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- PDB-7eeb: Structure of the CatSpermasome -

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Entry
Database: PDB / ID: 7eeb
TitleStructure of the CatSpermasome
Components
  • (Cation channel sperm-associated protein ...) x 8
  • (Transmembrane protein ...) x 2
  • EF-hand calcium-binding domain-containing protein 9
  • Enhanced green fluorescent protein,Cation channel sperm-associated protein 1
  • Kazal-like domain-containing protein
  • Unknown
KeywordsPROTEIN TRANSPORT / ion channel / membrane protein / calcium channel / protein complex
Function / homology
Function and homology information


CatSper complex / Sperm Motility And Taxes / sodium-independent organic anion transport / sperm principal piece / sodium-independent organic anion transmembrane transporter activity / fusion of sperm to egg plasma membrane involved in single fertilization / regulation of cilium beat frequency involved in ciliary motility / calcium ion sensor activity / flagellated sperm motility / male meiotic nuclear division ...CatSper complex / Sperm Motility And Taxes / sodium-independent organic anion transport / sperm principal piece / sodium-independent organic anion transmembrane transporter activity / fusion of sperm to egg plasma membrane involved in single fertilization / regulation of cilium beat frequency involved in ciliary motility / calcium ion sensor activity / flagellated sperm motility / male meiotic nuclear division / organic anion transport / organic anion transmembrane transporter activity / calcium-activated cation channel activity / fertilization / motile cilium / sperm capacitation / monoatomic ion channel complex / sodium ion transport / regulation of calcium ion transport / sperm flagellum / voltage-gated calcium channel activity / bioluminescence / acrosomal vesicle / generation of precursor metabolites and energy / establishment of localization in cell / cilium / calcium ion transport / spermatogenesis / basolateral plasma membrane / cell differentiation / calmodulin binding / calcium ion binding / endoplasmic reticulum / plasma membrane / cytoplasm
Similarity search - Function
Cation channel sperm-associated auxiliary subunit TMEM249 / Cation channel sperm-associated auxiliary subunit gamma / Cation channel sperm-associated protein 4 / Cation channel sperm-associated protein 1 / Cation channel sperm-associated protein 2 / Cation channel sperm-associated auxiliary subunit beta / Cation channel sperm-associated auxiliary subunit delta/epsilon / Cation channel sperm-associated auxiliary subunit zeta / Cation channel sperm-associated auxiliary subunit TMEM262 / EF-hand calcium-binding domain-containing protein 9 ...Cation channel sperm-associated auxiliary subunit TMEM249 / Cation channel sperm-associated auxiliary subunit gamma / Cation channel sperm-associated protein 4 / Cation channel sperm-associated protein 1 / Cation channel sperm-associated protein 2 / Cation channel sperm-associated auxiliary subunit beta / Cation channel sperm-associated auxiliary subunit delta/epsilon / Cation channel sperm-associated auxiliary subunit zeta / Cation channel sperm-associated auxiliary subunit TMEM262 / EF-hand calcium-binding domain-containing protein 9 / : / : / : / : / : / : / : / : / : / : / : / : / : / : / : / CATSPERD, beta-propeller domain / CATSPERG beta-propeller domain / CATSPERB, C-terminal domain / Cation channel sperm-associated auxiliary subunit TMEM249 / CATSPER protein subunit beta protein 1st domain / CATSPER subunit beta protein 2nd domain / CATSPERB head domain / CATSPERB Ig-like domain / CATSPERG N-terminal domain / CATSPERE first N-terminal domain / CATSPERE second N-terminal domain / CATSPERE beta-propeller domain / CATSPERG C-terminal domain / CATSPERE Ig-like domain / CATSPERD/E C-terminal domain / CATSPERG Ig-like domain / Organic anion transporter polypeptide / Organic Anion Transporter Polypeptide (OATP) family / Kazal-type serine protease inhibitor domain / Kazal domain superfamily / Kazal domain / Kazal domain profile. / MFS transporter superfamily / Voltage-dependent channel domain superfamily / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / EF-hand calcium-binding domain profile. / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair
Similarity search - Domain/homology
Cation channel sperm-associated auxiliary subunit TMEM249 / Cation channel sperm-associated protein 2 / Cation channel sperm-associated auxiliary subunit beta / Enhanced green fluorescent protein / Cation channel sperm-associated auxiliary subunit gamma 2 / Cation channel sperm-associated auxiliary subunit TMEM262 / Cation channel sperm-associated auxiliary subunit delta / Cation channel sperm-associated auxiliary subunit epsilon / Solute carrier organic anion transporter family member 6C1 / Cation channel sperm-associated protein 3 ...Cation channel sperm-associated auxiliary subunit TMEM249 / Cation channel sperm-associated protein 2 / Cation channel sperm-associated auxiliary subunit beta / Enhanced green fluorescent protein / Cation channel sperm-associated auxiliary subunit gamma 2 / Cation channel sperm-associated auxiliary subunit TMEM262 / Cation channel sperm-associated auxiliary subunit delta / Cation channel sperm-associated auxiliary subunit epsilon / Solute carrier organic anion transporter family member 6C1 / Cation channel sperm-associated protein 3 / Cation channel sperm-associated protein 4 / Cation channel sperm-associated protein 1 / Cation channel sperm-associated auxiliary subunit zeta / EF-hand calcium-binding domain-containing protein 9
Similarity search - Component
Biological speciesHuman cytomegalovirus
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsWu, J.P. / Ke, M.
CitationJournal: Nature / Year: 2021
Title: Structure of a mammalian sperm cation channel complex.
Authors: Shiyi Lin / Meng Ke / Yuqi Zhang / Zhen Yan / Jianping Wu /
Abstract: The cation channel of sperm (CatSper) is essential for sperm motility and fertility. CatSper comprises the pore-forming proteins CATSPER1-4 and multiple auxiliary subunits, including CATSPERβ, γ, ...The cation channel of sperm (CatSper) is essential for sperm motility and fertility. CatSper comprises the pore-forming proteins CATSPER1-4 and multiple auxiliary subunits, including CATSPERβ, γ, δ, ε, ζ, and EFCAB9. Here we report the cryo-electron microscopy (cryo-EM) structure of the CatSper complex isolated from mouse sperm. In the extracellular view, CATSPER1-4 conform to the conventional domain-swapped voltage-gated ion channel fold, following a counterclockwise arrangement. The auxiliary subunits CATSPERβ, γ, δ and ε-each of which contains a single transmembrane segment and a large extracellular domain-constitute a pavilion-like structure that stabilizes the entire complex through interactions with CATSPER4, 1, 3 and 2, respectively. Our EM map reveals several previously uncharacterized components, exemplified by the organic anion transporter SLCO6C1. We name this channel-transporter ultracomplex the CatSpermasome. The assembly and organization details of the CatSpermasome presented here lay the foundation for the development of CatSpermasome-related treatments for male infertility and non-hormonal contraceptives.
History
DepositionMar 18, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

