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- EMDB-59180: Structure of ZNFX1 in the ATP-bound, pre-ATP hydrolysis state -

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Basic information

Entry
Database: EMDB / ID: EMD-59180
TitleStructure of ZNFX1 in the ATP-bound, pre-ATP hydrolysis state
Map dataPost-processed, sharpened map of ZNFX1 bound to ATP, monomer refined by focused refinement from filamentous assembly
Sample
  • Complex: Human ZNFX1 protein in the pre-ATP hydrolysis state (auto-inhibited, bound to ATP)
    • Protein or peptide: NFX1-type zinc finger-containing protein 1
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsZNFX1 / RNA helicase / auto-inhibited / ubiquitin ligase / Zn fingers / armadillo repeat / dimer / ATPase / ATP / pre-ATP hydrolysis / ANTIVIRAL PROTEIN
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 / defense response to bacterium ...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 / defense response to bacterium / innate immune response / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsYip MCJ / Naydenova K / Randow F
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
UK Research and Innovation (UKRI) United Kingdom
CitationJournal: To Be Published
Title: ZNFX1, an immunoregulatory RNA helicase and E3 ubiquitin ligase, assembles into pleiomorphic polymers
Authors: Naydenova K / Mund T / Yip MCJ / Harper CM / Leigh KE / Hankinson J / Boyle KB / Heatley A / Otten EG / Lulla V / Modis Y / Randow F
History
DepositionJul 26, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_59180.png

Downloads & links

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Map

FileDownload / File: emd_59180.map.gz / Format: CCP4 / Size: 75.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed, sharpened map of ZNFX1 bound to ATP, monomer refined by focused refinement from filamentous assembly
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 270 pix.
= 366.606 Å		1.36 Å/pix.
x 270 pix.
= 366.606 Å		1.36 Å/pix.
x 270 pix.
= 366.606 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3578 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.10369706 - 0.15595224
Average (Standard dev.)0.000063044674 (±0.0020187846)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions270270270
Spacing270270270
CellA=B=C: 366.606 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map of ZNFX1 bound to ATP, monomer...

Fileemd_59180_additional_1.map
AnnotationUnsharpened map of ZNFX1 bound to ATP, monomer refined by focused refinement from filamentous assembly
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1 of ZNFX1 bound to ATP, monomer...

Fileemd_59180_half_map_1.map
AnnotationHalf-map 1 of ZNFX1 bound to ATP, monomer refined by focused refinement from filamentous assembly
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2 of ZNFX1 bound to ATP, monomer...

Fileemd_59180_half_map_2.map
AnnotationHalf-map 2 of ZNFX1 bound to ATP, monomer refined by focused refinement from filamentous assembly
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human ZNFX1 protein in the pre-ATP hydrolysis state (auto-inhibit...

EntireName: Human ZNFX1 protein in the pre-ATP hydrolysis state (auto-inhibited, bound to ATP)
Components
  • Complex: Human ZNFX1 protein in the pre-ATP hydrolysis state (auto-inhibited, bound to ATP)
    • Protein or peptide: NFX1-type zinc finger-containing protein 1
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Human ZNFX1 protein in the pre-ATP hydrolysis state (auto-inhibit...

