8P0V: Coiled-coil domain-containing protein 93

Structure of the human Commander complex coiled coils, DENND10 and partial Retriever subcomplex. Determined by electron microscopy at 6.5 Å resolution. Released 20 Mar 2024.

Method: Electron microscopy
Resolution: 6.5 Å
Organism: Homo sapiens
Chains: 5
Atoms: 9,072
Mol. weight: 314.97 kDa
Released: 20 Mar 2024

Explore 8P0V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8P0V contains 76 α-helices and 34 β-strands across 5 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 K: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	313-375	63
α-helix	380-423	44
α-helix	447-487	41
α-helix	491-550	60
α-helix	553-630	78

Chain L: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	2-15	14
α-helix	26-28	3
α-helix	31-45	15
α-helix	47-50	4
α-helix	57-58	2
α-helix	61-76	16
α-helix	86-89	4
α-helix	94-107	14
α-helix	322	1
α-helix	323-327	5
α-helix	328-391	64
α-helix	396-483	88
α-helix	487	1
α-helix	489	1
α-helix	490-547	58
α-helix	551-596	46
α-helix	599-626	28

Chain M: 19 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	2-11	10
β-strand	14-20	7	1
β-strand	26-28	3	1
β-strand	33	1	1
α-helix	37-46	10
α-helix	48-50	3
β-strand	59-64	6	1
β-strand	67-73	7	1
β-strand	87-93	7	1
α-helix	99-116	18
α-helix	119-132	14
β-strand	134-135	2	2
β-strand	143-144	2	2
α-helix	145-147	3
α-helix	150-155	6
α-helix	159-166	8
α-helix	169-178	10
β-strand	182-186	5	3
α-helix	190-202	13
α-helix	210-212	3
β-strand	214	1	3
α-helix	221-229	9
β-strand	233-237	5	3
α-helix	240-244	5
β-strand	251-254	4	3
β-strand	259-260	2	3
α-helix	266-269	4
α-helix	274-288	15
α-helix	294-315	22
β-strand	316-318	3	4
α-helix	319	1
β-strand	325-327	3	4
α-helix	329-334	6
α-helix	339-351	13

Chain N: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	5
α-helix	11-14	4
α-helix	20-25	6
β-strand	33-36	4	5
α-helix	43-52	10
β-strand	55-58	4	5
β-strand	72-77	6	6
β-strand	80-85	6	6
α-helix	87-89	3
α-helix	96-106	11
β-strand	110-112	3	6
β-strand	120-124	5	6
β-strand	127-131	5	6
β-strand	149-156	8	5
β-strand	159-168	10	5
β-strand	171-173	3	5
β-strand	175-176	2	7
β-strand	178-180	3	5

Chain O: 30 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
β-strand	8	1	8
α-helix	13-20	8
β-strand	21	1	6
α-helix	24	1
β-strand	25-26	2	7
α-helix	27-28	2
α-helix	461-474	14
α-helix	479-495	17
α-helix	499-516	18
α-helix	519-533	15
α-helix	538-541	4
α-helix	543-556	14
α-helix	560-565	6
α-helix	569-575	7
α-helix	579-596	18
α-helix	604-620	17
α-helix	627-643	17
α-helix	650-663	14
α-helix	668-689	22
α-helix	695-714	20
α-helix	718-734	17
α-helix	738-754	17
β-strand	759-761	3	9
β-strand	764-766	3	9
α-helix	768-784	17
α-helix	787-789	3
α-helix	796-807	12
α-helix	815-832	18
α-helix	846-850	5
α-helix	854-880	27
α-helix	884-901	18
β-strand	902	1	8
α-helix	907-923	17
α-helix	928-942	15
α-helix	948-956	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Coiled-coil domain-containing protein 93	K	protein	631	Homo sapiens	Q567U6 (AlphaFold model)
Coiled-coil domain-containing protein 22	L	protein	627	Homo sapiens	O60826 (AlphaFold model)
DENN domain-containing protein 10	M	protein	357	Homo sapiens	Q8TCE6 (AlphaFold model)
Vacuolar protein sorting-associated protein 29	N	protein	182	Homo sapiens	Q9UBQ0 (AlphaFold model)
VPS35 endosomal protein-sorting factor-like	O	protein	963	Homo sapiens	Q7Z3J2

