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- EMDB-75812: The composite map of cIL-U1A-Fab1R-PGA1-sfFab18 quaternary complex -

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Basic information

Entry
Database: EMDB / ID: EMD-75812
TitleThe composite map of cIL-U1A-Fab1R-PGA1-sfFab18 quaternary complex
Map dataComposite map of the full complex
Sample
  • Complex: cIL-U1A-Fab1R-PGA1-sfFab18 quaternary complex
    • Complex: U1 small nuclear ribonucleoprotein A
      • Protein or peptide: U1 small nuclear ribonucleoprotein A
    • Complex: Protein G
      • Protein or peptide: Protein G
    • Complex: sfFab18 light chain
      • Protein or peptide: sfFab18 light chain
    • Complex: sfFab18 heavy chain
      • Protein or peptide: sfFab18 heavy chain
    • Complex: Fab1R light chain
      • Protein or peptide: Fab1R light chain
    • Complex: Fab1R heavy chain
      • Protein or peptide: Fab1R heavy chain
    • Complex: cIL RNA (155-MER)
      • DNA: cIL RNA (155-MER)
Keywordsantibody / Fab / RNA / ribozyme / U1A / ribonucleoprotein (snRNP) complex / IMMUNE SYSTEM
Biological speciesHomo sapiens (human) / Streptococcus sp. 'group G' (bacteria) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 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
DepositionMar 3, 2026-
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_75812.png

Downloads & links

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Map

FileDownload / File: emd_75812.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of the full complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 8.6
Minimum - Maximum-26.781126 - 76.743889999999993
Average (Standard dev.)0.037289187 (±0.98744714)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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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
    • Complex: U1 small nuclear ribonucleoprotein A
      • Protein or peptide: U1 small nuclear ribonucleoprotein A
    • Complex: Protein G
      • Protein or peptide: Protein G
    • Complex: sfFab18 light chain
      • Protein or peptide: sfFab18 light chain
    • Complex: sfFab18 heavy chain
      • Protein or peptide: sfFab18 heavy chain
    • Complex: Fab1R light chain
      • Protein or peptide: Fab1R light chain
    • Complex: Fab1R heavy chain
      • Protein or peptide: Fab1R heavy chain
    • Complex: cIL RNA (155-MER)
      • DNA: cIL RNA (155-MER)

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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: all
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: U1 small nuclear ribonucleoprotein A

SupramoleculeName: U1 small nuclear ribonucleoprotein A / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Protein G

SupramoleculeName: Protein G / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Streptococcus sp. 'group G' (bacteria)

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Supramolecule #4: sfFab18 light chain

SupramoleculeName: sfFab18 light chain / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #5: sfFab18 heavy chain

SupramoleculeName: sfFab18 heavy chain / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #4
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #6: Fab1R light chain

SupramoleculeName: Fab1R light chain / type: complex / ID: 6 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #7: Fab1R heavy chain

SupramoleculeName: Fab1R heavy chain / type: complex / ID: 7 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #8: cIL RNA (155-MER)

SupramoleculeName: cIL RNA (155-MER) / type: complex / ID: 8 / Parent: 1 / Macromolecule list: #7

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Macromolecule #1: U1 small nuclear ribonucleoprotein A

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

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Macromolecule #2: Protein G

MacromoleculeName: Protein G / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Streptococcus sp. 'group G' (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
TPAVTTYKLV INGRTLSGYT TTTAVDAATA EKVFKQYAYV HEVDGEWTYD DATKTFTVTE KPEKLGG

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Macromolecule #3: sfFab18 light chain

MacromoleculeName: sfFab18 light chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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 #4: sfFab18 heavy chain

MacromoleculeName: sfFab18 heavy chain / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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 SSGLYSL(UNK)SV VTVPSSSLGT QTYICT

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Macromolecule #5: Fab1R light chain

MacromoleculeName: Fab1R light chain / type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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 #6: Fab1R heavy chain

MacromoleculeName: Fab1R heavy chain / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
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: cIL RNA (155-MER)

MacromoleculeName: cIL RNA (155-MER) / type: dna / ID: 7 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
UCCAGUAGGA ACACUAUACU ACUGGAUAAU CAAAGACAAA UCUGCCCGAA GGGCUUGAGA ACAUAACCCA UUGCACUCCG GGUAUGCAG AGGUGGCAGC CUCCGGUGGG UUAAAACCCA ACGUUCUCAA CAAUAGUGAC CCAUUGCACU CCGGGU

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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: Quantifoil R1.2/1.3 / Material: GRAPHENE OXIDE / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Support film - Film thickness: 50
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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: OTHER / Software - Name: cryoSPARC (ver. 3.3.1)
Details: The map resolution was estimated based on the gold-standard Fourier Shell Correlation (FSC) using the 0.143 cut-off criterion as implemented in cryoSPARC
Number images used: 430597
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: OTHER
Final 3D classificationNumber classes: 6

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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