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Assembly

Deposited unit
A: Enhanced green fluorescent protein,Cation channel sperm-associated protein 1
B: Cation channel sperm-associated protein 2
C: Cation channel sperm-associated protein 3
D: Cation channel sperm-associated protein 4
E: Cation channel sperm-associated protein subunit beta
F: Cation channel sperm-associated protein subunit gamma 2
G: Cation channel sperm-associated protein subunit delta
H: Cation channel sperm-associated protein subunit epsilon
L: Kazal-like domain-containing protein
J: Transmembrane protein 249
M: Transmembrane protein 262
N: Unknown
I: EF-hand calcium-binding domain-containing protein 9
K: Cation channel sperm-associated protein subunit zeta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)915,38444
Polymers901,51714
Non-polymers13,86730
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 3 types, 3 molecules ALI

#1: Protein Enhanced green fluorescent protein,Cation channel sperm-associated protein 1 / CatSper1


Mass: 109442.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human cytomegalovirus, (gene. exp.) Mus musculus (house mouse)
Gene: egfp, Catsper1 / Production host: Mus musculus (house mouse) / References: UniProt: C5MKY7, UniProt: Q91ZR5
#9: Protein Kazal-like domain-containing protein


Mass: 79055.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q3V161
#13: Protein EF-hand calcium-binding domain-containing protein 9


Mass: 26170.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9DAM2

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Cation channel sperm-associated protein ... , 8 types, 8 molecules BCDEFGHK

#2: Protein Cation channel sperm-associated protein 2 / CatSper2


Mass: 68651.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A2ARP9
#3: Protein Cation channel sperm-associated protein 3 / CatSper3


Mass: 45533.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q80W99
#4: Protein Cation channel sperm-associated protein 4 / CatSper4


Mass: 51179.273 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8BVN3
#5: Protein Cation channel sperm-associated protein subunit beta / CatSper-beta


Mass: 126250.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A2RTF1
#6: Protein Cation channel sperm-associated protein subunit gamma 2


Mass: 131550.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: C6KI89
#7: Protein Cation channel sperm-associated protein subunit delta / CatSper-delta / CatSperdelta / Transmembrane protein 146


Mass: 91186.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: E9Q9F6
#8: Protein Cation channel sperm-associated protein subunit epsilon / CatSper-epsilon / CatSperepsilon / C1orf101-like protein


Mass: 113913.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P0DP43
#14: Protein Cation channel sperm-associated protein subunit zeta / CatSper-zeta / CatSperzeta / Protein expressed in male leptotene and zygotene spermatocytes 622 / ...CatSper-zeta / CatSperzeta / Protein expressed in male leptotene and zygotene spermatocytes 622 / MLZ-622 / Testis-expressed protein 40


Mass: 22776.598 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q9CQP8

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Transmembrane protein ... , 2 types, 2 molecules JM

#10: Protein Transmembrane protein 249


Mass: 19918.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: A0A2R8VHF7
#11: Protein Transmembrane protein 262


Mass: 13489.028 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: D3Z338

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Protein/peptide , 1 types, 1 molecules N

#12: Protein/peptide Unknown


Mass: 2400.951 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Sugars , 6 types, 25 molecules

#15: Polysaccharide beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-3)-beta-D- ...beta-D-mannopyranose-(1-2)-beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-2DManpb1-3[DManpb1-3DManpb1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{[(2+1)][b-D-Manp]{}}[(6+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#16: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#17: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#18: Polysaccharide beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[DManpb1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#19: Polysaccharide beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-6)-[beta-D- ...beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3[DManpb1-6]DManpb1-6[DManpb1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{[(3+1)][b-D-Manp]{}[(6+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#22: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 5 molecules

#20: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Na
#21: Chemical ChemComp-9Z9 / (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en


Mass: 544.805 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H56O5 / Comment: detergent*YM

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: mouse CatSpermasome / Type: COMPLEX / Entity ID: #1-#14 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Homemade
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K / Details: blot for 8 s before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: cryoSPARC / Version: v3.0 / Category: CTF correction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 560730 / Symmetry type: POINT
RefinementHighest resolution: 2.9 Å

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