9L4J: Mouse SCMCcore complex contain ZBED3

Structure of mouse SCMCcore complex contain ZBED3. Determined by electron microscopy at 3.0 Å resolution. Released 1 Oct 2025.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Mus musculus
Chains: 4
Atoms: 11,293
Mol. weight: 174.07 kDa
Ligands: ZN
Released: 1 Oct 2025

Explore 9L4J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9L4J contains 62 α-helices and 70 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 49 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	98-109	12
α-helix	120-127	8
β-strand	140-145	6	1
α-helix	151-164	14
β-strand	173-178	6	1
β-strand	187-188	2	2
α-helix	190-197	8
α-helix	202-208	7
α-helix	212-214	3
β-strand	215-220	6	1
α-helix	222-227	6
β-strand	244-245	2	2
α-helix	246-254	9
β-strand	263-269	7	1
α-helix	273-276	4
β-strand	284-289	6	1
α-helix	293-301	9
α-helix	310-318	9
α-helix	321-326	6
α-helix	330-345	16
α-helix	347-349	3
α-helix	357-369	13
α-helix	374	1
α-helix	381-399	19
β-strand	405-406	2	3
α-helix	407-412	6
α-helix	417-423	7
β-strand	429-432	4	3
β-strand	439-442	4	3
α-helix	445-453	9
α-helix	455-458	4
α-helix	464-466	3
α-helix	489-497	9
α-helix	501-511	11
α-helix	519-531	13
α-helix	539-552	14
α-helix	555-561	7
β-strand	567-571	5	4
α-helix	576-585	10
β-strand	593-597	5	4
α-helix	624-636	13
β-strand	644-646	3	4
β-strand	651	1	5
α-helix	654-664	11
β-strand	673-675	3	4
β-strand	680	1	5
α-helix	682-684	3
α-helix	686-694	9
β-strand	700-702	3	4
α-helix	710-721	12
β-strand	729-731	3	4
α-helix	739-750	12
β-strand	757-759	3	4
α-helix	767-777	11
β-strand	786-788	3	4
α-helix	796-805	10
α-helix	806-808	3
β-strand	814-816	3	4
α-helix	823-835	13
β-strand	843-845	3	4
α-helix	855-863	9
β-strand	871-873	3	4
α-helix	880-891	12
β-strand	900-902	3	4
α-helix	910-912	3
α-helix	913-922	10
β-strand	928-930	3	4
α-helix	937-944	8
β-strand	957-959	3	4
α-helix	967-969	3
α-helix	970-979	10
β-strand	985-987	3	4
α-helix	995-1005	11
β-strand	1014-1016	3	4
α-helix	1019-1021	3
α-helix	1024-1036	13
β-strand	1041-1042	2	4
α-helix	1046-1048	3

Chain B: 4 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	158-173	16
α-helix	251-253	3
β-strand	255	1	6
β-strand	259	1	6
α-helix	264-266	3
β-strand	283-290	8	7
β-strand	298-302	5	8
β-strand	307-311	5	8
β-strand	315-320	6	8
β-strand	328	1	7
β-strand	333-336	4	8
β-strand	348-351	4	9
β-strand	357-361	5	9
β-strand	363	1	10
β-strand	367-372	6	9
β-strand	380-385	6	9
β-strand	390	1	10
β-strand	391-396	6	11
β-strand	401-406	6	11
β-strand	412-415	4	11
β-strand	421-424	4	11
β-strand	434-438	5	12
β-strand	441-445	5	12
β-strand	450-455	6	12
β-strand	461-466	6	12
β-strand	471-476	6	13
β-strand	482-487	6	13
β-strand	492-496	5	13
β-strand	503-506	4	13
α-helix	507-509	3
β-strand	513-518	6	14
β-strand	524-529	6	14
β-strand	533-538	6	14
β-strand	543-549	7	14
β-strand	554-559	6	7
β-strand	565-570	6	7
β-strand	573-580	8	7

Chain D: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	28-32	5	1
α-helix	38-40	3
β-strand	45-50	6	15
α-helix	51-58	8
α-helix	64-72	9
β-strand	76-77	2	15
β-strand	80-81	2	15
β-strand	86-91	6	15
α-helix	95-113	19

