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- PDB-8viv: Crystal structure of FBF-2 RBD in complex with gld-1 FBEa* RNA -

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Basic information

Entry
Database: PDB / ID: 8viv
TitleCrystal structure of FBF-2 RBD in complex with gld-1 FBEa* RNA
Components
  • Fem-3 mRNA-binding factor 2
  • RNA (5'-R(*CP*AP*UP*GP*UP*UP*GP*CP*CP*AP*U)-3')
KeywordsRNA BINDING PROTEIN / PUF protein
Function / homology
Function and homology information


sex differentiation / P granule / post-transcriptional regulation of gene expression / mRNA 3'-UTR binding / 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 / RNA (> 10) / Fem-3 mRNA-binding factor 2
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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: Nat Commun / Year: 2025
Title: A higher order PUF complex is central to regulation of C. elegans germline stem cells.
Authors: Chen Qiu / Sarah L Crittenden / Brian H Carrick / Lucas B Dillard / Stephany J Costa Dos Santos / Venkata P Dandey / Robert C Dutcher / Elizabeth G Viverette / Robert N Wine / Jennifer ...Authors: Chen Qiu / Sarah L Crittenden / Brian H Carrick / Lucas B Dillard / Stephany J Costa Dos Santos / Venkata P Dandey / Robert C Dutcher / Elizabeth G Viverette / Robert N Wine / Jennifer Woodworth / Zachary T Campbell / Marvin Wickens / Mario J Borgnia / Judith Kimble / Traci M Tanaka Hall /
Abstract: PUF RNA-binding proteins are broadly conserved stem cell regulators. Nematode PUF proteins maintain germline stem cells (GSCs) and, with key partner proteins, repress differentiation mRNAs, including ...PUF RNA-binding proteins are broadly conserved stem cell regulators. Nematode PUF proteins maintain germline stem cells (GSCs) and, with key partner proteins, repress differentiation mRNAs, including gld-1. Here we report that PUF protein FBF-2 and its partner LST-1 form a ternary complex that represses gld-1 via a pair of adjacent FBF binding elements (FBEs) in its 3'UTR. One LST-1 molecule links two FBF-2 molecules via motifs in the LST-1 intrinsically-disordered region; the gld-1 FBE pair includes a well-established 'canonical' FBE and a newly-identified noncanonical FBE. Remarkably, this FBE pair drives both full RNA repression in GSCs and full RNA activation upon differentiation. Discoveries of the LST-1-FBF-2 ternary complex, the gld-1 adjacent FBEs, and their in vivo significance predict an expanded regulatory repertoire of different assemblies of PUF-partner-RNA higher order complexes in nematode GSCs. This also suggests analogous PUF controls may await discovery in other biological contexts and organisms.
History
DepositionJan 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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*AP*UP*GP*UP*UP*GP*CP*CP*AP*U)-3')


Theoretical massNumber of molelcules
Total (without water)50,4632
Polymers50,4632
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-7 kcal/mol
Surface area19700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.569, 98.569, 107.140
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 (5'-R(*CP*AP*UP*GP*UP*UP*GP*CP*CP*AP*U)-3')


Mass: 3444.074 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Caenorhabditis elegans (invertebrata)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.23 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10% PEG 20000, 2% (v/v) dioxane, 0.1 M bicine, pH 9.0

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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: Oct 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 29170 / % possible obs: 99.4 % / Redundancy: 5 % / Biso Wilson estimate: 51.8 Å2 / CC1/2: 0.99 / CC star: 0.99 / Rpim(I) all: 0.07 / Rrim(I) all: 0.16 / Net I/σ(I): 13.5
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.7 % / Num. unique obs: 1511 / CC1/2: 0.5 / CC star: 0.816 / Rpim(I) all: 0.56 / Rrim(I) all: 1.24 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
SERGUIdata collection
Cootmodel building
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→36.27 Å / SU ML: 0.323 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.814
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.232 2185 7.49 %
Rwork0.1966 26985 -
obs0.1992 29170 97.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.78 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3189 212 0 92 3493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00193487
X-RAY DIFFRACTIONf_angle_d0.40484749
X-RAY DIFFRACTIONf_chiral_restr0.0314554
X-RAY DIFFRACTIONf_plane_restr0.0025572
X-RAY DIFFRACTIONf_dihedral_angle_d15.33961366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.250.37121340.34191616X-RAY DIFFRACTION94.19
2.25-2.30.30951270.31571609X-RAY DIFFRACTION93.89
2.3-2.360.32731300.28411669X-RAY DIFFRACTION96.1
2.36-2.420.30241350.27281653X-RAY DIFFRACTION96.18
2.42-2.490.29011360.23991658X-RAY DIFFRACTION96.19
2.49-2.570.25941290.23271667X-RAY DIFFRACTION96.46
2.57-2.670.26191400.23241684X-RAY DIFFRACTION97.49
2.67-2.770.25021420.24011684X-RAY DIFFRACTION98.12
2.77-2.90.22761320.20971717X-RAY DIFFRACTION98.14
2.9-3.050.2621440.22291693X-RAY DIFFRACTION98.66
3.05-3.240.24961290.21421684X-RAY DIFFRACTION97.16
3.24-3.490.2631420.21081721X-RAY DIFFRACTION99.68
3.49-3.840.23471420.1841734X-RAY DIFFRACTION99.89
3.85-4.40.20021440.16711740X-RAY DIFFRACTION99.58
4.4-5.540.2051380.1641729X-RAY DIFFRACTION99.41
5.54-36.270.19931410.17191727X-RAY DIFFRACTION97.55
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)
13.130191711472.981342135461.913411796073.532135143882.027433966611.338372395410.410667447716-0.233292635313-0.2953097151850.513585222727-0.119684697812-0.2952133003490.341412073596-0.095371782429-0.2829182921420.433021446193-0.0527593116922-0.0122421366370.4252076956250.04713462265470.438385122612-20.4964911336.778903073416.7611664808
24.60500575328-0.439559918517-1.86685870595.886908472541.880301288454.71060607860.1589279370790.2961374528690.1227983481430.0595403428159-0.06164628603080.173861445251-0.259320404725-0.156341611779-0.0878345096460.335633627432-0.02743208152590.02598512774690.352511188689-0.02781108421160.406431978243-7.2480572168663.157113618518.0679752158
30.5898675071031.47439537031.75082003313.510099910714.209360660095.035416203770.475735267158-0.4609576603580.01994032672510.777429331978-0.6941740253120.765719261140.805708924199-0.5063111638190.1714819280430.48941193976-0.08070935843620.02934717324680.624586084272-0.1697264075970.762063908465-7.8330595053841.55876467982.50846081848
42.773027243191.422644080891.531454464424.330786969353.214657108535.555158308180.1440307980020.258548970809-0.545777740727-0.02756862020150.392305701977-0.2809756493830.6001453442170.376750358704-0.4601632078360.538930176565-0.00222344541424-0.1459163774680.435946543509-0.04434636572790.783738770439-28.053457745910.7909425292-11.238284404
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 308 through 476 )AA308 - 476142 - 310
22chain 'A' and (resid 477 through 567 )AA477 - 567311 - 401
33chain 'B' and (resid 1 through 11 )BB1 - 11
44chain 'A' and (resid 167 through 307 )AA167 - 3071 - 141

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