8P0X: Human Commander complex Retriever Subcomplex

Structure of the human Commander complex Retriever Subcomplex. Determined by electron microscopy at 7.5 Å resolution. Released 20 Mar 2024.

Method: Electron microscopy
Resolution: 7.5 Å
Organism: Homo sapiens
Chains: 5
Atoms: 9,322
Mol. weight: 307.46 kDa
Released: 20 Mar 2024

Explore 8P0X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8P0X contains 78 α-helices and 47 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: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	447-487	41
α-helix	491-548	58
α-helix	549-551	3
α-helix	553-630	78

Chain L: 13 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	86-90	5
α-helix	94-105	12
α-helix	443-483	41
α-helix	487-489	3
α-helix	490-549	60
α-helix	551-597	47
α-helix	599-626	28

Chain N: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	1
α-helix	20-25	6
β-strand	33-36	4	1
α-helix	43-52	10
β-strand	56-58	3	1
β-strand	73-77	5	2
β-strand	80-84	5	2
α-helix	87-89	3
α-helix	96-106	11
β-strand	110-112	3	2
β-strand	120-122	3	2
β-strand	128-131	4	2
β-strand	151-156	6	1
β-strand	159-167	9	1
β-strand	172-179	8	1

Chain O: 48 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	13-20	8
β-strand	21	1	2
α-helix	24	1
β-strand	25-26	2	1
α-helix	27	1
α-helix	117-127	11
β-strand	134-139	6	3
α-helix	154-170	17
β-strand	173-179	7	3
α-helix	181-200	20
α-helix	204-219	16
α-helix	227-253	27
α-helix	259-261	3
α-helix	266-268	3
α-helix	271-285	15
β-strand	289	1	4
α-helix	290-307	18
α-helix	309-323	15
β-strand	326	1	5
α-helix	329-346	18
α-helix	349-369	21
α-helix	371-380	10
α-helix	384-387	4
α-helix	388-390	3
α-helix	392-403	12
α-helix	408-420	13
α-helix	425-434	10
α-helix	437-453	17
α-helix	461-474	14
α-helix	479-495	17
α-helix	499-516	18
α-helix	519-532	14
α-helix	536-541	6
α-helix	543-556	14
α-helix	560-566	7
α-helix	569-575	7
α-helix	579-596	18
β-strand	601	1	6
α-helix	604-620	17
α-helix	627-643	17
β-strand	644	1	6
α-helix	650-663	14
α-helix	668-689	22
α-helix	695-714	20
α-helix	718-734	17
α-helix	738-751	14
β-strand	758-761	4	7
β-strand	764-767	4	7
α-helix	768-783	16
α-helix	796-807	12
α-helix	815-832	18
β-strand	840	1	8
β-strand	843	1	8
α-helix	846-850	5
α-helix	854-881	28
α-helix	884-901	18
α-helix	907-922	16
α-helix	928-942	15
α-helix	947-956	10

Chain P: 9 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	9
β-strand	15-17	3	10
α-helix	20-22	3
β-strand	24-29	6	9
β-strand	34-49	16	11
α-helix	53-56	4
α-helix	58-64	7
β-strand	69-79	11	11
β-strand	82-84	3	11
β-strand	89-93	5	9
α-helix	106-108	3
β-strand	109	1	11
β-strand	114-126	13	11
α-helix	131-132	2
β-strand	133-139	7	11
β-strand	140-142	3	10
α-helix	143-146	4
β-strand	155-159	5	12
α-helix	161-163	3
α-helix	174-175	2
β-strand	176-182	7	12
β-strand	186-188	3	13
β-strand	192-202	11	12
β-strand	206-221	16	4
β-strand	224-231	8	4
β-strand	235-236	2	4
β-strand	239	1	5
α-helix	241-243	3
β-strand	246-253	8	12
β-strand	263-264	2	4
β-strand	268-280	13	4
β-strand	285-292	8	4
β-strand	293-295	3	13

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)
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 (AlphaFold model)
Vacuolar protein sorting-associated protein 26C	P	protein	297	Homo sapiens	O14972

Sequence of entity 1 (K), FASTA

>8P0X_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

>8P0X_2 Coiled-coil domain-containing protein 22 (chains L)
MEEADRILIHSLRQAGTAVPPDVQTLRAFTTELVVEAVVRCLRVINPAVGSGLSPLLPLA
MSARFRLAMSLAQACMDLGYPLELGYQNFLYPSEPDLRDLLLFLAERLPTDASEDADQPA
GDSAILLRAIGSQIRDQLALPWVPPHLRTPKLQHLQGSALQKPFHASRLVVPELSSRGEP
REFQASPLLLPVPTQVPQPVGRVASLLEHHALQLCQQTGRDRPGDEDWVHRTSRLPPQED
TRAQRQRLQKQLTEHLRQSWGLLGAPIQARDLGELLQAWGAGAKTGAPKGSRFTHSEKFT
FHLEPQAQATQVSDVPATSRRPEQVTWAAQEQELESLREQLEGVNRSIEEVEADMKTLGV
SFVQAESECRHSKLSTAEREQALRLKSRAVELLPDGTANLAKLQLVVENSAQRVIHLAGQ
WEKHRVPLLAEYRHLRKLQDCRELESSRRLAEIQELHQSVRAAAEEARRKEEVYKQLMSE
LETLPRDVSRLAYTQRILEIVGNIRKQKEEITKILSDTKELQKEINSLSGKLDRTFAVTD
ELVFKDAKKDDAVRKAYKYLAALHENCSQLIQTIEDTGTIMREVRDLEEQIETELGKKTL
SNLEKIREDYRALRQENAGLLGRVREA

Sequence of entity 3 (N), FASTA

>8P0X_3 Vacuolar protein sorting-associated protein 29 (chains N)
MLVLVLGDLHIPHRCNSLPAKFKKLLVPGKIQHILCTGNLCTKESYDYLKTLAGDVHIVR
GDFDENLNYPEQKVVTVGQFKIGLIHGHQVIPWGDMASLALLQRQFDVDILISGHTHKFE
AFEHENKFYINPGSATGAYNALETNIIPSFVLMDIQASTVVTYVYQLIGDDVKVERIEYK
KP

Sequence of entity 4 (O), FASTA

>8P0X_4 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

Sequence of entity 5 (P), FASTA

>8P0X_5 Vacuolar protein sorting-associated protein 26C (chains P)
MGTALDIKIKRANKVYHAGEVLSGVVVISSKDSVQHQGVSLTMEGTVNLQLSAKSVGVFE
AFYNSVKPIQIINSTIEMVKPGKFPSGKTEIPFEFPLHLKGNKVLYETYHGVFVNIQYTL
RCDMKRSLLAKDLTKTCEFIVHSAPQKGKFTPSPVDFTITPETLQNVKERALLPKFLLRG
HLNSTNCVITQPLTGELVVESSEAAIRSVELQLVRVETCGCAEGYARDATEIQNIQIADG
DVCRGLSVPIYMVFPRLFTCPTLETTNFKVEFEVNIVVLLHPDHLITENFPLKLCRI

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
8P0V 6.5 Å, Structure of the human Commander complex coiled coils, DENND10 and partial Retriever…

Browse structure collections

About this viewer

MolViewer shows 8P0X directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.