SupramoleculeName: Human ZNFX1 protein in the pre-ATP hydrolysis state (auto-inhibited, bound to ATP)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 224.607297 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MASWSHPQFE KGSAGSAAGS GAGWSHPQFE KENLYFQAME ERRPHLDARP RNSHTNHRGP VDGELPPRAR NQANNPPANA LRGGASHPG RHPRANNHPA AYWQREERFR AMGRNPHQGR RNQEGHASDE ARDQRHDQEN DTRWRNGNQD CRNRRPPWSN D NFQQWRTP ...String:
MASWSHPQFE KGSAGSAAGS GAGWSHPQFE KENLYFQAME ERRPHLDARP RNSHTNHRGP VDGELPPRAR NQANNPPANA LRGGASHPG RHPRANNHPA AYWQREERFR AMGRNPHQGR RNQEGHASDE ARDQRHDQEN DTRWRNGNQD CRNRRPPWSN D NFQQWRTP HQKPTEQPQQ AKKLGYKFLE SLLQKDPSEV VITLATSLGL KELLSHSSMK SNFLELICQV LRKACSSKMD RQ SVLHVLG ILKNSKFLKV CLPAYVVGMI TEPIPDIRNQ YPEHISNIIS LLQDLVSVFP ASSVQETSML VSLLPTSLNA LRA SGVDIE EETEKNLEKV QTIIEHLQEK RREGTLRVDT YTLVQPEAED HVESYRTMPI YPTYNEVHLD ERPFLRPNII SGKY DSTAI YLDTHFRLLR EDFVRPLREG ILELLQSFED QGLRKRKFDD IRIYFDTRII TPMCSSSGIV YKVQFDTKPL KFVRW QNSK RLLYGSLVCM SKDNFETFLF ATVSNREQED LCRGIVQLCF NEQSQQLLAE VQPSDSFLMV ETTAYFEAYR HVLEGL QEV QEEDVPFQRN IVECNSHVKE PRYLLMGGRY DFTPLIENPS ATGEFLRNVE GLRHPRINVL DPGQWPSKEA LKLDDSQ ME ALQFALTREL AIIQGPPGTG KTYVGLKIVQ ALLTNESVWQ ISLQKFPILV VCYTNHALDQ FLEGIYNCQK TSIVRVGG R SNSEILKQFT LRELRNKREF RRNLPMHLRR AYMSIMTQMK ESEQELHEGA KTLECTMRGV LREQYLQKYI SPQHWESLM NGPVQDSEWI CFQHWKHSMM LEWLGLGVGS FTQSVSPAGP ENTAQAEGDE EEEGEEESSL IEIAEEADLI QADRVIEEEE VVRPQRRKK EESGADQELA KMLLAMRLDH CGTGTAAGQE QATGEWQTQR NQKKKMKKRV KDELRKLNTM TAAEANEIED V WQLDLSSR WQLYRLWLQL YQADTRRKIL SYERQYRTSA ERMAELRLQE DLHILKDAQV VGMTTTGAAK YRQILQKVEP RI VIVEEAA EVLEAHTIAT LSKACQHLIL IGDHQQLRPS ANVYDLAKNF NLEVSLFERL VKVNIPFVRL NYQHRMCPEI ARL LTPHIY QDLENHPSVL KYEKIKGVSS NLFFVEHNFP EQEIQEGKSH QNQHEAHFVV ELCKYFLCQE YLPSQITILT TYTG QLFCL RKLMPAKTFA GVRVHVVDKY QGEENDIILL SLVRSNQEGK VGFLQISNRI CVALSRAKKG MYCIGNMQML AKVPL WSKI IHTLRENNQI GPMLRLCCQN HPETHTLVSK ASDFQKVPEG GCSLPCEFRL GCGHVCTRAC HPYDSSHKEF QCMKPC QKV ICQEGHRCPL VCFQECQPCQ VKVPKTIPRC GHEQMVPCSV PESDFCCQEP CSKSLRCGHR CSHPCGEDCV QLCSEMV TI KLKCGHSQPV KCGHVEGLLY GGLLVKCTTK CGTILDCGHP CPGSCHSCFE GRFHERCQQP CKRLLICSHK CQEPCIGE C PPCQRTCQNR CVHSQCKKKC GELCSPCVEP CVWRCQHYQC TKLCSEPCNR PPCYVPCTKL LVCGHPCIGL CGEPCPKKC RICHMDEVTQ IFFGFEDEPD ARFVQLEDCS HIFEVQALDR YMNEQKDDEV AIRLKVCPIC QVPIRKNLRY GTSIKQRLEE IEIIKEKIQ GSAGEIATSQ ERLKALLERK SLLHQLLPED FLMLKEKLAQ KNLSVKDLGL VENYISFYDH LASLWDSLKK M HVLEEKRV RTRLEQVHEW LAKKRLSFTS QELSDLRSEI QRLTYLVNLL TRYKIAEKKV KDSIAVEVYS VQNILEKTCK FT QEDEQLV QEKMEALKAT LPCSGLGISE EERVQIVSAI GYPRGHWFKC RNGHIYVIGD CGGAMERGTC PDCKEVIGGT NHT LERSNQ LASEMDGAQH AAWSDTANNL MNFEEIQGMM

UniProtKB: NFX1-type zinc finger-containing protein 1

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 29.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 404593
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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