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- EMDB-73618: Cryo-EM structure of the core region of cIL-U1A-Fab1R-PGA1-sfFab ... -

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Basic information

Entry
Database: EMDB / ID: EMD-73618
TitleCryo-EM structure of the core region of cIL-U1A-Fab1R-PGA1-sfFab quaternary complex at 2.9 A resolution
Map data
Sample
  • Complex: cIL-U1A-Fab1R-PGA1-sfFab18 quaternary complex
    • Protein or peptide: U1 small nuclear ribonucleoprotein A
    • RNA: Hairpin II of the U1 snRNA (U1hpII)
    • Protein or peptide: Protein G
    • Protein or peptide: sfFab18 light chain
    • Protein or peptide: sfFab18 heavy chain
    • Protein or peptide: Fab1R heavy chain
    • Protein or peptide: Fab1R light chain
  • Ligand: DECYL-BETA-D-MALTOPYRANOSIDE
Keywordsantibody / Fab / RNA / ribozyme / U1A / ribonucleoprotein (snRNP) complex / IMMUNE SYSTEM
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
U1 small nuclear ribonucleoprotein A
Similarity search - Component
Biological speciesHomo sapiens (human) / Streptococcus sp. 'group G' (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsFilippova EV / Kossiakoff AA
Funding support United States, 1 items
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: Ekaterina V Filippova / Daniel Krochmal / Somnath Mukherjee / Joseph A Piccirilli / Anthony A Kossiakoff /
Abstract: Recent advances in cryo-electron microscopy (cryo-EM) have made antigen-binding fragments (Fabs) essential tools in the field of structural biology. Fabs facilitate image alignment, thereby enhancing ...Recent advances in cryo-electron microscopy (cryo-EM) have made antigen-binding fragments (Fabs) essential tools in the field of structural biology. Fabs facilitate image alignment, thereby enhancing three-dimensional (3D) reconstruction, and increase the effective size of proteins, aiding in their structural elucidation. In this study, we sought to broaden the use of Fabs as fiducial markers to elucidate the structures of RNA molecules. Identifying an appropriate Fab for a specific RNA target can be particularly challenging due to RNA's inherent flexibility and tendency to assume multiple conformations, which complicate the process and prolong the structure determination timeline. To address this challenge, we designed a universal Fab that specifically recognizes a U1A-RNA epitope, thereby reducing the need for Fab selection tailored to each individual RNA target. We determined the cryo-EM structure of the class I ligase ribozyme complexed with a portable U1hpII loop bound to the U1A protein and the Fab. The resulting structure revealed that the Fab interacts with a conserved U1A-RNA binding region, which can be engineered into other RNA molecules. This strategy presents significant potential for streamlining the structural determination of various RNAs, which are essential for biological and biomedical research.
History
DepositionOct 27, 2025-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73618.png

Downloads & links

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Map

FileDownload / File: emd_73618.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.07 Å/pix.
x 360 pix.
= 384.48 Å		1.07 Å/pix.
x 360 pix.
= 384.48 Å		1.07 Å/pix.
x 360 pix.
= 384.48 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.46
Minimum - Maximum-1.088638 - 2.5280838
Average (Standard dev.)0.00094722747 (±0.027499149)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 384.47998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73618_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #2

Fileemd_73618_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73618_half_map_2.map
Projections & Slices
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Sample components

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Entire : cIL-U1A-Fab1R-PGA1-sfFab18 quaternary complex

EntireName: cIL-U1A-Fab1R-PGA1-sfFab18 quaternary complex
Components
  • Complex: cIL-U1A-Fab1R-PGA1-sfFab18 quaternary complex
    • Protein or peptide: U1 small nuclear ribonucleoprotein A
    • RNA: Hairpin II of the U1 snRNA (U1hpII)
    • Protein or peptide: Protein G
    • Protein or peptide: sfFab18 light chain
    • Protein or peptide: sfFab18 heavy chain
    • Protein or peptide: Fab1R heavy chain
    • Protein or peptide: Fab1R light chain
  • Ligand: DECYL-BETA-D-MALTOPYRANOSIDE

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Supramolecule #1: cIL-U1A-Fab1R-PGA1-sfFab18 quaternary complex

SupramoleculeName: cIL-U1A-Fab1R-PGA1-sfFab18 quaternary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 / Details: core region
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: U1 small nuclear ribonucleoprotein A

MacromoleculeName: U1 small nuclear ribonucleoprotein A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.20912 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
AVPETRPNHT IYINNLNEKI KKDELKKSLH AIFSRFGQIL DILVSRSLKM RGQAFVIFKE VSSATNALRS MQGFPFYDKP MRIQYAKTD SDIIAKMK

UniProtKB: U1 small nuclear ribonucleoprotein A

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Macromolecule #3: Protein G

MacromoleculeName: Protein G / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus sp. 'group G' (bacteria)
Molecular weightTheoretical: 7.359124 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
TPAVTTYKLV INGRTLSGYT TTTAVDAATA EKVFKQYAYV HEVDGEWTYD DATKTFTVTE KPEKLGG

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Macromolecule #4: sfFab18 light chain