Chain E: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	36-39	4
β-strand	42-43	2	16
α-helix	48-49	2
α-helix	52-54	3
β-strand	57-60	4	16
β-strand	66-68	3	16
α-helix	73-83	11
α-helix	84-88	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform 4 of NACHT, LRR and PYD domains-containing protein 5	A	protein	963	Mus musculus	Q9R1M5 (AlphaFold model)
Transducin-like enhancer protein 6	B	protein	427	Mus musculus	Q9WVB3 (AlphaFold model)
Oocyte-expressed protein homolog	D	protein	89	Mus musculus	Q9CWE6 (AlphaFold model)
Zinc finger BED domain-containing protein 3	E	protein	56	Mus musculus	Q9D0L1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9L4J_1 Isoform 4 of NACHT, LRR and PYD domains-containing protein 5 (chains A)
DLQDYKAHVIAKFDTSVDLHYDSPEMKLLSDAFKPYQKTFQPHTIILHGRPGVGKSALAR
SIVLGWAQGKLFQKMSFVIFFSVREIKWTEKSSLAQLIAKECPDSWDLVTKIMSQPERLL
FVIDGLDDMDSVLQHDDMTLSRDWKDEQPIYILMYSLLRKALLPQSFLIITTRNTGLEKL
KSMVVSPLYILVEGLSASRRSQLVLENISNESDRIQVFHSLIENHQLFDQCQAPSVCSLV
CEALQLQKKLGKRCTLPCQTLTGLYATLVFHQLTLKRPSQSALSQEEQITLVGLCMMAAE
GVWTMRSVFYDDDLKNYSLKESEILALFHMNILLQVGHNSEQCYVFSHLSLQDFFAALYY
VLEGLEEWNQHFCFIENQRSIMEVKRTDDTRLLGMKRFLFGLMNKDILKTLEVLFEYPVI
PTVEQKLQHWVSLIAQQVNGTSPMDTLDAFYCLFESQDEEFVGGALKRFQEVWLLINQKM
DLKVSSYCLKHCQNLKAIRVDIRDLLSVDNTLELCPVVTVQETQCKPLLMEWWGNFCSVL
GSLRNLKELDLGDSILSQRAMKILCLELRNQSCRIQKLTFKSAEVVSGLKHLWKLLFSNQ
NLKYLNLGNTPMKDDDMKLACEALKHPKCSVETLRLDSCELTIIGYEMISTLLISTTRLK
CLSLAKNRVGVKSMISLGNALSSSMCLLQKLILDNCGLTPASCHLLVSALFSNQNLTHLC
LSNNSLGTEGVQQLCQFLRNPECALQRLILNHCNIVDDAYGFLAMRLANNTKLTHLSLTM
NPVGDGAMKLLCEALKEPTCYLQELELVDCQLTQNCCEDLACMITTTKHLKSLDLGNNAL
GDKGVITLCEGLKQSSSSLRRLGLGACKLTSNCCEALSLAISCNPHLNSLNLVKNDFSTS
GMLKLCSAFQCPVSNLGIIGLWKQEYYARVRRQLEEVEFVKPHVVIDGDWYASDEDDRNW
WKN

Sequence of entity 2 (B), FASTA

>9L4J_2 Transducin-like enhancer protein 6 (chains B)
PQFCQGFLIQGLWELFMDSRQKNQQEHGGEDSSQESKDSGLCDFKPEPQPRHRNSLSDSA
DPFLIKSPSALLDYYQEDVSRPQPETQESSGRADKFLKPLSWGSEVLESSCNQPSTALWQ
LERFTVPQALQKVRVLKHQELLLVVAVSSFTRHVFTCSQSGIKVWNLVNQVAEDRDPESH
LKCSVQDNKVYLRTCLLSSNSRTLFAGGYNLPGVIVWDLAAPSLYEKCQLPCEGLSCQAL
ANTKENMALAGFTDGTVRIWDLRTQEIVRNLKGPTNSARNLVVKDDNIWTGGLDACLRCW
DLRMAKVSLEHLFQSQIMSLAHSPTEDWLLLGLANGQHCLFNSRKRDQVLTVDTKDNTIL
GLKFSPNGKWWASVGMGNFITVHSMPTGAKLFQVPEVGPVRCFDMTENGRLIITGSRDCA
SVYHIKY

Sequence of entity 3 (D), FASTA

>9L4J_3 Oocyte-expressed protein homolog (chains D)
SLRLRTRPWWFPIQEVSNPLVLYMEAWVAERVIGTDQAEISEIEWMCQALLTVDSVNSGN
LAEITIFGQPSAQTRMKNILLNMAAWHKE

Sequence of entity 4 (E), FASTA

>9L4J_4 Zinc finger BED domain-containing protein 3 (chains E)
SYSEAWGYFHLDPAQPRHRMMSAWATCRLCGLQVGGLPNFQMWTRALCQHLSDVHL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

Primary citation

Structural assembly of the subcortical maternal complex SCMC. Ou, G., Liu, Q., Jiao, H. et al. Structure (2026) 34:20-31.e7. DOI 10.1016/j.str.2025.09.009 · PubMed

Other PDB entries of the same protein (UniProt Q9R1M5 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8H96 2.78 Å, Structure of mouse SCMC core complex
8H94 2.9 Å, Structure of mouse SCMC bound with KH domain of FILIA
8XI3 3.0 Å, Structure of mouse SCMC-14-3-3gama complex
8H93 3.01 Å, Structure of dimeric mouse SCMC core complex
8H95 3.38 Å, Structure of mouse SCMC bound with full-length FILIA
24MC 3.4 Å, Structure of oocyte cytoplasmic lattices
12DL 3.5 Å, Native structure of the cytoplasmic lattice (CPL) asymmetric unit from mouse MII eggs
9XRL 3.74 Å, Structure of mouse cytoplasmic lattice (CPL) repeating unit
9SFP 4.2 Å, Native cytoplasmic lattices from mouse oocytes
9W2M 4.2 Å, Cryo-EM structure of the Cytoplasmic lattice(CPL) from mouse oocyte
9T63 4.7 Å, Asymmetric unit of a cytoplasmic lattice filament repeat unit
9T66 5.3 Å, Complex linking two repeat units of a cytoplasmic lattice filament

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