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- PDB-7s02: Crystal structure of FBF-2 in complex with LST-1 site A peptide a... -

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Basic information

Entry
Database: PDB / ID: 7s02
TitleCrystal structure of FBF-2 in complex with LST-1 site A peptide and FBE RNA
Components
  • FBE RNA
  • Fem-3 mRNA-binding factor 2
  • Lateral Signaling Target
KeywordsRNA BINDING PROTEIN / Pumilio RNA-binding proteins
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 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / RNA / Lateral Signaling Target / Fem-3 mRNA-binding factor 2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsQiu, C. / Hall, T.M.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) United States
CitationJournal: Nucleic Acids Res. / Year: 2022
Title: Bipartite interaction sites differentially modulate RNA-binding affinity of a protein complex essential for germline stem cell self-renewal.
Authors: Qiu, C. / Wine, R.N. / Campbell, Z.T. / Hall, T.M.T.
History
DepositionAug 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 29, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: FBE RNA
C: Lateral Signaling Target
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9845
Polymers53,8163
Non-polymers1682
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 Å2
ΔGint-7 kcal/mol
Surface area20730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.813, 93.813, 113.222
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein / RNA chain / Protein/peptide , 3 types, 3 molecules ABC

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


Mass: 47019.055 Da / Num. of mol.: 1 / 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 (E. coli) / References: UniProt: Q09312
#2: RNA chain FBE RNA


Mass: 2817.711 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Caenorhabditis elegans (invertebrata)
#3: Protein/peptide Lateral Signaling Target


Mass: 3979.517 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: lst-1, CELE_T22A3.3, T22A3.3 / Production host: Escherichia coli (E. coli) / References: UniProt: P91820

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Non-polymers , 3 types, 127 molecules

#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% (v/v) PEG 400, 0.1 M Tris, pH 8.5

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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: Jul 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 23853 / % possible obs: 99.7 % / Redundancy: 5 % / Biso Wilson estimate: 46.6 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.039 / Rrim(I) all: 0.09 / Χ2: 1.031 / Net I/σ(I): 9.7 / Num. measured all: 120279
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.34-2.385.20.76711910.7110.370.8530.93199.9
2.38-2.425.20.62612010.7980.3030.6970.98100
2.42-2.475.20.53611870.8480.2590.5960.9899.9
2.47-2.525.20.48911650.8730.2370.5451.0199.7
2.52-2.585.10.39412000.8950.1930.4390.998100
2.58-2.645.10.34711870.9180.1710.3881.032100
2.64-2.75.10.2911850.9430.1430.3241.062100
2.7-2.7750.2412000.9580.1210.2691.074100
2.77-2.864.90.18811840.9740.0940.2111.082100
2.86-2.954.80.17711890.9750.0890.1991.08499
2.95-3.054.50.14211770.980.0740.1611.08599.1
3.05-3.183.90.11111840.9830.0640.1291.051100
3.18-3.325.10.10112040.9910.0490.1121.088100
3.32-3.55.50.0812000.9940.0380.0891.034100
3.5-3.715.40.0711810.9940.0330.0780.994100
3.71-45.40.06412000.9950.030.0710.992100
4-4.45.30.05812020.9950.0280.0651.061100
4.4-5.045.10.05511860.9960.0270.0611.0699.5
5.04-6.354.40.05512000.9940.0290.0631.05798
6.35-505.30.04912300.9940.0240.0550.99699.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
SERGUIdata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3k5q

3k5q


Resolution: 2.34→36.12 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2247 2020 8.48 %
Rwork0.1784 21789 -
obs0.1823 23809 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.18 Å2 / Biso mean: 57.3614 Å2 / Biso min: 30.97 Å2
Refinement stepCycle: final / Resolution: 2.34→36.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3259 171 11 125 3566
Biso mean--60.17 55.3 -
Num. residues----417
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.34-2.40.30411400.271515611701100
2.4-2.460.29721450.240815661711100
2.46-2.540.28061410.241715531694100
2.54-2.620.26611390.224115451684100
2.62-2.710.26281470.22615501697100
2.71-2.820.27111470.220915531700100
2.82-2.950.25241430.22891551169499
2.95-3.10.30311390.21811537167699
3.1-3.30.23081480.196515531701100
3.3-3.550.24771420.193215581700100
3.55-3.910.23111480.164315771725100
3.91-4.470.18341420.140915711713100
4.47-5.630.18581460.14491547169399
5.63-36.120.18721530.14871567172099
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)
15.06431.6551.19587.0961.53592.78-0.10761.2135-0.8393-1.23980.4987-0.8859-0.00880.5073-0.41540.5881-0.00770.01580.7311-0.15340.5645-4.507822.4154-25.6862
22.39010.82622.40871.34511.25814.43220.1903-0.3359-0.25660.15570.09340.05750.1567-0.4998-0.29490.30020.0090.00740.3630.06340.35292.545232.13233.4607
36.3737-0.47160.93420.9601-0.18541.33730.2609-0.63610.20250.0304-0.1283-0.04290.0455-0.0011-0.13910.33310.0306-0.05280.4595-0.08680.336936.779434.047920.3471
44.6969-3.0127-0.11067.46452.35783.09080.34180.21570.3772-0.4541-0.2336-0.4852-0.18890.1763-0.08960.36530.018-0.00750.47230.02820.375453.126735.592315.248
52.7737-1.07792.34680.7919-0.80571.6953-0.18090.7722-0.18350.25710.1171-0.12070.0773-0.04740.08060.57990.1216-0.23930.7402-0.1810.699325.245225.05241.296
65.02574.75435.5619.07437.18498.52020.2635-1.2742-0.70330.3319-0.1639-0.2436-0.5907-0.8267-0.19110.7184-0.04740.01880.70820.06260.555840.708424.917431.7895
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 167 through 212 )A167 - 212
2X-RAY DIFFRACTION2chain 'A' and (resid 213 through 409 )A213 - 409
3X-RAY DIFFRACTION3chain 'A' and (resid 410 through 527 )A410 - 527
4X-RAY DIFFRACTION4chain 'A' and (resid 528 through 569 )A528 - 569
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 9 )B1 - 9
6X-RAY DIFFRACTION6chain 'C' and (resid 31 through 41 )C31 - 41

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