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- PDB-4f02: Crystal structure of the PABP-binding site of eIF4G in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4f02
TitleCrystal structure of the PABP-binding site of eIF4G in complex with RRM1-2 of PABP and poly(A)
Components
  • Eukaryotic translation initiation factor 4 gamma 1
  • Polyadenylate-binding protein 1
  • RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
KeywordsTranslation/RNA / Translation initiation / mRNA / eukaryotic initiation factors (eIFs) / Paip1 and Paip2 / Translation-RNA complex
Function / homology
Function and homology information


positive regulation of eukaryotic translation initiation factor 4F complex assembly / positive regulation of mRNA cap binding / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / positive regulation of translation in response to endoplasmic reticulum stress / cap-dependent translational initiation / macromolecule biosynthetic process / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay ...positive regulation of eukaryotic translation initiation factor 4F complex assembly / positive regulation of mRNA cap binding / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / mCRD-mediated mRNA stability complex / positive regulation of translation in response to endoplasmic reticulum stress / cap-dependent translational initiation / macromolecule biosynthetic process / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / translation activator activity / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / CRD-mediated mRNA stabilization / eukaryotic initiation factor 4E binding / regulation of cellular response to stress / eukaryotic translation initiation factor 4F complex / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / translation factor activity, RNA binding / Deadenylation of mRNA / miRNA-mediated gene silencing by inhibition of translation / positive regulation of cytoplasmic translation / mRNA stabilization / poly(A) binding / M-decay: degradation of maternal mRNAs by maternally stored factors / regulatory ncRNA-mediated gene silencing / positive regulation of protein localization to cell periphery / poly(U) RNA binding / regulation of translational initiation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Ribosomal scanning and start codon recognition / Translation initiation complex formation / : / negative regulation of peptidyl-threonine phosphorylation / mTORC1-mediated signalling / cell leading edge / cellular response to nutrient levels / regulation of presynapse assembly / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of G1/S transition of mitotic cell cycle / behavioral fear response / positive regulation of viral genome replication / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation initiation factor binding / energy homeostasis / translational initiation / catalytic step 2 spliceosome / positive regulation of neuron differentiation / positive regulation of protein metabolic process / translation initiation factor activity / negative regulation of autophagy / mRNA 3'-UTR binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / lung development / cytoplasmic ribonucleoprotein granule / ISG15 antiviral mechanism / neuron differentiation / mRNA splicing, via spliceosome / Regulation of expression of SLITs and ROBOs / cytoplasmic stress granule / lamellipodium / positive regulation of peptidyl-serine phosphorylation / positive regulation of cell growth / postsynapse / response to ethanol / molecular adaptor activity / ribosome / ribonucleoprotein complex / translation / focal adhesion / mRNA binding / RNA binding / extracellular exosome / ATP binding / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Initiation factor 4G / : / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Polyadenylate-binding protein/Hyperplastic disc protein / Poly-adenylate binding protein, unique domain / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / PABC (PABP) domain / Initiation factor eIF-4 gamma, MA3 ...Initiation factor 4G / : / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Polyadenylate-binding protein/Hyperplastic disc protein / Poly-adenylate binding protein, unique domain / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / PABC (PABP) domain / Initiation factor eIF-4 gamma, MA3 / MA3 domain / MI domain profile. / Domain in DAP-5, eIF4G, MA-3 and other proteins. / eIF4-gamma/eIF5/eIF2-epsilon / Domain at the C-termini of GCD6, eIF-2B epsilon, eIF-4 gamma and eIF-5 / W2 domain / W2 domain profile. / MIF4G domain / RNA recognition motif domain, eukaryote / RNA recognition motif / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / RRM (RNA recognition motif) domain / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Polyadenylate-binding protein 1 / Eukaryotic translation initiation factor 4 gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSafaee, N. / Kozlov, G. / Gehring, K.B.
CitationJournal: Mol.Cell / Year: 2012
Title: Interdomain Allostery Promotes Assembly of the Poly(A) mRNA Complex with PABP and eIF4G.
Authors: Safaee, N. / Kozlov, G. / Noronha, A.M. / Xie, J. / Wilds, C.J. / Gehring, K.
History
DepositionMay 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyadenylate-binding protein 1
B: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
C: Eukaryotic translation initiation factor 4 gamma 1
D: Polyadenylate-binding protein 1
E: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
F: Eukaryotic translation initiation factor 4 gamma 1


Theoretical massNumber of molelcules
Total (without water)60,8726
Polymers60,8726
Non-polymers00
Water3,531196
1
A: Polyadenylate-binding protein 1
B: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
C: Eukaryotic translation initiation factor 4 gamma 1


Theoretical massNumber of molelcules
Total (without water)30,4363
Polymers30,4363
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-10 kcal/mol
Surface area11260 Å2
2
D: Polyadenylate-binding protein 1
E: RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')
F: Eukaryotic translation initiation factor 4 gamma 1


Theoretical massNumber of molelcules
Total (without water)30,4363
Polymers30,4363
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-8 kcal/mol
Surface area11270 Å2
Unit cell
Length a, b, c (Å)130.191, 130.191, 86.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Polyadenylate-binding protein 1 / PABP-1 / Poly(A)-binding protein 1


