8H93: Dimeric mouse SCMC core complex

Structure of dimeric mouse SCMC core complex. Determined by electron microscopy at 3.01 Å resolution. Released 10 Jan 2024.

Method: Electron microscopy
Resolution: 3.01 Å
Organism: Mus musculus
Chains: 6
Atoms: 22,191
Mol. weight: 406.98 kDa
Released: 10 Jan 2024

Explore 8H93 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8H93 contains 102 α-helices and 132 β-strands across 6 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: 43 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	98-108	11
α-helix	120-128	9
β-strand	140-145	6	1
α-helix	151-164	14
β-strand	174-178	5	1
α-helix	179-181	3
β-strand	187-188	2	2
α-helix	190-197	8
α-helix	201-207	7
β-strand	216-220	5	1
α-helix	223-228	6
β-strand	244-245	2	2
α-helix	246-254	9
β-strand	263-269	7	1
α-helix	273-279	7
β-strand	284-289	6	1
α-helix	293-303	11
α-helix	310-319	10
α-helix	321-327	7
α-helix	330-345	16
α-helix	357-372	16
α-helix	378-380	3
α-helix	381-400	20
β-strand	406	1	3
α-helix	407-412	6
α-helix	417-424	8
β-strand	430-432	3	3
β-strand	439-441	3	3
α-helix	445-461	17
α-helix	486-498	13
α-helix	501-511	11
α-helix	519-531	13
α-helix	539-551	13
α-helix	555-561	7
β-strand	567-571	5	4
α-helix	575-585	11
β-strand	593-597	5	4
α-helix	624-638	15
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	685-694	10
β-strand	700-704	5	4
α-helix	710-721	12
β-strand	729-733	5	4
α-helix	739-750	12
β-strand	757-761	5	4
α-helix	767-778	12
β-strand	786-790	5	4
α-helix	796-806	11
β-strand	814-818	5	4
α-helix	824-835	12
β-strand	843-847	5	4
α-helix	853-864	12
β-strand	871-875	5	4
α-helix	881-892	12
β-strand	900-903	4	4
α-helix	913-922	10
β-strand	928-931	4	4
α-helix	938-949	12
β-strand	957-961	5	4
α-helix	969-977	9
β-strand	985-989	5	4
α-helix	995-1006	12
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: 5 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	158-175	18
α-helix	251-253	3
β-strand	255	1	6
β-strand	259	1	6
α-helix	262-266	5
α-helix	270-272	3
β-strand	284-290	7	7
β-strand	296-300	5	8
β-strand	307-312	6	8
β-strand	315-320	6	8
β-strand	327-328	2	7
β-strand	333-336	4	8
β-strand	346-351	6	9
β-strand	358-362	5	9
β-strand	368-371	4	9
β-strand	380	1	9
β-strand	391-396	6	10
β-strand	401-406	6	10
β-strand	410-415	6	10
β-strand	420-426	7	10
β-strand	434-438	5	11
β-strand	441-445	5	11
β-strand	451-455	5	11
β-strand	460-465	6	11
β-strand	471-475	5	12
β-strand	483-487	5	12
β-strand	491-495	5	12
β-strand	503-508	6	12
α-helix	512	1
β-strand	513-518	6	13
β-strand	524-529	6	13
β-strand	533-538	6	13
β-strand	544-549	6	13
β-strand	565-569	5	7
β-strand	574-579	6	7

Chain C: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	28-32	5	1
α-helix	38-41	4
β-strand	45-50	6	14
α-helix	51-58	8
α-helix	63-72	10
β-strand	75-79	5	14
β-strand	86-92	7	14
α-helix	95-113	19

