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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: Filippova EV / Krochmal D / Mukherjee S / Piccirilli JA / Kossiakoff AA
History
DepositionMar 3, 2026-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 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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