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- PDB-6pun: Crystal structure of a ternary complex of FBF-2 with LST-1 (site ... -

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Basic information

Entry
Database: PDB / ID: 6pun
TitleCrystal structure of a ternary complex of FBF-2 with LST-1 (site B) and compact FBE RNA
Components
  • Fem-3 mRNA-binding factor 2
  • LST-1
  • RNA (5'-R(*CP*UP*GP*UP*GP*AP*AP*U)-3')
KeywordsRNA BINDING PROTEIN/RNA / PUF / protein-RNA complex / RNA BINDING PROTEIN-RNA complex
Function / homology
Function and homology information


sex differentiation / P granule / post-transcriptional regulation of gene expression / G-protein alpha-subunit binding / mRNA 3'-UTR binding / regulation of gene expression / cell differentiation / negative regulation of translation / nucleus / cytoplasm
Similarity search - Function
Pumilio, RNA binding domain / Pumilio homology domain / Pumilio homology domain (PUM-HD) profile. / Pumilio-family RNA binding repeat / Pumilio RNA-binding repeat profile. / Pumilio RNA-binding repeat / Pumilio-like repeats / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical ...Pumilio, RNA binding domain / Pumilio homology domain / Pumilio homology domain (PUM-HD) profile. / Pumilio-family RNA binding repeat / Pumilio RNA-binding repeat profile. / Pumilio RNA-binding repeat / Pumilio-like repeats / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
RNA / Lateral Signaling Target / Fem-3 mRNA-binding factor 2 / Uncharacterized protein
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.099 Å
AuthorsQiu, C. / Campbell, Z.T. / Hall, T.M.T.
CitationJournal: Elife / Year: 2019
Title: A crystal structure of a collaborative RNA regulatory complex reveals mechanisms to refine target specificity.
Authors: Qiu, C. / Bhat, V.D. / Rajeev, S. / Zhang, C. / Lasley, A.E. / Wine, R.N. / Campbell, Z.T. / Tanaka Hall, T.M.T.
History
DepositionJul 18, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fem-3 mRNA-binding factor 2
B: RNA (5'-R(*CP*UP*GP*UP*GP*AP*AP*U)-3')
C: Fem-3 mRNA-binding factor 2
D: RNA (5'-R(*CP*UP*GP*UP*GP*AP*AP*U)-3')
E: LST-1
F: LST-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,09612
Polymers105,7336
Non-polymers3636
Water2,990166
1
A: Fem-3 mRNA-binding factor 2
B: RNA (5'-R(*CP*UP*GP*UP*GP*AP*AP*U)-3')
E: LST-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1688
Polymers52,8663
Non-polymers3015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-18 kcal/mol
Surface area20560 Å2
MethodPISA
2
C: Fem-3 mRNA-binding factor 2
D: RNA (5'-R(*CP*UP*GP*UP*GP*AP*AP*U)-3')
F: LST-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9294
Polymers52,8663
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-12 kcal/mol
Surface area19820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.751, 74.380, 81.547
Angle α, β, γ (deg.)107.170, 104.400, 101.760
Int Tables number1
Space group name H-MP1

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Components

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Protein / RNA chain / Protein/peptide , 3 types, 6 molecules ACBDEF

#1: Protein Fem-3 mRNA-binding factor 2


Mass: 47019.055 Da / Num. of mol.: 2 / Fragment: UNP residues 164-575
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: fbf-2, F21H12.5 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-CodonPuls(DE3)-RIL / References: UniProt: Q09312
#2: RNA chain RNA (5'-R(*CP*UP*GP*UP*GP*AP*AP*U)-3')


Mass: 2527.545 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Caenorhabditis elegans (invertebrata)
#3: Protein/peptide LST-1


Mass: 3319.860 Da / Num. of mol.: 2 / Fragment: UNP residues 64-88
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Production host: Escherichia coli (E. coli) / References: UniProt: Q86RT0, UniProt: P91820*PLUS