Chain D: 42 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	98-108	11
α-helix	120-128	9
β-strand	140-145	6	15
α-helix	151-164	14
β-strand	176-178	3	15
β-strand	187	1	16
α-helix	190-197	8
α-helix	202-210	9
β-strand	218-220	3	15
α-helix	223-228	6
β-strand	245	1	16
α-helix	246-254	9
β-strand	264-269	6	15
α-helix	270-272	3
α-helix	273-279	7
β-strand	284-289	6	15
α-helix	293-303	11
α-helix	310-319	10
α-helix	321-327	7
α-helix	330-345	16
α-helix	357-372	16
α-helix	378-380	3
α-helix	381-399	19
α-helix	407-412	6
α-helix	417-424	8
β-strand	431	1	17
β-strand	440	1	17
α-helix	445-458	14
α-helix	459-461	3
α-helix	489-497	9
α-helix	501-511	11
α-helix	519-531	13
α-helix	539-551	13
α-helix	555-561	7
β-strand	567-572	6	18
α-helix	575-585	11
β-strand	593-598	6	18
α-helix	624-638	15
β-strand	644-645	2	19
β-strand	646	1	18
β-strand	651	1	20
α-helix	654-664	11
β-strand	673-675	3	19
β-strand	680	1	20
α-helix	685-694	10
β-strand	700-704	5	19
α-helix	710-721	12
β-strand	729-733	5	19
α-helix	741-750	10
β-strand	757-761	5	19
α-helix	767-778	12
β-strand	786-788	3	19
α-helix	796-806	11
β-strand	814-817	4	19
α-helix	824-835	12
β-strand	843-846	4	19
α-helix	854-864	11
β-strand	871-874	4	19
α-helix	881-891	11
β-strand	900-903	4	19
α-helix	911-922	12
β-strand	928-931	4	19
α-helix	937-950	14
β-strand	957-961	5	19
α-helix	970-978	9
β-strand	985-989	5	19
α-helix	995-1005	11
β-strand	1014-1016	3	19
α-helix	1019-1021	3
α-helix	1024-1036	13
β-strand	1041-1042	2	19

Chain E: 4 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	158-173	16
α-helix	251-253	3
β-strand	255	1	21
β-strand	259	1	21
α-helix	264-266	3
β-strand	283-291	9	22
α-helix	295-296	2
β-strand	300	1	23
β-strand	307-312	6	23
β-strand	315-320	6	23
β-strand	327-328	2	22
β-strand	333-336	4	23
β-strand	346-351	6	24
β-strand	357-362	6	24
β-strand	367	1	25
β-strand	369-372	4	24
β-strand	380-382	3	24
β-strand	385	1	25
β-strand	395-396	2	26
β-strand	401-405	5	26
β-strand	410-415	6	26
β-strand	420-426	7	26
β-strand	432	1	27
β-strand	436-437	2	27
β-strand	441-445	5	27
β-strand	450-455	6	27
β-strand	460-466	7	27
β-strand	471-476	6	28
β-strand	482-487	6	28
β-strand	491-496	6	28
β-strand	504-508	5	28
β-strand	515-518	4	29
β-strand	524-528	5	29
β-strand	534-538	5	29
β-strand	544-548	5	29
β-strand	556	1	22
β-strand	559	1	22
β-strand	565-566	2	22
β-strand	569	1	22
β-strand	573-580	8	22

