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- PDB-4krf: Structure of Human Argonaute-1 let-7 complex -

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Basic information

Entry
Database: PDB / ID: 4krf
TitleStructure of Human Argonaute-1 let-7 complex
Components
  • Protein argonaute-1
  • RNA (5'-R(P*UP*GP*AP*GP*GP*UP*AP*GP*UP*AP*GP*GP*UP*UP*GP*UP*AP*UP*AP*GP*UP*U)-3')
KeywordsTRANSCRIPTION/RNA / eukaryotic Argonaute / GENE REGULATION / RNAi / Slicer / TRANSCRIPTION-RNA 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-mediated gene silencing by inhibition of translation / miRNA processing / pre-miRNA processing / RISC complex / Regulation of RUNX1 Expression and Activity / miRNA binding / MicroRNA (miRNA) biogenesis / nuclear-transcribed mRNA catabolic process / 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 / TP53 Regulates Metabolic Genes / Transcriptional regulation by small RNAs / MAPK6/MAPK4 signaling / P-body / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Oncogene Induced Senescence / Pre-NOTCH Transcription and Translation / cytoplasmic ribonucleoprotein granule / 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. / Response regulator / Beta Complex / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
RNA / RNA (> 10) / Protein argonaute-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.101 Å
AuthorsFaehnle, C.R. / Elkayam, E. / Joshua-Tor, L.
CitationJournal: Cell Rep / Year: 2013
Title: The making of a slicer: activation of human argonaute-1.
Authors: Faehnle, C.R. / Elkayam, E. / Haase, A.D. / Hannon, G.J. / Joshua-Tor, L.
History
DepositionMay 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 1.2Feb 28, 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
A: Protein argonaute-1
R: RNA (5'-R(P*UP*GP*AP*GP*GP*UP*AP*GP*UP*AP*GP*GP*UP*UP*GP*UP*AP*UP*AP*GP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)104,5392
Polymers104,5392
Non-polymers00
Water6,612367
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-34 kcal/mol
Surface area38280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.390, 97.730, 72.700
Angle α, β, γ (deg.)90.000, 110.890, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Protein argonaute-1 / Argonaute1 / hAgo1 / Eukaryotic translation initiation factor 2C 1 / eIF-2C 1 / eIF2C 1 / Putative ...Argonaute1 / hAgo1 / Eukaryotic translation initiation factor 2C 1 / eIF-2C 1 / eIF2C 1 / Putative RNA-binding protein Q99


Mass: 97420.367 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGO1, EIF2C1 / Plasmid: Multi-Bac, pFL / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: Q9UL18
#2: RNA chain RNA (5'-R(P*UP*GP*AP*GP*GP*UP*AP*GP*UP*AP*GP*GP*UP*UP*GP*UP*AP*UP*AP*GP*UP*U)-3')