Sequence of entity 1 (K), FASTA

>8P0V_1 Coiled-coil domain-containing protein 93 (chains K)
MGLPRGPEGQGLPEVETREDEEQNVKLTEILELLVAAGYFRARIKGLSPFDKVVGGMTWC
ITTCNFDVDVDLLFQENSTIGQKIALSEKIVSVLPRMKCPHQLEPHQIQGMDFIHIFPVV
QWLVKRAIETKEEMGDYIRSYSVSQFQKTYSLPEDDDFIKRKEKAIKTVVDLSEVYKPRR
KYKRHQGAEELLDEESRIHATLLEYGRRYGFSRQSKMEKAEDKKTALPAGLSATEKADAH
EEDELRAAEEQRIQSLMTKMTAMANEESRLTASSVGQIVGLCSAEIKQIVSEYAEKQSEL
SAEESPEKLGTSQLHRRKVISLNKQIAQKTKHLEELRASHTSLQARYNEAKKTLTELKTY
SEKLDKEQAALEKIESKADPSILQNLRALVAMNENLKSQEQEFKAHCREEMTRLQQEIEN
LKAERAPRGDEKTLSSGEPPGTLTSAMTHDEDLDRRYNMEKEKLYKIRLLQARRNREIAI
LHRKIDEVPSRAELIQYQKRFIELYRQISAVHKETKQFFTLYNTLDDKKVYLEKEISLLN
SIHENFSQAMASPAARDQFLRQMEQIVEGIKQSRMKMEKKKQENKMRRDQLNDQYLELLE
KQRLYFKTVKEFKEEGRKNEMLLSKVKAKAS

Sequence of entity 2 (L), FASTA

>8P0V_2 Coiled-coil domain-containing protein 22 (chains L)
MEEADRILIHSLRQAGTAVPPDVQTLRAFTTELVVEAVVRCLRVINPAVGSGLSPLLPLA
MSARFRLAMSLAQACMDLGYPLELGYQNFLYPSEPDLRDLLLFLAERLPTDASEDADQPA
GDSAILLRAIGSQIRDQLALPWVPPHLRTPKLQHLQGSALQKPFHASRLVVPELSSRGEP
REFQASPLLLPVPTQVPQPVGRVASLLEHHALQLCQQTGRDRPGDEDWVHRTSRLPPQED
TRAQRQRLQKQLTEHLRQSWGLLGAPIQARDLGELLQAWGAGAKTGAPKGSRFTHSEKFT
FHLEPQAQATQVSDVPATSRRPEQVTWAAQEQELESLREQLEGVNRSIEEVEADMKTLGV
SFVQAESECRHSKLSTAEREQALRLKSRAVELLPDGTANLAKLQLVVENSAQRVIHLAGQ
WEKHRVPLLAEYRHLRKLQDCRELESSRRLAEIQELHQSVRAAAEEARRKEEVYKQLMSE
LETLPRDVSRLAYTQRILEIVGNIRKQKEEITKILSDTKELQKEINSLSGKLDRTFAVTD
ELVFKDAKKDDAVRKAYKYLAALHENCSQLIQTIEDTGTIMREVRDLEEQIETELGKKTL
SNLEKIREDYRALRQENAGLLGRVREA