Chain F: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	28-32	5	15
α-helix	38-41	4
β-strand	47-50	4	30
α-helix	51-58	8
α-helix	62-72	11
β-strand	75-79	5	30
β-strand	86-92	7	30
α-helix	95-113	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NACHT, LRR and PYD domains-containing protein 5	A, D	protein	1059	Mus musculus	Q9R1M5 (AlphaFold model)
Transducin-like enhancer protein 6	B, E	protein	581	Mus musculus	Q9WVB3 (AlphaFold model)
Oocyte-expressed protein homolog	C, F	protein	164	Mus musculus	Q9CWE6 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>8H93_1 NACHT, LRR and PYD domains-containing protein 5 (chains A, D)
MGPPEKDSKAILKARGLEEEQKSESTMSPSENVSRAILKDSGSEEVEQASERKMTSPEND
SKSIQKDQGPEQEQTSETLQSKEEDEVTEADKDNGGDLQDYKAHVIAKFDTSVDLHYDSP
EMKLLSDAFKPYQKTFQPHTIILHGRPGVGKSALARSIVLGWAQGKLFQKMSFVIFFSVR
EIKWTEKSSLAQLIAKECPDSWDLVTKIMSQPERLLFVIDGLDDMDSVLQHDDMTLSRDW
KDEQPIYILMYSLLRKALLPQSFLIITTRNTGLEKLKSMVVSPLYILVEGLSASRRSQLV
LENISNESDRIQVFHSLIENHQLFDQCQAPSVCSLVCEALQLQKKLGKRCTLPCQTLTGL
YATLVFHQLTLKRPSQSALSQEEQITLVGLCMMAAEGVWTMRSVFYDDDLKNYSLKESEI
LALFHMNILLQVGHNSEQCYVFSHLSLQDFFAALYYVLEGLEEWNQHFCFIENQRSIMEV
KRTDDTRLLGMKRFLFGLMNKDILKTLEVLFEYPVIPTVEQKLQHWVSLIAQQVNGTSPM
DTLDAFYCLFESQDEEFVGGALKRFQEVWLLINQKMDLKVSSYCLKHCQNLKAIRVDIRD
LLSVDNTLELCPVVTVQETQCKPLLMEWWGNFCSVLGSLRNLKELDLGDSILSQRAMKIL
CLELRNQSCRIQKLTFKSAEVVSGLKHLWKLLFSNQNLKYLNLGNTPMKDDDMKLACEAL
KHPKCSVETLRLDSCELTIIGYEMISTLLISTTRLKCLSLAKNRVGVKSMISLGNALSSS
MCLLQKLILDNCGLTPASCHLLVSALFSNQNLTHLCLSNNSLGTEGVQQLCQFLRNPECA
LQRLILNHCNIVDDAYGFLAMRLANNTKLTHLSLTMNPVGDGAMKLLCEALKEPTCYLQE
LELVDCQLTQNCCEDLACMITTTKHLKSLDLGNNALGDKGVITLCEGLKQSSSSLRRLGL
GACKLTSNCCEALSLAISCNPHLNSLNLVKNDFSTSGMLKLCSAFQCPVSNLGIIGLWKQ
EYYARVRRQLEEVEFVKPHVVIDGDWYASDEDDRNWWKN

Sequence of entity 2 (B, E), FASTA

>8H93_2 Transducin-like enhancer protein 6 (chains B, E)
MTSHRQSSDTFGGILPSTLSSRYLSIVNQLPEEFSSVVSEMMVHLENIFSLAENFFQAIE
RFSRTPDLLERNKMSIGVGAEGDSWPCHVSHEAPMGSAQTTENSAKEEDKQVPESAALQH
PKFKSTPGPQLPTRRRFLSESDELQDPQPVWDAEPQFCQGFLIQGLWELFMDSRQKNQQE
HGGEDSSQESKDSGLCDFKPEPQPRHRNSLSDSADPFLIKSPSALLDYYQEDVSRPQPET
QESSGRADKFLKPLSWGSEVLESSCNQPSTALWQLERFTVPQALQKVRVLKHQELLLVVA
VSSFTRHVFTCSQSGIKVWNLVNQVAEDRDPESHLKCSVQDNKVYLRTCLLSSNSRTLFA
GGYNLPGVIVWDLAAPSLYEKCQLPCEGLSCQALANTKENMALAGFTDGTVRIWDLRTQE
IVRNLKGPTNSARNLVVKDDNIWTGGLDACLRCWDLRMAKVSLEHLFQSQIMSLAHSPTE
DWLLLGLANGQHCLFNSRKRDQVLTVDTKDNTILGLKFSPNGKWWASVGMGNFITVHSMP
TGAKLFQVPEVGPVRCFDMTENGRLIITGSRDCASVYHIKY

Sequence of entity 3 (C, F), FASTA

>8H93_3 Oocyte-expressed protein homolog (chains C, F)
MASHTADADAKPDSDSQKLLNVLPVSLRLRTRPWWFPIQEVSNPLVLYMEAWVAERVIGT
DQAEISEIEWMCQALLTVDSVNSGNLAEITIFGQPSAQTRMKNILLNMAAWHKENELQRA
VKVKEVEEFLKIRASSILSKLSKKGLKLAGFPLPLEGRETQMES

Primary citation

Structural basis of the subcortical maternal complex and its implications in reproductive disorders. Chi, P., Ou, G., Qin, D. et al. Nat Struct Mol Biol (2024) 31:115-124. DOI 10.1038/s41594-023-01153-x · 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
9L4J 3.0 Å, Structure of mouse SCMCcore complex contain ZBED3
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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