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- EMDB-77053: Cryo-EM structure of human ZNFX1 dimer in complex with ssRNA and ATPgS -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-77053
TitleCryo-EM structure of human ZNFX1 dimer in complex with ssRNA and ATPgS
Map dataThe composite map
Sample
  • Complex: ZNFX1 and ssRNA complex
    • Protein or peptide: NFX1-type zinc finger-containing protein 1
    • RNA: RNA
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
KeywordsRNA helicase / E3 Ligase / RNA
Function / homology
Function and homology information


nuclear RNA-directed RNA polymerase complex / regulatory ncRNA-mediated heterochromatin formation / negative regulation of viral genome replication / helicase activity / activation of innate immune response / RING-type E3 ubiquitin transferase / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic stress granule / defense response to virus / innate immune response ...nuclear RNA-directed RNA polymerase complex / regulatory ncRNA-mediated heterochromatin formation / negative regulation of viral genome replication / helicase activity / activation of innate immune response / RING-type E3 ubiquitin transferase / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic stress granule / defense response to virus / innate immune response / defense response to bacterium / mitochondrial outer membrane / RNA binding / zinc ion binding
Similarity search - Function
: / ZNFX1 domain / Zinc finger, NF-X1-type / ZnF_NFX / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / UPF1-type helicase core domain profile. / DNA2/NAM7 helicase, helicase domain / AAA domain ...: / ZNFX1 domain / Zinc finger, NF-X1-type / ZnF_NFX / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / UPF1-type helicase core domain profile. / DNA2/NAM7 helicase, helicase domain / AAA domain / DNA2/NAM7-like helicase / : / DNA2/NAM7 helicase-like, C-terminal / AAA domain / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NFX1-type zinc finger-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsWang F / He Q / Li H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131754 United States
CitationJournal: Nat Commun / Year: 2026
Title: Cryo-EM structures of autoinhibited and RNA-activated ZNFX1 helicase
Authors: He Q / Wang F / Rassool FV / Baylin SB / Li H
History
DepositionMay 5, 2026-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77053.png

Downloads & links

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Map

FileDownload / File: emd_77053.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe composite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 440 pix.
= 364.32 Å		0.83 Å/pix.
x 440 pix.
= 364.32 Å		0.83 Å/pix.
x 440 pix.
= 364.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.09
Minimum - Maximum-0.38029885 - 1.2236751
Average (Standard dev.)0.004862721 (±0.019430751)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 364.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: The shaperend EM map by EMREADY

Fileemd_77053_additional_1.map
AnnotationThe shaperend EM map by EMREADY
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : ZNFX1 and ssRNA complex

EntireName: ZNFX1 and ssRNA complex
Components
  • Complex: ZNFX1 and ssRNA complex
    • Protein or peptide: NFX1-type zinc finger-containing protein 1
    • RNA: RNA
  • Ligand: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

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Supramolecule #1: ZNFX1 and ssRNA complex

SupramoleculeName: ZNFX1 and ssRNA complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 400 KDa

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Macromolecule #1: NFX1-type zinc finger-containing protein 1

