9M1L: TBC-DE-Arl2-alpha-beta-tubulin complex with GTP

Name: PDB 9M1L: Cryo-EM structure of the TBC-DE-Arl2-alpha-beta-tubulin complex with GTP
Published: 2025-10-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: chaperone

Cryo-EM structure of the TBC-DE-Arl2-alpha-beta-tubulin complex with GTP. Determined by electron microscopy at 2.55 Å resolution. Released 22 Oct 2025.

Method: Electron microscopy
Resolution: 2.55 Å
Organisms: Homo sapiens, Sus scrofa
Chains: 5
Atoms: 21,090
Mol. weight: 314.64 kDa
Ligands: MG, GTP
Released: 22 Oct 2025

Explore 9M1L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9M1L contains 135 α-helices and 85 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 a: 18 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	17
α-helix	10-28	19
α-helix	49-51	3
β-strand	53-54	2	18
β-strand	62-63	2	18
β-strand	65-68	4	17
α-helix	72-79	8
β-strand	93	1	17
α-helix	103-104	2
α-helix	105-109	5
α-helix	112-128	17
β-strand	132-138	7	17
α-helix	144-160	17
β-strand	167	1	17
β-strand	169	1	19
α-helix	183-193	11
β-strand	202	1	19
α-helix	206-215	10
α-helix	224-243	20
α-helix	252-258	7
β-strand	269-273	5	10
β-strand	277	1	20
α-helix	288-294	7
β-strand	301	1	10
α-helix	307-309	3
β-strand	312-321	10	10
α-helix	325-337	13
β-strand	351-356	6	10
β-strand	368	1	20
β-strand	373-381	9	10
α-helix	382-384	3
α-helix	385-400	16
α-helix	406-409	4
α-helix	415-435	21

Chain b: 17 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	21
α-helix	11-28	18
β-strand	30	1	22
β-strand	36	1	22
α-helix	41-43	3
α-helix	47-49	3
β-strand	51-53	3	23
β-strand	59-61	3	23
β-strand	63-67	5	21
α-helix	72-77	6
β-strand	90-92	3	21
α-helix	103-107	5
α-helix	113-125	13
β-strand	130-136	7	21
β-strand	138	1	24
α-helix	145-158	14
β-strand	163-166	4	21
β-strand	169	1	24
α-helix	181-194	14
β-strand	198-200	3	21
α-helix	204-213	10
α-helix	222-236	15
α-helix	250-257	8
β-strand	265-266	2	21
β-strand	267-271	5	25
α-helix	286-293	8
β-strand	299	1	25
β-strand	310-312	3	26
β-strand	314-318	5	25
α-helix	323-330	8
β-strand	350-354	5	25
β-strand	364-369	6	25
β-strand	370-371	2	26
α-helix	372-374	3
α-helix	375-390	16
α-helix	396-401	6
α-helix	405-426	22

Chain D: 74 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	33-41	9
α-helix	50-64	15
α-helix	65-67	3
α-helix	71-73	3
α-helix	75-77	3
α-helix	80-90	11
α-helix	96-112	17
α-helix	115-118	4
α-helix	126-128	3
α-helix	129-137	9
α-helix	147-160	14
α-helix	167-170	4
α-helix	185-196	12
α-helix	203-214	12
α-helix	225-238	14
α-helix	244-262	19
α-helix	273-281	9
α-helix	291-308	18
α-helix	356-366	11
α-helix	367-370	4
α-helix	374-388	15
α-helix	393-404	12
α-helix	405-407	3
α-helix	413-429	17
α-helix	434-436	3
α-helix	437-447	11
β-strand	452-453	2	1
β-strand	458-459	2	1
α-helix	461-474	14
α-helix	480-497	18
α-helix	504-520	17
α-helix	527-533	7
α-helix	542-544	3
α-helix	545-549	5
α-helix	550-554	5
α-helix	561-569	9
α-helix	571-573	3
α-helix	578-593	16
α-helix	595-597	3
α-helix	598-602	5
α-helix	603-609	7
α-helix	615-638	24
α-helix	643-645	3
α-helix	649-665	17
α-helix	672-688	17
α-helix	698-712	15
α-helix	719-721	3
α-helix	722-737	16
α-helix	750-761	12
α-helix	769-780	12
α-helix	791-802	12
α-helix	812-829	18
β-strand	831	1	2
β-strand	840	1	2
α-helix	845-855	11
α-helix	868-887	20
α-helix	891-893	3
α-helix	896-909	14
α-helix	916-930	15
β-strand	932	1	3
β-strand	935	1	3
α-helix	936	1
α-helix	942-948	7
α-helix	951-953	3
α-helix	962-964	3
α-helix	966-969	4
α-helix	970-974	5
α-helix	980-989	10
α-helix	996-1009	14
α-helix	1010-1012	3
α-helix	1016-1032	17
α-helix	1040-1053	14
α-helix	1059-1061	3
α-helix	1066-1078	13
α-helix	1085-1097	13
α-helix	1104-1117	14
α-helix	1122-1138	17
α-helix	1145-1154	10
α-helix	1164-1178	15
α-helix	1180-1183	4

