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- PDB-9yxv: Cryo-EM structure of the core region of cIL-U1A-Fab1R-PGA1-sfFab ... -

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Basic information

Entry
Database: PDB / ID: 9yxv
TitleCryo-EM structure of the core region of cIL-U1A-Fab1R-PGA1-sfFab quaternary complex at 2.9 A resolution
Components
  • Fab1R heavy chain
  • Fab1R light chain
  • Hairpin II of the U1 snRNA (U1hpII)
  • Protein G
  • U1 small nuclear ribonucleoprotein A
  • sfFab18 heavy chain
  • sfFab18 light chain
KeywordsIMMUNE SYSTEM / antibody / Fab / RNA / ribozyme / U1A / ribonucleoprotein (snRNP) complex
Function / homology
Function and homology information


U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm ...U1 snRNP binding / U1 snRNP / U1 snRNA binding / U4/U6 x U5 tri-snRNP complex / mRNA Splicing - Major Pathway / spliceosomal complex / mRNA splicing, via spliceosome / DNA binding / RNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
U1 small nuclear ribonucleoprotein A, RNA recognition motif 2 / U1 small nuclear ribonucleoprotein A, RNA recognition motif 1 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
RNA / RNA (> 10) / U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptococcus sp. 'group G' (bacteria)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsFilippova, E.V. / Kossiakoff, A.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nucleic Acids Res. / Year: 2026
Title: A universal Fab targeting a conserved U1A-RNA epitope for RNA structure determination by cryo-EM
Authors: Filippova, E.V. / Krochmal, D. / Mukherjee, S. / Piccirilli, J.A. / Kossiakoff, A.A.
History
DepositionOct 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0May 27, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: U1 small nuclear ribonucleoprotein A
B: Hairpin II of the U1 snRNA (U1hpII)
C: Protein G
D: sfFab18 light chain
E: sfFab18 heavy chain
H: Fab1R heavy chain
L: Fab1R light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,8738
Polymers127,3907
Non-polymers4831
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 2 molecules AC

#1: Protein U1 small nuclear ribonucleoprotein A / U1A


Mass: 11209.120 Da / Num. of mol.: 1 / Mutation: Y31H, Q36R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNRPA / Plasmid: pHFT2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09012
#3: Protein Protein G


Mass: 7359.124 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. 'group G' (bacteria) / Plasmid: pHFT2 / Production host: Escherichia coli BL21(DE3) (bacteria)

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Antibody , 4 types, 4 molecules DEHL

#4: Antibody sfFab18 light chain


Mass: 26082.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSFV4 / Production host: Escherichia coli BL21(DE3) (bacteria)
#5: Antibody sfFab18 heavy chain


Mass: 24998.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSFV4 / Production host: Escherichia coli BL21(DE3) (bacteria)
#6: Antibody Fab1R heavy chain


Mass: 28280.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSFV4 / Production host: Escherichia coli BL21(DE3) (bacteria)
#7: Antibody Fab1R light chain


Mass: 23775.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pSFV4 / Production host: Escherichia coli BL21(DE3) (bacteria)

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RNA chain / Sugars , 2 types, 2 molecules B

#2: RNA chain Hairpin II of the U1 snRNA (U1hpII)


Mass: 5684.419 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#8: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H42O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: cIL-U1A-Fab1R-PGA1-sfFab18 quaternary complex / Type: COMPLEX / Details: core region / Entity ID: #1-#7 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3) / Plasmid: pSFV4
Buffer solutionpH: 7.4 / Details: 10 mM HEPES, 75 mM NaCl, 5 mM MgCl2
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 900 nm
Image recordingAverage exposure time: 6.6 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 10696

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Processing

EM software
IDNameVersionCategory
1cryoSPARC3.3.1particle selection
2EPUimage acquisition
4cryoSPARC3.3.1CTF correction
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
10Cootmodel refinement
14cryoSPARC3.3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 327742
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.9 Å / Resolution method: OTHER / Num. of particles: 430597 / Algorithm: FOURIER SPACE / Details: FSC 0.143 CUT-OFF obtained from cryoSPARC / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13hhn

3hhn

13hhn1PDBexperimental model
26u8c

6u8c

16u8c2PDBexperimental model
35bjz

5bjz

15bjz3PDBexperimental model
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036732
ELECTRON MICROSCOPYf_angle_d0.6079200
ELECTRON MICROSCOPYf_dihedral_angle_d15.7991029
ELECTRON MICROSCOPYf_chiral_restr0.0411043
ELECTRON MICROSCOPYf_plane_restr0.0051114

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