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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: Filippova EV / Krochmal D / Mukherjee S / Piccirilli JA / Kossiakoff AA
History
DepositionOct 27, 2025-
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_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)

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: 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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_73618_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73618_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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: 24.998895 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 SSGLYSL(UNK)SV VTVPSSSLGT QTYICT

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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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