.2705-1.3557-1.29858.38135.39518.5115-0.0507-1.1239-0.23190.58830.1353-0.45270.56150.4389-0.08460.45420.0711-0.20330.86460.35980.403433.511889.80776.283
88.1663-1.22595.33473.2415-1.38128.4660.13970.6085-0.456-1.124-0.0511-0.20710.51830.5641-0.08860.86540.08990.35840.4813-0.2060.3974-2.836853.470512.0906
95.02240.29752.81732.08180.10798.43550.06220.0212-0.4571-0.84530.0228-0.06090.20870.0175-0.0850.98020.15840.0760.4274-0.19181.0585-7.773828.756420.2482
102.22290.43380.13424.95442.88518.6054-0.0167-0.85-0.08170.02580.1064-0.463-0.0060.2269-0.08970.42740.1864-0.18220.97590.07551.064758.209794.751-1.8651
114.8547-3.017-0.25167.8278-1.45838.17020.4547-1.0472-0.40070.36640.0137-0.62480.17730.1352-0.46840.3151-0.09-0.09781.2797-0.08120.9488-10.86518.306656.121
127.6992-2.4296-0.55714.3142-1.21447.95390.03710.3793-0.6571-0.91020.4739-0.37950.02530.22-0.5111.2796-0.0912-0.0820.2769-0.09731.015368.661897.8433-37.7616
134.56082.92961.58699.13790.50540.58860.1879-0.9424-0.60850.5835-0.39291.3750.47380.36240.2051.16890.08850.12921.76390.4561.2568-32.1084-2.938562.224
149.14233.2101-0.08423.6531.53160.9658-0.53830.82361.1445-0.89280.2391-0.60850.27360.49260.29921.6790.09490.38881.16280.13291.295189.9141119.0832-43.8386
153.9087-0.0422-2.17078.67051.89082.2582-0.10840.25890.57120.07740.0868-0.205-0.71130.06890.02160.7036-0.1193-0.13151.0496-0.05341.1236-37.016639.538356.8917
168.14130.28331.72593.5074-1.62461.9970.13890.0704-0.15410.2494-0.10520.50450.0952-0.663-0.03371.0492-0.1203-0.06140.6838-0.09191.084247.4378123.9896-38.5319
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 14122 - 155
2X-RAY DIFFRACTION2AA144 - 271158 - 285
3X-RAY DIFFRACTION3AA274 - 412288 - 426
4X-RAY DIFFRACTION4BB8 - 14122 - 155
5X-RAY DIFFRACTION5BB144 - 271158 - 285
6X-RAY DIFFRACTION6BB274 - 412288 - 426
7X-RAY DIFFRACTION7EE440 - 6347 - 201
8X-RAY DIFFRACTION8FF440 - 6347 - 201
9X-RAY DIFFRACTION9GG440 - 6347 - 201
10X-RAY DIFFRACTION10HH440 - 6347 - 201
11X-RAY DIFFRACTION11CC274 - 412288 - 426
12X-RAY DIFFRACTION12DD274 - 412288 - 426
13X-RAY DIFFRACTION13CC8 - 14122 - 155
14X-RAY DIFFRACTION14DD8 - 14122 - 155
15X-RAY DIFFRACTION15CC144 - 270158 - 284
16X-RAY DIFFRACTION16DD144 - 270158 - 284

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