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- EMDB-63452: Cryo-EM structure of the cytosolic ARMH2-EFCAB9-CATSPERz subcompl... -

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Basic information

Entry
Database: EMDB / ID: EMD-63452
TitleCryo-EM structure of the cytosolic ARMH2-EFCAB9-CATSPERz subcomplex of the mouse CatSpermasome
Map data
Sample
  • Complex: ARMH2-EFCAB9-CATSPERZ complex
    • Protein or peptide: EF-hand calcium-binding domain-containing protein 9
    • Protein or peptide: Armadillo-like helical domain containing 2
    • Protein or peptide: Cation channel sperm-associated auxiliary subunit zeta
KeywordsCatSper / sperm motility / male fertility / channel / ARMH2 / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


CatSper complex / calcium ion sensor activity / male meiotic nuclear division / flagellated sperm motility / sperm capacitation / sperm principal piece / spermatogenesis / calmodulin binding / calcium ion binding / cytoplasm
Similarity search - Function
Armadillo-like helical domain-containing protein 2 / Armadillo-like helical domain-containing protein 2 / Cation channel sperm-associated auxiliary subunit zeta / EF-hand calcium-binding domain-containing protein 9 / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Armadillo-like helical domain containing 2 / Cation channel sperm-associated auxiliary subunit zeta / EF-hand calcium-binding domain-containing protein 9
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.77 Å
AuthorsZhao Q / Lin S / Xu Q / Wu J
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32271261 China
CitationJournal: Nat Commun / Year: 2025
Title: ARMH2 is a cytosolic component of CatSper crucial for sperm function.
Authors: Qingqing Zhao / Shiyi Lin / Hang Kang / Yanfei Ru / Qikui Xu / Zijing Yu / Xiaofang Huang / Carlo De Rito / Giulia Sassi / Shaojie Wang / Shuya Sun / Rui Sun / Honghan Cheng / Yi Zhu / ...Authors: Qingqing Zhao / Shiyi Lin / Hang Kang / Yanfei Ru / Qikui Xu / Zijing Yu / Xiaofang Huang / Carlo De Rito / Giulia Sassi / Shaojie Wang / Shuya Sun / Rui Sun / Honghan Cheng / Yi Zhu / Mingxi Liu / Yongdeng Zhang / Min Jiang / Riccardo Percudani / Jean-Ju Chung / Xuhui Zeng / Zhen Yan / Jianping Wu /
Abstract: Sperm capacitation and fertilization are highly regulated by Ca signaling. CatSper, a sperm-specific calcium channel, plays a crucial role in sperm hyperactivated motility and fertility by mediating ...Sperm capacitation and fertilization are highly regulated by Ca signaling. CatSper, a sperm-specific calcium channel, plays a crucial role in sperm hyperactivated motility and fertility by mediating Ca influx into sperm. CatSper is the most complicated ion channel known, comprising the pore-forming CATSPER1-4 and multiple auxiliary subunits. However, our previous structural study of mouse CatSper suggests the presence of potential component(s) that remain to be identified. The identity and functional significance of the missing piece(s) of CatSper remain elusive. Here, by combining cryo-EM, mass spectrometry, AlphaFold structure prediction, and coevolutionary analysis, we identify armadillo-like helical domain containing 2 (ARMH2) as a cytosolic component of CatSper. ARMH2 forms a cytosolic ternary subcomplex with EFCAB9 and CATSPERζ, which contributes to the stable assembly of the linear arrangement of CatSper nanodomains along the sperm tail and regulates the pH and Ca sensitivity of the channel. Loss of ARMH2 leads to compromised physiological activation of CatSper, thereby resulting in asthenozoospermia and severe subfertility. These findings show that ARMH2 is crucial for sperm function and provide fresh insights into the composition and functional regulation of CatSper. The integrated methodology employed in identifying ARMH2 also provides valuable approaches for discovering uncharacterized components in other protein complexes.
History
DepositionFeb 15, 2025-
Header (metadata) releaseDec 31, 2025-
Map releaseDec 31, 2025-
UpdateDec 31, 2025-
Current statusDec 31, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63452.png

Downloads & links

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Map

FileDownload / File: emd_63452.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 384 pix.
= 417.408 Å		1.09 Å/pix.
x 384 pix.
= 417.408 Å		1.09 Å/pix.
x 384 pix.
= 417.408 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.087 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.422
Minimum - Maximum-1.7276806 - 2.0131574
Average (Standard dev.)-0.00028750347 (±0.019704005)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 417.40802 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63452_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63452_half_map_2.map
Projections & Slices
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Sample components