MacromoleculeName: sfFab18 light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.082279 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: IMKKNIAFLL ASMFVFSIAT NAYASDIQMT QSPSSLSASV GDRVTITCRA SQSVSSAVAW YQQKPGKAPK LLIYSASSLY SGVPSRFSG SRSGTDFTLT ISSLQPEDFA TYYCQQTMTY PITFGQGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC L LNNFYPRE ...String:
IMKKNIAFLL ASMFVFSIAT NAYASDIQMT QSPSSLSASV GDRVTITCRA SQSVSSAVAW YQQKPGKAPK LLIYSASSLY SGVPSRFSG SRSGTDFTLT ISSLQPEDFA TYYCQQTMTY PITFGQGTKV EIKRTVAAPS VFIFPPSDEQ LKSGTASVVC L LNNFYPRE AKVQWKVDNA LQSGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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Macromolecule #5: sfFab18 heavy chain

MacromoleculeName: sfFab18 heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.724973 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MKKNIAFLLA SMFVFSIATN AYAEISEVQL VESGGGLVQP GGSLRLSCAA SGFNFASASI HWVRQAPGKG LEWVASIYSY SGYTYYADS VKGRFTISAD TSKNTAYLQM NSLRAEDTAV YYCARNYDYP YWYSEEAFDY WGQGTLVTVS SASTKGPSVF P LAPSSKST ...String:
MKKNIAFLLA SMFVFSIATN AYAEISEVQL VESGGGLVQP GGSLRLSCAA SGFNFASASI HWVRQAPGKG LEWVASIYSY SGYTYYADS VKGRFTISAD TSKNTAYLQM NSLRAEDTAV YYCARNYDYP YWYSEEAFDY WGQGTLVTVS SASTKGPSVF P LAPSSKST SGGTAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PS NTKVDKK VEPKSCDKTH T

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Macromolecule #6: Fab1R heavy chain

MacromoleculeName: Fab1R heavy chain / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.280682 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GDFMKKNIAF LLASMFVFSI ATNAYAEISE VQLVESGGGL VQPGGSLRLS CAASGFNIYS SSIHWVRQAP GKGLEWVASI YPYSGYTSY ADSVKGRFTI SADTSKNTAY LQMNSLRAED TAVYYCARSP WGWFWQYGQY SVALDYWGQG TLVTVSSAST K GPSVFPLA ...String:
GDFMKKNIAF LLASMFVFSI ATNAYAEISE VQLVESGGGL VQPGGSLRLS CAASGFNIYS SSIHWVRQAP GKGLEWVASI YPYSGYTSY ADSVKGRFTI SADTSKNTAY LQMNSLRAED TAVYYCARSP WGWFWQYGQY SVALDYWGQG TLVTVSSAST K GPSVFPLA PSSKSTSGGT AALGCLVKDY FPEPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CN VNHKPSN TKVDKKVEPK SCDKTHT

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Macromolecule #7: Fab1R light chain

MacromoleculeName: Fab1R light chain / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.775441 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: AQPAMASDIQ MTQSPSSLSA SVGDRVTITC RASQSVSSAV AWYQQKPGKA PKLLIYSASS LYSGVPSRFS GSRSGTDFTL TISSLQPED FATYYCQQSS FYPITFGQGT KVEIKRTVAA PSVFIFPPSD LRTGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV ...String:
AQPAMASDIQ MTQSPSSLSA SVGDRVTITC RASQSVSSAV AWYQQKPGKA PKLLIYSASS LYSGVPSRFS GSRSGTDFTL TISSLQPED FATYYCQQSS FYPITFGQGT KVEIKRTVAA PSVFIFPPSD LRTGTASVVC LLNNFYPREA KVQWKVDNAL Q SGNSQESV TEQDSKDSTY SLSSTLTLSK ADYEKHKVYA CEVTHQGLSS PVTKSFNRGE C

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

MacromoleculeName: Hairpin II of the U1 snRNA (U1hpII) / type: rna / ID: 2 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 5.684419 KDa
SequenceString:
ACCCAUUGCA CUCCGGGU

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Macromolecule #8: DECYL-BETA-D-MALTOPYRANOSIDE

MacromoleculeName: DECYL-BETA-D-MALTOPYRANOSIDE / type: ligand / ID: 8 / Number of copies: 1 / Formula: DMU
Molecular weightTheoretical: 482.562 Da
Chemical component information

ChemComp-DMU:
DECYL-BETA-D-MALTOPYRANOSIDE / detergent*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 7.4 / Details: 10 mM HEPES, 75 mM NaCl, 5 mM MgCl2
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER / Pretreatment - Pressure: 0.02 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 2 / Number real images: 10696 / Average exposure time: 6.6 sec. / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 327742
CTF correctionSoftware - Name: cryoSPARC (ver. 3.3.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio reconstruction by cryoSPARC.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: OTHER / Software - Name: cryoSPARC (ver. 3.3.1) / Details: FSC 0.143 CUT-OFF obtained from cryoSPARC / Number images used: 430597
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: OTHER
Final 3D classificationNumber classes: 6
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

3hhn

source_name: PDB, initial_model_type: experimental model

6u8c

source_name: PDB, initial_model_type: experimental model

5bjz

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9yxv:
Cryo-EM structure of the core region of cIL-U1A-Fab1R-PGA1-sfFab quaternary complex at 2.9 A resolution

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