6LT0: C9ORF72-SMCR8-WDR41

cryo-EM structure of C9ORF72-SMCR8-WDR41. Determined by electron microscopy at 3.2 Å resolution. Released 15 Apr 2020.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: Homo sapiens
Chains: 6
Atoms: 17,774
Mol. weight: 422.65 kDa
Released: 15 Apr 2020

Explore 6LT0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6LT0 contains 76 α-helices and 118 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.

Chains A and D: 1 helix, 31 β-strands

Element	Residues	Length	Sheet
β-strand	35-40	6	1
β-strand	46-53	8	2
β-strand	56-61	6	2
β-strand	66-70	5	2
β-strand	76-80	5	2
β-strand	87-92	6	3
β-strand	106-110	5	3
β-strand	115-118	4	3
β-strand	127-129	3	3
β-strand	141-142	2	4
β-strand	147-148	2	4
β-strand	156-157	2	5
β-strand	167-168	2	5
β-strand	179-182	4	6
β-strand	187-191	5	6
β-strand	196-197	2	6
β-strand	225-230	6	7
β-strand	235-240	6	7
β-strand	245-249	5	7
β-strand	273-276	4	7
β-strand	291-292	2	8
β-strand	295-297	3	8
β-strand	306-308	3	8
β-strand	314-315	2	8
β-strand	329-332	4	9
β-strand	336-339	4	9
β-strand	347-350	4	9
β-strand	397-400	4	9
β-strand	408-413	6	1
β-strand	419-423	5	1
β-strand	427-432	6	1
α-helix	441-452	12

Chains B and E: 21 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	60-63	4	10
β-strand	83	1	10
α-helix	97-100	4
β-strand	115-117	3	10
β-strand	130-137	8	10
β-strand	153-159	7	10
α-helix	162-166	5
α-helix	169-173	5
α-helix	180-187	8
α-helix	331-344	14
α-helix	350-364	15
α-helix	368-371	4
α-helix	702-714	13
α-helix	721-729	9
β-strand	732	1	11
β-strand	733-736	4	12
α-helix	740-750	11
α-helix	751-753	3
β-strand	764	1	12
α-helix	776-779	4
β-strand	782-785	4	12
α-helix	796-800	5
α-helix	801-803	3
β-strand	807	1	11
β-strand	810-811	2	12
β-strand	816	1	12
β-strand	817-819	3	13
α-helix	826-830	5
α-helix	841-863	23
α-helix	865-868	4
α-helix	877-886	10
α-helix	887-891	5
α-helix	898-915	18
β-strand	926	1	1
α-helix	930-932	3
β-strand	933-935	3	13

Chains C and F: 16 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	14-17	4	14
β-strand	27	1	10
β-strand	29	1	14
β-strand	30	1	10
β-strand	44-47	4	14
α-helix	57-67	11
β-strand	81-87	7	10
β-strand	92-98	7	10
β-strand	111-117	7	10
α-helix	125-127	3
α-helix	128-147	20
α-helix	174-192	19
α-helix	201-203	3
α-helix	216-229	14
β-strand	234-237	4	15
α-helix	242-251	10
α-helix	252-254	3
α-helix	257-262	6
β-strand	280-281	2	15
α-helix	295-299	5
β-strand	306-309	4	15
β-strand	314-316	3	15
α-helix	321-336	16
β-strand	369	1	15
α-helix	376-384	9
α-helix	394-419	26
α-helix	430-436	7
α-helix	442-454	13
α-helix	459-463	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
WD repeat-containing protein 41	A, D	protein	459	Homo sapiens	Q9HAD4 (AlphaFold model)
Guanine nucleotide exchange protein SMCR8	B, E	protein	937	Homo sapiens	Q8TEV9 (AlphaFold model)
Guanine nucleotide exchange C9orf72	C, F	protein	481	Homo sapiens	Q96LT7 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>6LT0_1 WD repeat-containing protein 41 (chains A, D)
MLRWLIGGGREPQGLAEKSPLQTIGEEQTQNPYTELLVLKAHHDIVRFLVQLDDYRFASA
GDDGIVVVWNAQTGEKLLELNGHTQKITAIITFPSLESCEEKNQLILTASADRTVIVWDG
DTTRQVQRISCFQSTVKCLTVLQRLDVWLSGGNDLCVWNRKLDLLCKTSHLSDTGISALV
EIPKNCVVAAVGKELIIFRLVAPTEGSLEWDILEVKRLLDHQDNILSLINVNDLSFVTGS
HVGELIIWDALDWTMQAYERNFWDPSPQLDTQQEIKLCQKSNDISIHHFTCDEENVFAAV
GRGLYVYSLQMKRVIACQKTAHDSNVLHVARLPNRQLISCSEDGSVRIWELREKQQLAAE
PVPTGFFNMWGFGRVSKQASQPVKKQQENATSCSLELIGDLIGHSSSVEMFLYFEDHGLV
TCSADHLIILWKNGERESGLRSLRLFQKLEENGDLYLAV