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Entire : ARMH2-EFCAB9-CATSPERZ complex

EntireName: ARMH2-EFCAB9-CATSPERZ complex
Components
  • Complex: ARMH2-EFCAB9-CATSPERZ complex
    • Protein or peptide: EF-hand calcium-binding domain-containing protein 9
    • Protein or peptide: Armadillo-like helical domain containing 2
    • Protein or peptide: Cation channel sperm-associated auxiliary subunit zeta

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Supramolecule #1: ARMH2-EFCAB9-CATSPERZ complex

SupramoleculeName: ARMH2-EFCAB9-CATSPERZ complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: EF-hand calcium-binding domain-containing protein 9

MacromoleculeName: EF-hand calcium-binding domain-containing protein 9 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.170482 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: MKLTPGCFLW YLYMDKIYCL LSLRNVKALM VYFHLLDVHH RNTLNDVLFF HFLQHVTNLN KSQIGMIFDL LDWTAVGEIG FDQFYVLIC ILLAHQDHLE DHFMYRHSRP VFELLDLDGE MNIGAANFQN YRFLFNIKKQ ELRDLFHDFD ITGDRLLNYK E FKLYTIFC ...String:
MKLTPGCFLW YLYMDKIYCL LSLRNVKALM VYFHLLDVHH RNTLNDVLFF HFLQHVTNLN KSQIGMIFDL LDWTAVGEIG FDQFYVLIC ILLAHQDHLE DHFMYRHSRP VFELLDLDGE MNIGAANFQN YRFLFNIKKQ ELRDLFHDFD ITGDRLLNYK E FKLYTIFC TDKSIDRKKR RKDREAARER EKEKGKDKEK YLHLKKIYSS MLSHRSIL

UniProtKB: EF-hand calcium-binding domain-containing protein 9

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Macromolecule #2: Armadillo-like helical domain containing 2

MacromoleculeName: Armadillo-like helical domain containing 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.780201 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: MSYENWGICG RICSICSQTC QLFRTLSESL RSFWDNKVKR RFFASPQKEE VPTSTADYIF HREKILELGS ILKNKRLSLD KRAQAAQKI GLLSFTGGMS AAQFASEYMT EVAFLLQKKK AMSFRTKILL LQSVACWCYL NPDSQRKVRQ LEIIPTLIDF L EESFQSSN ...String:
MSYENWGICG RICSICSQTC QLFRTLSESL RSFWDNKVKR RFFASPQKEE VPTSTADYIF HREKILELGS ILKNKRLSLD KRAQAAQKI GLLSFTGGMS AAQFASEYMT EVAFLLQKKK AMSFRTKILL LQSVACWCYL NPDSQRKVRQ LEIIPTLIDF L EESFQSSN KTEINTHRLC QFWVCYALTV ITCNNLAIMR ELRSYRSLKF HLQLVATENW SGWPENFAEV LYFLIGFHRN

UniProtKB: Armadillo-like helical domain containing 2

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Macromolecule #3: Cation channel sperm-associated auxiliary subunit zeta

MacromoleculeName: Cation channel sperm-associated auxiliary subunit zeta
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 22.776598 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: MEESVKPVPK HANHRRSSVR SSLYGDVRDL WSTATMSTAN VSVSDVCEDF DEEGKSVRNR IRKYSQTISI RDSLNLEPEE IQQQARREL ELCHGRSLEH GEDHEESETS LASSTSESLI FSLWKPHRTY WTEQQNRLPL PLMELMETEV LDILKKALIT Y RSTIGRNH ...String:
MEESVKPVPK HANHRRSSVR SSLYGDVRDL WSTATMSTAN VSVSDVCEDF DEEGKSVRNR IRKYSQTISI RDSLNLEPEE IQQQARREL ELCHGRSLEH GEDHEESETS LASSTSESLI FSLWKPHRTY WTEQQNRLPL PLMELMETEV LDILKKALIT Y RSTIGRNH FMTKELQGYI EGIRKRRNKR LYFLDQ

UniProtKB: Cation channel sperm-associated auxiliary subunit zeta

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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: 7.4
VitrificationCryogen name: ETHANE

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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: 2.0 µm / Nominal defocus min: 1.5 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83920
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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