MacromoleculeName: NFX1-type zinc finger-containing protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 220.537 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: MEERRPHLDA RPRNSHTNHR GPVDGELPPR ARNQANNPPA NALRGGASHP GRHPRANNHP AAYWQREERF RAMGRNPHQG RRNQEGHAS DEARDQRHDQ ENDTRWRNGN QDCRNRRPPW SNDNFQQWRT PHQKPTEQPQ QAKKLGYKFL ESLLQKDPSE V VITLATSL ...String:
MEERRPHLDA RPRNSHTNHR GPVDGELPPR ARNQANNPPA NALRGGASHP GRHPRANNHP AAYWQREERF RAMGRNPHQG RRNQEGHAS DEARDQRHDQ ENDTRWRNGN QDCRNRRPPW SNDNFQQWRT PHQKPTEQPQ QAKKLGYKFL ESLLQKDPSE V VITLATSL GLKELLSHSS MKSNFLELIC QVLRKACSSK MDRQSVLHVL GILKNSKFLK VCLPAYVVGM ITEPIPDIRN QY PEHISNI ISLLQDLVSV FPASSVQETS MLVSLLPTSL NALRASGVDI EEETEKNLEK VQTIIEHLQE KRREGTLRVD TYT LVQPEA EDHVESYRTM PIYPTYNEVH LDERPFLRPN IISGKYDSTA IYLDTHFRLL REDFVRPLRE GILELLQSFE DQGL RKRKF DDIRIYFDTR IITPMCSSSG IVYKVQFDTK PLKFVRWQNS KRLLYGSLVC MSKDNFETFL FATVSNREQE DLCRG IVQL CFNEQSQQLL AEVQPSDSFL MVETTAYFEA YRHVLEGLQE VQEEDVPFQR NIVECNSHVK EPRYLLMGGR YDFTPL IEN PSATGEFLRN VEGLRHPRIN VLDPGQWPSK EALKLDDSQM EALQFALTRE LAIIQGPPGT GKTYVGLKIV QALLTNE SV WQISLQKFPI LVVCYTNHAL DQFLEGIYNC QKTSIVRVGG RSNSEILKQF TLRELRNKRE FRRNLPMHLR RAYMSIMT Q MKESEQELHE GAKTLECTMR GVLREQYLQK YISPQHWESL MNGPVQDSEW ICFQHWKHSM MLEWLGLGVG SFTQSVSPA GPENTAQAEG DEEEEGEEES SLIEIAEEAD LIQADRVIEE EEVVRPQRRK KEESGADQEL AKMLLAMRLD HCGTGTAAGQ EQATGEWQT QRNQKKKMKK RVKDELRKLN TMTAAEANEI EDVWQLDLSS RWQLYRLWLQ LYQADTRRKI LSYERQYRTS A ERMAELRL QEDLHILKDA QVVGMTTTGA AKYRQILQKV EPRIVIVEEA AEVLEAHTIA TLSKACQHLI LIGDHQQLRP SA NVYDLAK NFNLEVSLFE RLVKVNIPFV RLNYQHRMCP EIARLLTPHI YQDLENHPSV LKYEKIKGVS SNLFFVEHNF PEQ EIQEGK SHQNQHEAHF VVELCKYFLC QEYLPSQITI LTTYTGQLFC LRKLMPAKTF AGVRVHVVDK YQGEENDIIL LSLV RSNQE GKVGFLQISN RICVALSRAK KGMYCIGNMQ MLAKVPLWSK IIHTLRENNQ IGPMLRLCCQ NHPETHTLVS KASDF QKVP EGGCSLPCEF RLGCGHVCTR ACHPYDSSHK EFQCMKPCQK VICQEGHRCP LVCFQECQPC QVKVPKTIPR CGHEQM VPC SVPESDFCCQ EPCSKSLRCG HRCSHPCGED CVQLCSEMVT IKLKCGHSQP VKCGHVEGLL YGGLLVKCTT KCGTILD CG HPCPGSCHSC FEGRFHERCQ QPCKRLLICS HKCQEPCIGE CPPCQRTCQN RCVHSQCKKK CGELCSPCVE PCVWRCQH Y QCTKLCSEPC NRPPCYVPCT KLLVCGHPCI GLCGEPCPKK CRICHMDEVT QIFFGFEDEP DARFVQLEDC SHIFEVQAL DRYMNEQKDD EVAIRLKVCP ICQVPIRKNL RYGTSIKQRL EEIEIIKEKI QGSAGEIATS QERLKALLER KSLLHQLLPE DFLMLKEKL AQKNLSVKDL GLVENYISFY DHLASLWDSL KKMHVLEEKR VRTRLEQVHE WLAKKRLSFT SQELSDLRSE I QRLTYLVN LLTRYKIAEK KVKDSIAVEV YSVQNILEKT CKFTQEDEQL VQEKMEALKA TLPCSGLGIS EEERVQIVSA IG YPRGHWF KCRNGHIYVI GDCGGAMERG TCPDCKEVIG GTNHTLERSN QLASEMDGAQ HAAWSDTANN LMNFEEIQGM M

UniProtKB: NFX1-type zinc finger-containing protein 1

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Macromolecule #2: RNA

MacromoleculeName: RNA / type: rna / ID: 2 / Number of copies: 2
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 19.496188 KDa
SequenceString:
UGUGUGUGUG UGUGUGUGUG UGUGUGUGUG UGUGUGUGUG UGUGUGUGUG UGUGUGUGUG

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Macromolecule #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: AGS
Molecular weightTheoretical: 523.247 Da
Chemical component information

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*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

BufferpH: 7.5
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
25.0 mMHEPES4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 10642983
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: OTHER / Software - Name: cryoSPARC / Number images used: 263896
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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