9M1J: TBC-DE-Arl2-beta-tubulin complex

Name: PDB 9M1J: Cryo-EM structure of the TBC-DE-Arl2-beta-tubulin complex
Published: 2025-10-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: chaperone

Cryo-EM structure of the TBC-DE-Arl2-beta-tubulin complex. Determined by electron microscopy at 2.14 Å resolution. Released 22 Oct 2025.

Method: Electron microscopy
Resolution: 2.14 Å
Organisms: Homo sapiens, Sus scrofa
Chains: 4
Atoms: 16,686
Mol. weight: 245.29 kDa
Ligands: GTP, MG
Released: 22 Oct 2025

Explore 9M1J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9M1J contains 114 α-helices and 55 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 b: 21 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	10
α-helix	10-28	19
β-strand	30	1	11
β-strand	36	1	11
α-helix	41-43	3
β-strand	51-53	3	12
β-strand	59-61	3	12
β-strand	63-66	4	10
α-helix	70-77	8
α-helix	87-89	3
β-strand	90-91	2	10
α-helix	101-102	2
α-helix	103-107	5
α-helix	113-125	13
β-strand	129-136	8	10
α-helix	143-147	5
α-helix	148-158	11
β-strand	164-167	4	10
β-strand	169-170	2	13
α-helix	181-192	12
β-strand	198-200	3	10
β-strand	202-203	2	13
α-helix	204-211	8
α-helix	222-236	15
α-helix	250-257	8
β-strand	260	1	14
β-strand	263	1	14
β-strand	265-266	2	10
β-strand	267-271	5	15
α-helix	286-293	8
α-helix	296-298	3
β-strand	299	1	15
α-helix	305-307	3
β-strand	310-318	9	15
α-helix	323-333	11
β-strand	349-350	2	15
β-strand	353-354	2	15
α-helix	357-358	2
β-strand	364-371	8	15
α-helix	374-389	16
α-helix	396-399	4
α-helix	405-426	22

Chain D: 74 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	22-23	2	1
α-helix	24-25	2
α-helix	33-41	9
α-helix	42-45	4
α-helix	51-66	16
α-helix	71-74	4
α-helix	76-78	3
α-helix	80-89	10
α-helix	96-112	17
α-helix	118-121	4
α-helix	126-137	12
α-helix	147-161	15
α-helix	167-170	4
α-helix	185-196	12
α-helix	203-215	13
α-helix	225-238	14
α-helix	244-262	19
α-helix	266-269	4
α-helix	270-272	3
α-helix	275-281	7
α-helix	291-308	18
α-helix	358-369	12
α-helix	374-387	14
α-helix	393-404	12
α-helix	413-429	17
α-helix	434-436	3
α-helix	437-447	11
β-strand	452-454	3	2
β-strand	457-459	3	2
α-helix	461-477	17
α-helix	484-500	17
α-helix	504-521	18
α-helix	527-533	7
α-helix	538-540	3
α-helix	542-545	4
α-helix	549-554	6
α-helix	557-559	3
α-helix	561-570	10
α-helix	577-591	15
α-helix	595-597	3
α-helix	598-602	5
α-helix	603-609	7
α-helix	615-638	24
α-helix	649-655	7
α-helix	658-664	7
α-helix	673-689	17
α-helix	698-712	15
α-helix	719-721	3
α-helix	723-739	17
α-helix	750-761	12
α-helix	762-765	4
α-helix	769-779	11
α-helix	785-787	3
α-helix	791-802	12
β-strand	805	1	3
β-strand	808	1	3
α-helix	812-829	18
α-helix	846-854	9
α-helix	855-857	3
β-strand	861	1	4
β-strand	866	1	4
α-helix	868-888	21
α-helix	891-893	3
α-helix	896-910	15
α-helix	915-929	15
β-strand	932	1	5
β-strand	935	1	5
α-helix	936	1
α-helix	942-948	7
α-helix	962-964	3
α-helix	966-969	4
α-helix	970-974	5
α-helix	981-990	10
α-helix	995-1009	15
α-helix	1016-1032	17
α-helix	1040-1051	12
α-helix	1066-1078	13
α-helix	1085-1097	13
α-helix	1098-1100	3
α-helix	1104-1117	14
α-helix	1122-1138	17
α-helix	1145-1156	12
α-helix	1164-1178	15

Chain E: 13 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	131-133	3	6
α-helix	147-151	5
β-strand	157-159	3	6
α-helix	168-177	10
β-strand	183-185	3	6
β-strand	208-210	3	6
α-helix	218-224	7
α-helix	225-227	3
β-strand	233-235	3	6
β-strand	256-258	3	6
α-helix	269-272	4
α-helix	273-275	3
β-strand	281-283	3	6
β-strand	311-314	4	6
α-helix	323-328	6
β-strand	338-339	2	6
α-helix	351-361	11
β-strand	367	1	7
β-strand	372	1	7
α-helix	375-395	21
α-helix	409-414	6
α-helix	418-424	7
β-strand	445-451	7	8
β-strand	462-466	5	8
β-strand	470	1	9
α-helix	471-482	12
α-helix	486-488	3
β-strand	490-494	5	8
β-strand	503-505	3	8
β-strand	511	1	9
β-strand	522-526	5	8

Chain G: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3-14	12
β-strand	16	1	1
β-strand	19-23	5	1
α-helix	29-34	6
β-strand	50-57	8	1
β-strand	60-67	8	1
α-helix	74-77	4
β-strand	86-92	7	1
α-helix	99-109	11
β-strand	119-125	7	1
α-helix	135-142	8
β-strand	153-156	4	1
α-helix	166-177	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin-specific chaperone D	D	protein	1168	Homo sapiens	Q9BTW9 (AlphaFold model)
Tubulin-specific chaperone E	E	protein	399	Homo sapiens	Q15813 (AlphaFold model)
ADP-ribosylation factor-like protein 2	G	protein	184	Homo sapiens	P36404 (AlphaFold model)
Tubulin beta chain	b	protein	431	Sus scrofa	Q767L7 (AlphaFold model)

