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- EMDB-59183: Helical polymer of human ZNFX1 proteins -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-59183
TitleHelical polymer of human ZNFX1 proteins
Map dataHalf-map 2 of ZNFX1 filament, reconstructed using a single-particle approach
Sample
  • Complex: Helical filament of ZNFX1 protein
    • Protein or peptide: ZNFX1 (NFX1-type zinc finger-containing protein 1)
KeywordsZNFX1 / Helical filament / RNA helicase / ubiquitin ligase / Zn fingers / armadillo repeat / 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: 9.4 Å
AuthorsLeigh KE / Harper CM / Naydenova K / Modis Y / 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_59183.png

Downloads & links

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Map

FileDownload / File: emd_59183.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHalf-map 2 of ZNFX1 filament, reconstructed using a single-particle approach
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.18 Å/pix.
x 200 pix.
= 435. Å		2.18 Å/pix.
x 200 pix.
= 435. Å		2.18 Å/pix.
x 200 pix.
= 435. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.175 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.12787732 - 0.50111353
Average (Standard dev.)0.0071159727 (±0.039965)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 435.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Unsharpened map of ZNFX1 filament, reconstructed using a...

Fileemd_59183_half_map_1.map
AnnotationUnsharpened map of ZNFX1 filament, reconstructed using a single-particle approach
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1 of ZNFX1 filament, reconstructed using a...

Fileemd_59183_half_map_2.map
AnnotationHalf-map 1 of ZNFX1 filament, reconstructed using a single-particle approach
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Helical filament of ZNFX1 protein

EntireName: Helical filament of ZNFX1 protein
Components
  • Complex: Helical filament of ZNFX1 protein
    • Protein or peptide: ZNFX1 (NFX1-type zinc finger-containing protein 1)

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Supramolecule #1: Helical filament of ZNFX1 protein

SupramoleculeName: Helical filament of ZNFX1 protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: ZNFX1 (NFX1-type zinc finger-containing protein 1)

MacromoleculeName: ZNFX1 (NFX1-type zinc finger-containing protein 1) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MASWSHPQFE KGSAGSAAGS GAGWSHPQFE KENLYFQAME ERRPHLDARP RNSHTNHRGP VDGELPPRAR NQANNPPANA LRGGASHPGR HPRANNHPAA YWQREERFRA MGRNPHQGRR NQEGHASDEA RDQRHDQEND TRWRNGNQDC RNRRPPWSND NFQQWRTPHQ ...String:
MASWSHPQFE KGSAGSAAGS GAGWSHPQFE KENLYFQAME ERRPHLDARP RNSHTNHRGP VDGELPPRAR NQANNPPANA LRGGASHPGR HPRANNHPAA YWQREERFRA MGRNPHQGRR NQEGHASDEA RDQRHDQEND TRWRNGNQDC RNRRPPWSND NFQQWRTPHQ KPTEQPQQAK KLGYKFLESL LQKDPSEVVI TLATSLGLKE LLSHSSMKSN FLELICQVLR KACSSKMDRQ SVLHVLGILK NSKFLKVCLP AYVVGMITEP IPDIRNQYPE HISNIISLLQ DLVSVFPASS VQETSMLVSL LPTSLNALRA SGVDIEEETE KNLEKVQTII EHLQEKRREG TLRVDTYTLV QPEAEDHVES YRTMPIYPTY NEVHLDERPF LRPNIISGKY DSTAIYLDTH FRLLREDFVR PLREGILELL QSFEDQGLRK RKFDDIRIYF DTRIITPMCS SSGIVYKVQF DTKPLKFVRW QNSKRLLYGS LVCMSKDNFE TFLFATVSNR EQEDLCRGIV QLCFNEQSQQ LLAEVQPSDS FLMVETTAYF EAYRHVLEGL QEVQEEDVPF QRNIVECNSH VKEPRYLLMG GRYDFTPLIE NPSATGEFLR NVEGLRHPRI NVLDPGQWPS KEALKLDDSQ MEALQFALTR ELAIIQGPPG TGKTYVGLKI VQALLTNESV WQISLQKFPI LVVCYTNHAL DQFLEGIYNC QKTSIVRVGG RSNSEILKQF TLRELRNKRE FRRNLPMHLR RAYMSIMTQM KESEQELHEG AKTLECTMRG VLREQYLQKY ISPQHWESLM NGPVQDSEWI CFQHWKHSMM LEWLGLGVGS FTQSVSPAGP ENTAQAEGDE EEEGEEESSL IEIAEEADLI QADRVIEEEE VVRPQRRKKE ESGADQELAK MLLAMRLDHC GTGTAAGQEQ ATGEWQTQRN QKKKMKKRVK DELRKLNTMT AAEANEIEDV WQLDLSSRWQ LYRLWLQLYQ ADTRRKILSY ERQYRTSAER MAELRLQEDL HILKDAQVVG MTTTGAAKYR QILQKVEPRI VIVEEAAEVL EAHTIATLSK ACQHLILIGD HQQLRPSANV YDLAKNFNLE VSLFERLVKV NIPFVRLNYQ HRMCPEIARL LTPHIYQDLE NHPSVLKYEK IKGVSSNLFF VEHNFPEQEI QEGKSHQNQH EAHFVVELCK YFLCQEYLPS QITILTTYTG QLFCLRKLMP AKTFAGVRVH VVDKYQGEEN DIILLSLVRS NQEGKVGFLQ ISNRICVALS RAKKGMYCIG NMQMLAKVPL WSKIIHTLRE NNQIGPMLRL CCQNHPETHT LVSKASDFQK VPEGGCSLPC EFRLGCGHVC TRACHPYDSS HKEFQCMKPC QKVICQEGHR CPLVCFQECQ PCQVKVPKTI PRCGHEQMVP CSVPESDFCC QEPCSKSLRC GHRCSHPCGE DCVQLCSEMV TIKLKCGHSQ PVKCGHVEGL LYGGLLVKCT TKCGTILDCG HPCPGSCHSC FEGRFHERCQ QPCKRLLICS HKCQEPCIGE CPPCQRTCQN RCVHSQCKKK CGELCSPCVE PCVWRCQHYQ CTKLCSEPCN RPPCYVPCTK LLVCGHPCIG LCGEPCPKKC RICHMDEVTQ IFFGFEDEPD ARFVQLEDCS HIFEVQALDR YMNEQKDDEV AIRLKVCPIC QVPIRKNLRY GTSIKQRLEE IEIIKEKIQG SAGEIATSQE RLKALLERKS LLHQLLPEDF LMLKEKLAQK NLSVKDLGLV ENYISFYDHL ASLWDSLKKM HVLEEKRVRT RLEQVHEWLA KKRLSFTSQE LSDLRSEIQR LTYLVNLLTR YKIAEKKVKD SIAVEVYSVQ NILEKTCKFT QEDEQLVQEK MEALKATLPC SGLGISEEER VQIVSAIGYP RGHWFKCRNG HIYVIGDCGG AMERGTCPDC KEVIGGTNHT LERSNQLASE MDGAQHAAWS DTANNLMNFE EIQGMM

UniProtKB: NFX1-type zinc finger-containing protein 1

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 9.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 10752
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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