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- PDB-4f26: Crystal structure of the second RRM domain of human PABPC1 a pH 9.0 -

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Basic information

Entry
Database: PDB / ID: 4f26
TitleCrystal structure of the second RRM domain of human PABPC1 a pH 9.0
ComponentsPolyadenylate-binding protein 1
KeywordsTRANSLATION / RRM fold / translation initiation / RNA-binding / eIF4G-binding / sytoplasm
Function / homology
Function and homology information


mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / translation activator activity / CRD-mediated mRNA stabilization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / poly(A) binding / positive regulation of cytoplasmic translation ...mCRD-mediated mRNA stability complex / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / translation activator activity / CRD-mediated mRNA stabilization / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / poly(A) binding / positive regulation of cytoplasmic translation / mRNA stabilization / regulatory ncRNA-mediated gene silencing / poly(U) RNA binding / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Translation initiation complex formation / cell leading edge / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of viral genome replication / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / catalytic step 2 spliceosome / mRNA 3'-UTR binding / AUF1 (hnRNP D0) binds and destabilizes mRNA / mRNA splicing, via spliceosome / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / lamellipodium / ribonucleoprotein complex / focal adhesion / mRNA binding / RNA binding / extracellular exosome / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
: / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain / Poly-adenylate binding protein, unique domain / RNA recognition motif domain, eukaryote / RNA recognition motif ...: / PABP, RNA recognition motif 2 / Polyadenylate binding protein, human types 1, 2, 3, 4 / Poly(A)-binding protein C-terminal (PABC) domain profile. / C-terminal domain of Poly(A)-binding protein. Present also in Drosophila hyperplastics discs protein. / Polyadenylate-binding protein/Hyperplastic disc protein / PABC (PABP) domain / Poly-adenylate binding protein, unique domain / RNA recognition motif domain, eukaryote / RNA recognition motif / 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 / Nucleotide-binding alpha-beta plait domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyadenylate-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKozlov, G. / Safaee, N. / Gehring, K.
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 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Polyadenylate-binding protein 1


Theoretical massNumber of molelcules
Total (without water)12,6801
Polymers12,6801
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.955, 69.487, 41.787
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 Polyadenylate-binding protein 1 / PABP-1 / Poly(A)-binding protein 1


Mass: 12680.360 Da / Num. of mol.: 1 / Fragment: RRM2 domain (un residues 99-119)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PABPC1, PAB1, PABP1, PABPC2 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P11940
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 1.52 Å3/Da / Density % sol: 18.85 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 25% PEG 1500 and 0.1 M MMT buffer , pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9772 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 4, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9772 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 5177 / Num. obs: 5162 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 16.9
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.279 / Mean I/σ(I) obs: 5.3 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1cvj

1cvj


Resolution: 2→18.8 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.902 / SU B: 11.156 / SU ML: 0.148 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.21 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28606 243 4.5 %RANDOM
Rwork0.21561 ---
all0.219 5177 --
obs0.21866 5162 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.221 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2---0.06 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→18.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms606 0 0 9 615
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.022615
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.942820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.764576
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93724.83931
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.4815115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.798153
X-RAY DIFFRACTIONr_chiral_restr0.130.287
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02462
X-RAY DIFFRACTIONr_nbd_refined0.2030.2236
X-RAY DIFFRACTIONr_nbtor_refined0.3150.2419
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.221
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.223
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2220.23
X-RAY DIFFRACTIONr_mcbond_it0.9871.5385
X-RAY DIFFRACTIONr_mcangle_it1.6952599
X-RAY DIFFRACTIONr_scbond_it2.9853252
X-RAY DIFFRACTIONr_scangle_it4.5674.5221
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 19 -
Rwork0.254 362 -
obs--98.2 %
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)
13.1181-1.01920.9221.1462-0.50592.42320.04140.2826-0.058-0.0725-0.1228-0.15360.0004-0.09120.08140.0431-0.01020.01270.04250.00990.0595-14.557113.2103-9.2692
25.5594-1.0851-0.14392.6799-0.55531.7728-0.08790.02410.2650.01320.036-0.1563-0.0206-0.15170.05190.0979-0.0041-0.03420.0509-0.01240.0896-14.239715.6374-5.0857
32.82440.75721.221212.11961.34054.5933-0.0118-0.06590.0002-0.1546-0.11330.31280.1898-0.00720.1250.07080.01460.00130.05740.02840.0441-16.019710.927-1.0898
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A99 - 129
2X-RAY DIFFRACTION2A130 - 160
3X-RAY DIFFRACTION3A161 - 175

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