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Non-polymers , 4 types, 172 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 17-20% w/v PEG3350, 0.2 M magnesium chloride, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2018
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.099→50 Å / Num. obs: 50128 / % possible obs: 96.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 41.24 Å2 / Rmerge(I) obs: 0.108 / Rpim(I) all: 0.045 / Rrim(I) all: 0.118 / Χ2: 1.294 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.146.50.74925140.8650.3120.8130.93697.1
2.14-2.186.60.67925240.8920.2820.7360.9298.6
2.18-2.226.50.56925560.9170.2380.6180.97998.5
2.22-2.266.40.4925680.9360.2060.5331.08497.5
2.26-2.316.40.43525210.9390.1830.4731.05798.7
2.31-2.376.30.3625340.9640.1520.3911.11397.6
2.37-2.426.30.31425040.9690.1330.3421.22997.9
2.42-2.495.90.26224870.9760.1150.2871.30595.3
2.49-2.565.90.25521890.9740.1120.2791.33184.6
2.56-2.656.60.21524640.9820.0890.2331.43495
2.65-2.747.20.18725400.9880.0740.2011.42498.5
2.74-2.857.10.16725860.990.0670.181.52899.4
2.85-2.987.20.14925720.990.060.1611.44799.6
2.98-3.147.10.12725410.9920.0510.1371.47999.3
3.14-3.3370.11125700.9930.0450.121.59499.4
3.33-3.596.80.09725850.9940.040.1051.7999.3
3.59-3.956.60.08925620.9940.0370.0971.40698.7
3.95-4.5260.07724730.9950.0340.0851.26396.3
4.52-5.76.40.07722760.9940.0330.0841.287.9
5.7-5070.09225620.990.0380.0991.19699

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
SERGUIdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3V74

3v74


Resolution: 2.099→42.691 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 28.51
RfactorNum. reflection% reflection
Rfree0.2404 2000 3.99 %
Rwork0.1984 --
obs0.2001 50104 96.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.71 Å2 / Biso mean: 54.4985 Å2 / Biso min: 25.79 Å2
Refinement stepCycle: final / Resolution: 2.099→42.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6502 317 23 166 7008
Biso mean--67.48 50.12 -
Num. residues----830
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.099-2.15150.33251410.2966338994
2.1515-2.20960.35691440.2733346199
2.2096-2.27470.29681440.2508348098
2.2747-2.34810.25431460.2336351298
2.3481-2.4320.26981450.2251345798
2.432-2.52940.24381340.2301325091
2.5294-2.64450.27181350.2237324691
2.6445-2.78390.26881460.2184349699
2.7839-2.95820.21191460.2161352299
2.9582-3.18660.251480.2147354399
3.1866-3.50710.2421470.205353599
3.5071-4.01430.21941450.1769350499
4.0143-5.05630.2391330.1638319089
5.0563-42.6910.21161460.1796351999
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)
10.39750.37340.31560.81020.95481.9832-0.0269-0.0019-0.00270.02560.064-0.01080.02060.2084-0.04650.28570.02820.02430.33320.00420.3419-21.6104-18.828830.6786
20.1098-0.01780.05951.18051.55582.11490.0081-0.07080.0850.3205-0.23270.34770.4884-0.3750.20480.5413-0.06610.08050.5574-0.08570.4034-31.7057-18.39437.9916
30.65920.1734-0.18820.99780.50671.8456-0.0268-0.04420.11110.0261-0.02350.0688-0.12380.06690.0550.2805-0.0298-0.0410.33750.01660.3488-33.18627.987112.4524
40.3883-0.01210.28131.0571.04982.22370.0864-0.28670.2660.0278-0.0217-0.1815-0.39440.26920.00880.5492-0.17490.00540.5444-0.05730.3666-24.166313.808115.0217
51.43320.447-0.13511.985-0.20051.8019-0.04020.17390.22820.11640.0305-0.3421-0.67750.41570.02890.7221-0.148-0.07250.6416-0.06820.6738-23.38978.130751.0508
61.83980.49360.33233.6566-0.49863.0039-0.1558-0.1639-0.030.45170.0455-0.50050.1432-0.19850.13230.68820.0059-0.01440.7237-0.10410.7821-28.756716.700644.9447
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 167 through 568)A167 - 568
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 8)B1 - 8
3X-RAY DIFFRACTION3(chain 'C' and resid 167 through 564)C167 - 564
4X-RAY DIFFRACTION4(chain 'D' and resid 2 through 8)D2 - 8
5X-RAY DIFFRACTION5(chain 'E' and resid 76 through 80)E76 - 80
6X-RAY DIFFRACTION6(chain 'F' and resid 75 through 80)F75 - 80

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