Sequence of entity 3 (M), FASTA

>8P0V_3 DENN domain-containing protein 10 (chains M)
MAAAEVADTQLMLGVGLIEKDTNGEVLWVWCYPSTTATLRNLLLRKCCLTDENKLLHPFV
FGQYRRTWFYITTIEVPDSSILKKVTHFSIVLTAKDFNPEKYAAFTRILCRMYLKHGSPV
KMMESYIAVLTKGICQSEENGSFLSKDFDARKAYLAGSIKDIVSQFGMETVILHTALMLK
KRIVVYHPKIEAVQEFTRTLPALVWHRQDWTILHSYVHLNADELEALQMCTGYVAGFVDL
EVSNRPDLYDVFVNLAESEITIAPLAKEAMAMGKLHKEMGQLIVQSAEDPEKSESHVIQD
IALKTREIFTNLAPFSEVSADGEKRVLNLEALKQKRFPPATENFLYHLAAAEQMLKI

Sequence of entity 4 (N), FASTA

>8P0V_4 Vacuolar protein sorting-associated protein 29 (chains N)
MLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVR
GDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKFE
AFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYK
KP

Sequence of entity 5 (O), FASTA

>8P0V_5 VPS35 endosomal protein-sorting factor-like (chains O)
MAVFPWHSRNRNYKAEFASCRLEAVPLEFGDYHPLKPITVTESKTKKVNRKGSTSSTSSS
SSSSVVDPLSSVLDGTDPLSMFAATADPAALAAAMDSSRRKRDRDDNSVVGSDFEPWTNK
RGEILARYTTTEKLSINLFMGSEKGKAGTATLAMSEKVRTRLEELDDFEEGSQKELLNLT
QQDYVNRIEELNQSLKDAWASDQKVKALKIVIQCSKLLSDTSVIQFYPSKFVLITDILDT
FGKLVYERIFSMCVDSRSVLPDHFSPENANDTAKETCLNWFFKIASIRELIPRFYVEASI
LKCNKFLSKTGISECLPRLTCMIRGIGDPLVSVYARAYLCRVGMEVAPHLKETLNKNFFD
FLLTFKQIHGDTVQNQLVVQGVELPSYLPLYPPAMDWIFQCISYHAPEALLTEMMERCKK
LGNNALLLNSVMSAFRAEFIATRSMDFIGMIKECDESGFPKHLLFRSLGLNLALADPPES
DRLQILNEAWKVITKLKNPQDYINCAEVWVEYTCKHFTKREVNTVLADVIKHMTPDRAFE
DSYPQLQLIIKKVIAHFHDFSVLFSVEKFLPFLDMFQKESVRVEVCKCIMDAFIKHQQEP
TKDPVILNALLHVCKTMHDSVNALTLEDEKRMLSYLINGFIKMVSFGRDFEQQLSFYVES
RSMFCNLEPVLVQLIHSVNRLAMETRKVMKGNHSRKTAAFVRACVAYCFITIPSLAGIFT
RLNLYLHSGQVALANQCLSQADAFFKAAISLVPEVPKMINIDGKMRPSESFLLEFLCNFF
STLLIVPDHPEHGVLFLVRELLNVIQDYTWEDNSDEKIRIYTCVLHLLSAMSQETYLYHI
DKVDSNDSLYGGDSKFLAENNKLCETVMAQILEHLKTLAKDEALKRQSSLGLSFFNSILA
HGDLRNNKLNQLSVNLWHLAQRHGCADTRTMVKTLEYIKKQSKQPDMTHLTELALRLPLQ
TRT

Primary citation

Structure and interactions of the endogenous human Commander complex. Laulumaa, S., Kumpula, E.P., Huiskonen, J.T. et al. Nat Struct Mol Biol (2024) 31:925-938. DOI 10.1038/s41594-024-01246-1 · PubMed

Other PDB entries of the same protein (UniProt Q567U6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8P0W 2.9 Å, Structure of the human Commander complex COMMD ring
8F2U 3.53 Å, Human CCC complex
8P0X 7.5 Å, Structure of the human Commander complex Retriever Subcomplex

Browse structure collections

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