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

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Basic information

Entry
Database: PDB / ID: 7rzz
TitleCrystal structure of FBF-2 in complex with LST-1 site A peptide and compact FBE RNA
Components
  • Fem-3 mRNA-binding factor 2
  • Lateral Signaling Target
  • RNA
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 / RNA binding / 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
RNA / Lateral signaling target 1 protein / Fem-3 mRNA-binding factor 2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 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 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Assembly

Deposited unit
A: Fem-3 mRNA-binding factor 2
B: RNA
C: Lateral Signaling Target


Theoretical massNumber of molelcules
Total (without water)53,8713
Polymers53,8713
Non-polymers00
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-6 kcal/mol
Surface area20370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.169, 93.169, 111.278
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#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 RNA


Mass: 2872.750 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30% (v/v) PEG 400, 0.1 M CHES, pH 9.5

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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: Jun 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→35.7 Å / Num. obs: 26102 / % possible obs: 99.5 % / Redundancy: 5.1 % / Biso Wilson estimate: 42.65 Å2 / Rpim(I) all: 0.031 / Net I/σ(I): 14.5
Reflection shellResolution: 2.39→2.48 Å / Num. unique obs: 2118 / Rpim(I) all: 0.186 / % possible all: 99.4

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIX1.19.2-4158refinement
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3k5q

3k5q


Resolution: 2.39→35.7 Å / SU ML: 0.2743 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 22.4784
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2151 1991 9.21 %
Rwork0.171 19632 -
obs0.1751 21623 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.93 Å2
Refinement stepCycle: LAST / Resolution: 2.39→35.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3266 171 0 95 3532
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213519
X-RAY DIFFRACTIONf_angle_d0.44634782
X-RAY DIFFRACTIONf_chiral_restr0.033557
X-RAY DIFFRACTIONf_plane_restr0.0038581
X-RAY DIFFRACTIONf_dihedral_angle_d8.4225539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.39-2.450.26371340.23041364X-RAY DIFFRACTION99.07
2.45-2.510.30681450.21891402X-RAY DIFFRACTION99.42
2.51-2.590.27321420.19841414X-RAY DIFFRACTION99.62
2.59-2.670.25231450.20651361X-RAY DIFFRACTION99.67
2.67-2.770.26121500.19961418X-RAY DIFFRACTION99.81
2.77-2.880.26381430.20391391X-RAY DIFFRACTION99.87
2.88-3.010.25691440.20631430X-RAY DIFFRACTION99.49
3.01-3.170.2231420.19161388X-RAY DIFFRACTION99.54
3.17-3.370.25931450.18561403X-RAY DIFFRACTION99.49
3.37-3.630.23771440.17411393X-RAY DIFFRACTION99.55
3.63-3.990.19531360.15521401X-RAY DIFFRACTION99.29
3.99-4.560.16441360.1411416X-RAY DIFFRACTION99.42
4.57-5.740.18711410.15281412X-RAY DIFFRACTION99.11
5.75-35.720.17651440.15031439X-RAY DIFFRACTION99.56
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)
12.95818630386-1.62519842941-2.249155732623.802727133833.87432736037.13913028150.1232625354470.165553070254-0.0810606567157-0.087695556119-0.0352283108631-0.1232757255740.0331430498270.0980036218996-0.09141001361360.244693019810.0542163308309-0.00534533419240.3024360583730.005328434495510.368037574234-21.8803068662-17.3906133288-8.25083208411
20.253211937137-1.51231157224-0.1618931404453.903619423921.06474529840.467319194879-0.092456230186-0.1081701314940.02321876098050.1004758128540.198178196134-0.0123701253963-0.006844588455860.0195632235139-0.1075313555470.364584101222-0.01627520526010.05974290075880.321523224158-0.006632941591680.339113255209-45.12054778589.8990464571419.4695999588
38.96857946674-7.81569634142-5.385080962227.994653331555.762218138475.8559812956-0.114206368763-0.3834947496360.300586659970.6153659364830.0696676103454-0.6233954446370.3880336039480.3938208650060.03032972693360.565794844429-0.0560584168120.1934335649660.373766869326-0.05384490685010.404619515392-34.775464174612.03891140834.1247726283
49.220630416646.13340013414-6.119340574289.78524950405-5.478486478424.41771375918-0.2233323153530.458353059446-0.504196443863-0.234529572052-0.0786556046282-0.4475735736920.753097316808-0.01392945569740.5917303445040.5015857693180.0381323466361-0.0621239560010.58522519893-0.0304958237440.434741509387-38.229260270123.881659655728.7708249999
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 168 through 323 )AA168 - 3231 - 151
22chain 'A' and (resid 324 through 568 )AA324 - 566152 - 394
33chain 'B' and (resid 1 through 9 )BB1 - 9
44chain 'C' and (resid 27 through 41 )CC27 - 411 - 15

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