Sequence of entity 2 (B, E), FASTA

>6LT0_2 Guanine nucleotide exchange protein SMCR8 (chains B, E)
MISAPDVVAFTKEEEYEEEPYNEPALPEEYSVPLFPFASQGANPWSKLSGAKFSRDFILI
SEFSEQVGPQPLLTIPNDTKVFGTFDLNYFSLRIMSVDYQASFVGHPPGSAYPKLNFVED
SKVVLGDSKEGAFAYVHHLTLYDLEARGFVRPFCMAYISADQHKIMQQFQELSAEFSRAS
ECLKTGNRKAFAGELEKKLKDLDYTRTVLHTETEIQKKANDKGFYSSQAIEKANELASVE
KSIIEHQDLLKQIRSYPHRKLKGHDLCPGEMEHIQDQASQASTTSNPDESADTDLYTCRP
AYTPKLIKAKSTKCFDKKLKTLEELCDTEYFTQTLAQLSHIEHMFRGDLCYLLTSQIDRA
LLKQQHITNFLFEDFVEVDDRMVEKQESIPSKPSQDRPPSSSLEECPIPKVLISVGSYKS
SVESVLIKMEQELGDEEYKEVEVTELSSFDPQENLDYLDMDMKGSISSGESIEVLGTEKS
TSVLSKSDSQASLTVPLSPQVVRSKAVSHRTISEDSIEVLSTCPSEALIPDDFKASYPSA
INEEESYPDGNEGAIRFQASISPPELGETEEGSIENTPSQIDSSCCIGKESDGQLVLPST
PAHTHSDEDGVVSSPPQRHRQKDQGFRVDFSVENANPSSRDNSCEGFPAYELDPSHLLAS
RDISKTSLDNYSDTTSYVSSVASTSSDRIPSAYPAGLSSDRHKKRAGQNALKFIRQYPFA
HPAIYSLLSGRTLVVLGEDEAIVRKLVTALAIFVPSYGCYAKPVKHWASSPLHIMDFQKW
KLIGLQRVASPAGAGTLHALSRYSRYTSILDLDNKTLRCPLYRGTLVPRLADHRTQIKRG
STYYLHVQSMLTQLCSKAFLYTFCHHLHLPTHDKETEELVASRQMSFLKLTLGLVNEDVR
VVQYLAELLKLHYMQESPGTSHPMLRFDYVPSFLYKI

Sequence of entity 3 (C, F), FASTA

>6LT0_3 Guanine nucleotide exchange C9orf72 (chains C, F)
MSTLCPPPSPAVAKTEIALSGKSPLLAATFAYWDNILGPRVRHIWAPKTEQVLLSDGEIT
FLANHTLNGEILRNAESGAIDVKFFVLSEKGVIIVSLIFDGNWNGDRSTYGLSIILPQTE
LSFYLPLHRVCVDRLTHIIRKGRIWMHKERQENVQKIILEGTERMEDQGQSIIPMLTGEV
IPVMELLSSMKSHSVPEEIDIADTVLNDDDIGDSCHEGFLLNAISSHLQTCGCSVVVGSS
AEKVNKIVRTLCLFLTPAERKCSRLCEAESSFKYESGLFVQGLLKDSTGSFVLPFRQVMY
APYPTTHIDVDVNTVKQMPPCHEHIYNQRRYMRSELTAFWRATSEEDMAQDTIIYTDESF
TPDLNIFQDVLHRDTLVKAFLDQVFQLKPGLSLRSTFLAQFLLVLHRKALTLIKYIEDDT
QKGKKPFKSLRNLKIDLDLTAEGDLNIIMALAEKIKPGLHSFIFGRPFYTSVQERDVLMT
F

Primary citation

Cryo-EM structure of C9ORF72-SMCR8-WDR41 reveals the role as a GAP for Rab8a and Rab11a. Tang, D., Sheng, J., Xu, L. et al. Proc Natl Acad Sci U S A (2020) 117:9876-9883. DOI 10.1073/pnas.2002110117 · PubMed

Other PDB entries of the same protein (UniProt Q9HAD4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8W3V 2.2 Å, Crystal structure of human WDR41
6V4U 3.8 Å, Cryo-EM structure of SMCR8-C9orf72-WDR41 complex
7MGE 3.94 Å, Structure of C9orf72:SMCR8:WDR41 in complex with ARF1

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