Mass: 7118.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: let-7 miRNA
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 13% PEG 3350, 9% iso-propanol, 0.1M Tris pH 9.0, vapor diffusion, hanging drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.075 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 50618 / Num. obs: 50618 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 40.298 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 16.85
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.160.322.434394255864.1
2.16-2.210.2323.215395297877.4
2.21-2.280.1874.036622330387.9
2.28-2.350.1685.128295350296.2
2.35-2.430.1426.629752348199.1
2.43-2.510.137.8610587342599.7
2.51-2.610.11210.1111487327299.7
2.61-2.710.09711.4210893318399.6
2.71-2.830.07714.2910690300099.8
2.83-2.970.06516.369952291199.5
2.97-3.130.05319.959695275899.7
3.13-3.320.04323.58909260599.4
3.32-3.550.03728.638631245799.2
3.55-3.840.03232.177906230299.5
3.84-4.20.0335.167164209499.5
4.2-4.70.02838.476807192899.7
4.7-5.430.02837.75789169599.3
5.43-6.640.0336.244938143299.7
6.64-9.40.02739.653790110999.1
9.40.02244.3205262597.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
CBASSdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.101→40.568 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8372 / SU ML: 0.25 / σ(F): 1.99 / Phase error: 23.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2173 2003 3.96 %Random
Rwork0.1755 ---
obs0.1772 50614 94.4 %-
all-50614 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 134.54 Å2 / Biso mean: 38.0837 Å2 / Biso min: 12.73 Å2
Refinement stepCycle: LAST / Resolution: 2.101→40.568 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6580 259 0 367 7206
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037025
X-RAY DIFFRACTIONf_angle_d0.7239574
X-RAY DIFFRACTIONf_chiral_restr0.0481065
X-RAY DIFFRACTIONf_plane_restr0.0031189
X-RAY DIFFRACTIONf_dihedral_angle_d11.4762700
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.101-2.15370.3294920.23952364245664
2.1537-2.21190.2711180.21112816293477
2.2119-2.2770.29151340.20383215334988
2.277-2.35050.25051450.19313525367096
2.3505-2.43450.28751540.1923641379599
2.4345-2.53190.24041460.188236353781100
2.5319-2.64710.25591520.184236553807100
2.6471-2.78670.22341520.1936703822100
2.7867-2.96120.23921460.188936623808100
2.9612-3.18980.21871550.18436773832100
3.1898-3.51060.23061510.177836533804100
3.5106-4.01820.18091500.159536623812100
4.0182-5.0610.16491490.148137053854100
5.061-40.5680.211590.172237313890100
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)
12.7641-0.1434-0.61571.31861.5133.35490.1161-0.38130.4508-0.1281-0.03850.0509-0.24740.4099-0.08470.15860.00480.05110.320.00350.263120.147410.1732-36.7117
22.3863-0.20881.04632.9964-0.78154.2759-0.00720.00020.2513-0.3054-0.0557-0.0615-0.54040.05220.07740.3274-0.00040.06380.2193-0.03110.174822.766427.2187-64.3762
31.8241-0.57581.88010.4705-1.05712.90760.1109-0.2349-0.3888-0.11510.26980.23150.2015-0.6052-0.2760.3196-0.018-0.03430.44010.02870.291-4.321512.0239-70.7109
43.3984-1.90673.36432.7344-3.77127.1484-0.15550.02780.07680.10150.38060.1875-0.2633-0.611-0.11790.276-0.0587-0.04620.48820.0250.2989-12.391915.9353-78.0832
51.62971.8426-1.88722.0394-2.04012.2147-0.31670.0602-0.2639-0.54530.0271-0.14590.46320.24240.31040.33910.08930.06660.2554-0.00090.264721.31623.0796-55.738
62.0725-0.6510.90661.0331-0.7312.26050.0833-0.3139-0.6174-0.02980.17140.47310.2496-0.5281-0.10230.2264-0.0532-0.01060.31180.07510.4193-19.3623-3.4172-31.8924
72.56840.1261-0.08982.11330.67912.54910.1939-0.0410.2439-0.12490.0625-0.0348-0.41850.0743-0.11540.2682-0.01580.1160.1455-0.03560.255-1.815720.3738-30.3638
82.75360.0961-1.56660.7983-0.40581.67490.047-0.22470.0433-0.1057-0.0738-0.01460.03460.2505-0.01480.17360.01650.01770.1720.01130.154410.23325.756-36.5532
95.14940.06310.09456.0812-1.79783.41080.0992-0.0750.3588-0.0658-0.17060.341-0.4981-0.57820.01010.22690.07530.00680.2435-0.05420.2373-16.802816.0164-38.3124
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 19:43)A19 - 43
2X-RAY DIFFRACTION2(chain A and resid 44:169)A44 - 169
3X-RAY DIFFRACTION3(chain A and resid 170:301)A170 - 301
4X-RAY DIFFRACTION4(chain A and resid 302:362)A302 - 362
5X-RAY DIFFRACTION5(chain A and resid 363:411)A363 - 411
6X-RAY DIFFRACTION6(chain A and resid 412:578)A412 - 578
7X-RAY DIFFRACTION7(chain A and resid 579:697)A579 - 697
8X-RAY DIFFRACTION8(chain A and resid 698:803)A698 - 803
9X-RAY DIFFRACTION9(chain A and resid 804:857)A804 - 857

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