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- PDB-1si2: Crystal structure of the PAZ domain of human eIF2c1 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 1si2
TitleCrystal structure of the PAZ domain of human eIF2c1 in complex with a 9-mer siRNA-like duplex of deoxynucleotide overhang
Components
  • 5'-R(*CP*GP*UP*GP*AP*CP*U)-D(P*CP*T)-3'
  • Eukaryotic translation initiation factor 2C 1
KeywordsGENE REGULATION/RNA/DNA / PROTEIN-RNA COMPLEX / RNA INTERFERENCE / DOUBLE HELIX / OVERHANG / GENE REGULATION-RNA-DNA COMPLEX
Function / homology
Function and homology information


Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of PTEN mRNA translation / Small interfering RNA (siRNA) biogenesis / Transcriptional Regulation by MECP2 / RNA secondary structure unwinding / RISC-loading complex / RISC complex assembly ...Regulation of CDH11 mRNA translation by microRNAs / Regulation of NPAS4 mRNA translation / Post-transcriptional silencing by small RNAs / Competing endogenous RNAs (ceRNAs) regulate PTEN translation / Regulation of PTEN mRNA translation / Small interfering RNA (siRNA) biogenesis / Transcriptional Regulation by MECP2 / RNA secondary structure unwinding / RISC-loading complex / RISC complex assembly / miRNA processing / pre-miRNA processing / miRNA-mediated gene silencing by inhibition of translation / RISC complex / Regulation of RUNX1 Expression and Activity / nuclear-transcribed mRNA catabolic process / MicroRNA (miRNA) biogenesis / miRNA binding / RNA polymerase II complex binding / Regulation of MECP2 expression and activity / Transcriptional Regulation by VENTX / core promoter sequence-specific DNA binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / negative regulation of angiogenesis / P-body / TP53 Regulates Metabolic Genes / Transcriptional regulation by small RNAs / MAPK6/MAPK4 signaling / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Oncogene Induced Senescence / cytoplasmic ribonucleoprotein granule / Pre-NOTCH Transcription and Translation / double-stranded RNA binding / Ca2+ pathway / Oxidative Stress Induced Senescence / Estrogen-dependent gene expression / single-stranded RNA binding / positive regulation of transcription by RNA polymerase II / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
paz domain / Protein argonaute, Mid domain / Argonaute-like, PIWI domain / Mid domain of argonaute / paz domain / Argonaute linker 2 domain / Protein argonaute, N-terminal / N-terminal domain of argonaute / Argonaute linker 2 domain / DUF1785 ...paz domain / Protein argonaute, Mid domain / Argonaute-like, PIWI domain / Mid domain of argonaute / paz domain / Argonaute linker 2 domain / Protein argonaute, N-terminal / N-terminal domain of argonaute / Argonaute linker 2 domain / DUF1785 / Argonaute, linker 1 domain / Argonaute linker 1 domain / Piwi domain / Piwi domain profile. / Piwi domain / Piwi / PAZ domain superfamily / PAZ / PAZ domain / PAZ domain / PAZ domain profile. / Beta Complex / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Mainly Beta
Similarity search - Domain/homology
DNA/RNA hybrid / Protein argonaute-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsYe, K. / Ma, J.B. / Patel, D.
CitationJournal: Nature / Year: 2004
Title: Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain.
Authors: Ma, J.B. / Ye, K. / Patel, D.J.
History
DepositionFeb 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
B: 5'-R(*CP*GP*UP*GP*AP*CP*U)-D(P*CP*T)-3'
A: Eukaryotic translation initiation factor 2C 1


Theoretical massNumber of molelcules
Total (without water)19,9812
Polymers19,9812
Non-polymers00
Water28816
1
B: 5'-R(*CP*GP*UP*GP*AP*CP*U)-D(P*CP*T)-3'
A: Eukaryotic translation initiation factor 2C 1

B: 5'-R(*CP*GP*UP*GP*AP*CP*U)-D(P*CP*T)-3'
A: Eukaryotic translation initiation factor 2C 1


Theoretical massNumber of molelcules
Total (without water)39,9614
Polymers39,9614
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_675-x+1,-y+2,z1
Unit cell
Length a, b, c (Å)100.051, 100.051, 34.438
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
DetailsThe biological assemble consists of two PAZ domains bound to each end of a 9-mer siRNA-like duplex generated from the protein monomer and the 9-mer single stranded RNA in the asymmetric unit by the operation: -X+1,-Y+2,Z.

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Components

#1: DNA/RNA hybrid 5'-R(*CP*GP*UP*GP*AP*CP*U)-D(P*CP*T)-3'


Mass: 2790.730 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein Eukaryotic translation initiation factor 2C 1 / EIF2C 1 / EIF-2C 1 / PUTATIVE RNA-BINDING PROTEIN Q99 / ARGONAUTE 1


Mass: 17189.984 Da / Num. of mol.: 1 / Fragment: PAZ domain (residues 225-369)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EIF2C1 / Plasmid: pET19b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9UL18
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.49 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG 1000, potassium chloride, HEPES-NaOH, Dithiothreitol, pH 7.60, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 100011
2potassium chloride11
3HEPES-NaOH11
4Dithiothreitol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.981 / Wavelength: 0.981 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 13, 2003
RadiationMonochromator: DIAMOND (111) DOUBLE-CRYSTAL / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 6263 / Num. obs: 6225 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 62.3 Å2 / Rsym value: 0.087 / Net I/σ(I): 27.8
Reflection shellResolution: 2.6→2.69 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.696 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
CNS1.1refinement
HKL-2000data reduction
CNS1.1phasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→19.71 Å / Rfactor Rfree error: 0.011 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.261 581 9.9 %RANDOM
Rwork0.221 ---
obs0.2247 5873 93.8 %-
all-6263 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.026 Å2 / ksol: 0.326947 e/Å3
Displacement parametersBiso mean: 51.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å28.79 Å20 Å2
2--0.89 Å20 Å2
3----1.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms977 184 0 16 1177
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.13
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.571.5
X-RAY DIFFRACTIONc_mcangle_it2.722
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.92.5
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.049 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.342 48 8.7 %
Rwork0.313 504 -
obs--88.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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