Sequence of entity 1 (D), FASTA

>9M1J_1 Tubulin-specific chaperone D (chains D)
ETLAFGAALEAFGESAETRALLGRLREVHGGGAEREVALERFRVIMDKYQEQPHLLDPHL
EWMMNLLLDIVQDQTSPASLVHLAFKFLYIITKVRGYKTFLRLFPHEVADVEPVLDLVTI
QNPKDHEAWETRYMLLLWLSVTCLIPFDFSRLDGNLLTQPGQARMSIMDRILQIAESYLI
VSDKARDAAAVLVSRFITRPDVKQSKMAEFLDWSLCNLARSSFQTMQGVITMDGTLQALA
QIFKHGKREDCLPYAATVLRCLDGCRLPESNQTLLRKLGVKLVQRLGLTFLKPKVAAWRY
QRGCRSLAANLQLLTQGQSEQKPLILTEDDDEDDDVPEGVERVIEQLLVGLKDKDTVVRW
SAAKGIGRMAGRLPRALADDVVGSVLDCFSFQETDKAWHGGCLALAELGRRGLLLPSRLV
DVVAVILKALTYDEKRGACSVGTNVRDAACYVCWAFARAYEPQELKPFVTAISSALVIAA
VFDRDINCRRAASAAFQENVGRQGTFPHGIDILTTADYFAVGNRSNCFLVISVFIAGFPE
YTQPMIDHLVTMKISHWDGVIRELAARALHNLAQQAPEFSATQVFPRLLSMTLSPDLHMR
HGSILACAEVAYALYKLAAQENRPVTDHLDEQAVQGLKQIHQQLYDRQLYRGLGGQLMRQ
AVCVLIEKLSLSKMPFRGDTVIDGWQWLINDTLRHLHLISSHSRQQMKDAAVSALAALCS
EYYMKEPGEADPAIQEELITQYLAELRNPEEMTRCGFSLALGALPGFLLKGRLQQVLTGL
RAVTHTSPEDVSFAESRRDGLKAIARICQTVGVKAGAPDEAVCGENVSQIYCALLGCMDD
YTTDSRGDVGTWVRKAAMTSLMDLTLLLARSQPELIEAHTCERIMCCVAQQASEKIDRFR
AHAASVFLTLLHFDSPPIPHVPHRGELEKLFPRSDVASVNWSAPSQAFPRITQLLGLPTY
RYHVLLGLVVSLGGLTESTIRHSTQSLFEYMKGIQSDPQALGSFSGTLLQIFEDNLLNER
VSVPLLKTLDHVLTHGCFDIFTTEEDHPFAVKLLALCKKEIKNSKDIQKLLSGIAVFCEM
VQFPGDVRRQALLQLCLLLCHRFPLIRKTTASQVYETLLTYSDVVGADVLDEVVTVLSDT
AWDAELAVVREQRNRLCDLLGVPRPQLV

Sequence of entity 2 (E), FASTA

>9M1J_2 Tubulin-specific chaperone E (chains E)
LQEVSLRNCAVSCAGEKGGVAEACPNIRKVDLSKNLLSSWDEVIHIADQLRHLEVLNVSE
NKLKFPSGSVLTGTLSVLKVLVLNQTGITWAEVLRCVAGCPGLEELYLESNNIFISERPT
DVLQTVKLLDLSSNQLIDENQLYLIAHLPRLEQLILSDTGISSLHFPDAGIGCKTSMFPS
LKYLVVNDNQISQWSFFNELEKLPSLRALSCLRNPLTKEDKEAETARLLIIASIGQLKTL
NKCEILPEERRRAELDYRKAFGNEWKQAGGHKDPEKNRLSEEFLTAHPRYQFLCLKYGAP
EDWELKTQQPLMLKNQLLTLKIKYPHQLDQKVLEKQLPGSMTIQKVKGLLSRLLKVPVSD
LLLSYESPKKPGREIELENDLKSLQFYSVENGDCLLVRW

Sequence of entity 3 (G), FASTA

>9M1J_3 ADP-ribosylation factor-like protein 2 (chains G)
MGLLTILKKMKQKERELRLLMLGLDNAGKTTILKKFNGEDIDTISPTLGFNIKTLEHRGF
KLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADRQRMQDCQRELQSLLVEERLAGATL
LIFANKQDLPGALSSNAIREVLELDSIRSHHWCIQGCSAVTGENLLPGIDWLLDDISSRI
FTAD

Sequence of entity 4 (b), FASTA

>9M1J_4 Tubulin beta chain (chains b)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQVFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMAVTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAE

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	1

Primary citation

Structural dissection of alpha beta-tubulin heterodimer assembly and disassembly by human tubulin-specific chaperones. Seong, Y., Kim, H., Byun, K. et al. Science (2025) 390:eady2708-eady2708. DOI 10.1126/science.ady2708 · PubMed

Other PDB entries of the same protein (UniProt Q9BTW9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9M1M 2.21 Å, Cryo-EM structure of the TBC-DEC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
9M1N 2.24 Å, Cryo-EM structure of the TBC-DC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
9M1K 2.45 Å, Cryo-EM structure of the TBC-DE-Arl2-beta-tubulin complex with GTP
9M1I 2.48 Å, Cryo-EM structure of the TBC-D-Arl2-beta-tubulin complex
9M1L 2.55 Å, Cryo-EM structure of the TBC-DE-Arl2-alpha-beta-tubulin complex with GTP

Browse structure collections

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