Mass: 23833.131 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PABPC1, PAB1, PABP1, PABPC2 / Production host: Escherichia coli (E. coli) / References: UniProt: P11940
#2: RNA chain RNA (5'-R(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')


Mass: 3576.306 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Oligo-rA11
#3: Protein/peptide Eukaryotic translation initiation factor 4 gamma 1 / / eIF-4-gamma 1 / eIF-4G 1 / eIF-4G1 / p220


Mass: 3026.406 Da / Num. of mol.: 2 / Fragment: unp residues 178-203 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q04637
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 3.02 Å3/Da / Density % sol: 59.32 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.03 M Tris, 1.3 M (NH4)2SO4, 5% glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 29, 2010
Details: DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror.
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2→36.11 Å / Num. all: 47356 / Num. obs: 47356 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2→2.03 Å / % possible all: 97.6

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→36.11 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.931 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.139 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23016 2532 5.1 %RANDOM
Rwork0.20413 ---
all0.22 50142 --
obs0.20541 47356 97.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.392 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.14 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 2→36.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3058 393 0 196 3647
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223550
X-RAY DIFFRACTIONr_angle_refined_deg2.1232.1034857
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3415389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64323.245151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19615573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9031532
X-RAY DIFFRACTIONr_chiral_restr0.1420.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212555
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_it0.861.51932
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51823100
X-RAY DIFFRACTIONr_scbond_it2.71931618
X-RAY DIFFRACTIONr_scangle_it4.2044.51755
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.997→2.049 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.22 -
Rwork0.229 3272
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)
11.8324-0.9517-0.90821.89330.3082.7907-0.03950.0213-0.07140.0177-0.00930.1142-0.0810.08260.04880.0433-0.01170.01790.0255-0.00790.0084-12.37845.8913.805
21.3551-0.5880.13282.7538-0.96921.3773-0.1236-0.1626-0.34730.1405-0.00990.12070.1141-0.01640.13350.1056-0.00260.07820.12130.04850.1107-4.60332.21127.061
35.24480.1057-0.75062.6927-3.605410.0905-0.2263-0.0273-0.9187-0.3867-0.12640.10651.28430.21940.35260.24660.04180.13070.10970.05970.242-0.33823.3120.668
43.64420.4104-0.9077-0.47220.97131.74720.0151-0.10740.0917-0.0526-0.03590.0189-0.09310.08160.02070.07780.0130.03980.07520.00710.0214-0.9842.50614.399
55.2771.75033.836814.4728-3.9485.96570.0160.11260.57680.818-0.24610.8632-0.48280.02940.23010.3155-0.01030.20910.27220.14950.3487-13.82721.94138.941
616.9562-4.27715.38051.1127-6.554237.90870.7577-0.22620.1620.3558-0.2251-0.16280.7781-0.1232-0.53270.8405-0.13670.07450.41140.35520.4529-7.98215.57945.327
710.6456-12.581418.33539.94831.558734.3657-0.8710.04380.72690.29520.6983-1.7687-1.77970.74140.17270.6863-0.14130.41250.52780.04770.39-9.30726.77545.035
80.99060.5937-0.20271.5693-0.13572.2794-0.04240.0524-0.0515-0.0842-0.0079-0.0595-0.0806-0.03240.05040.06440.00870.02980.04860.00580.010114.96849.168-2.656
92.2051-0.42310.18282.94391.13841.81560.14120.1802-0.3089-0.1245-0.12120.02760.1830.0875-0.020.16220.04060.02090.1502-0.04550.0529.68431.494-14.299
103.50780.09010.0196-0.1090.24043.2140.0040.119-0.34940.0545-0.04860.00740.4877-0.07640.04460.1447-0.01840.04150.1238-0.03070.04735.5634.94-4.049
1124.28838.1285-0.272633.35123.68216.49670.3570.457-0.3954-0.4826-0.0535-1.23940.21060.2786-0.30340.36460.18090.07820.2988-0.09420.131219.57122.996-26.262
12-0.8738-2.7666-8.91437.6526-0.551431.0056-0.0861.2806-0.6668-2.84330.9404-1.01570.2595-0.5348-0.85440.57960.08970.15521.3016-0.65910.545116.13418.675-31.984
1315.9874-39.4189-9.747588.8164-20.812317.5731-0.64550.09121.0174-1.68881.41360.80780.8464-0.4976-0.76810.85080.08860.15251.03990.05550.159614.7829.427-32.867
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 55
2X-RAY DIFFRACTION2A56 - 184
3X-RAY DIFFRACTION3B1 - 4
4X-RAY DIFFRACTION4B5 - 8
5X-RAY DIFFRACTION5C179 - 183
6X-RAY DIFFRACTION6C184 - 191
7X-RAY DIFFRACTION7C192 - 198
8X-RAY DIFFRACTION8D11 - 65
9X-RAY DIFFRACTION9D66 - 183
10X-RAY DIFFRACTION10E2 - 8
11X-RAY DIFFRACTION11F179 - 184
12X-RAY DIFFRACTION12F185 - 193
13X-RAY DIFFRACTION13F194 - 198

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