Chain E: 18 helices, 35 β-strands

Element	Residues	Length	Sheet
β-strand	13-16	4	6
β-strand	19-28	10	6
β-strand	35-41	7	6
β-strand	53	1	7
β-strand	56	1	7
β-strand	68-70	3	6
α-helix	72-74	3
β-strand	76	1	6
β-strand	79	1	8
α-helix	81-89	9
β-strand	105-106	2	9
β-strand	109-110	2	9
β-strand	111-113	3	10
α-helix	116-124	9
α-helix	126-128	3
β-strand	131-133	3	11
β-strand	139	1	8
α-helix	147-151	5
β-strand	157-159	3	11
β-strand	167	1	12
α-helix	168-177	10
β-strand	183-185	3	11
β-strand	192	1	12
α-helix	198-199	2
β-strand	208-210	3	11
α-helix	218-224	7
β-strand	233-235	3	11
β-strand	256-258	3	11
α-helix	267-272	6
β-strand	281-283	3	11
β-strand	311-313	3	11
α-helix	323-328	6
β-strand	336-338	3	11
α-helix	352-361	10
β-strand	367-368	2	11
β-strand	372	1	11
α-helix	375-388	14
α-helix	390-395	6
α-helix	409-414	6
α-helix	418-424	7
α-helix	441-444	4
β-strand	445-448	4	13
β-strand	449-451	3	14
α-helix	459-460	2
β-strand	463-466	4	13
β-strand	470	1	15
α-helix	471-482	12
β-strand	490	1	16
β-strand	492-494	3	14
β-strand	503-504	2	14
β-strand	511	1	15
β-strand	522-524	3	14
β-strand	526	1	16

Chain G: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-15	13
β-strand	16-23	8	4
α-helix	30-37	8
β-strand	50-57	8	4
β-strand	60-67	8	4
α-helix	71-74	4
α-helix	77-79	3
β-strand	86-92	7	4
α-helix	103-106	4
β-strand	119-125	7	4
α-helix	132-134	3
α-helix	135-141	7
β-strand	155-156	2	4
β-strand	158	1	5
β-strand	163	1	5
α-helix	165-177	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin-specific chaperone D	D	protein	1192	Homo sapiens	Q9BTW9 (AlphaFold model)
ADP-ribosylation factor-like protein 2	G	protein	184	Homo sapiens	P36404 (AlphaFold model)
Tubulin-specific chaperone E	E	protein	527	Homo sapiens	Q15813 (AlphaFold model)
Tubulin alpha-1B chain	a	protein	451	Sus scrofa	Q2XVP4 (AlphaFold model)
Tubulin beta chain	b	protein	444	Sus scrofa	Q767L7

Sequence of entity 1 (D), FASTA

>9M1L_1 Tubulin-specific chaperone D (chains D)
MALSDEPAAGGPEEEAEDETLAFGAALEAFGESAETRALLGRLREVHGGGAEREVALERF
RVIMDKYQEQPHLLDPHLEWMMNLLLDIVQDQTSPASLVHLAFKFLYIITKVRGYKTFLR
LFPHEVADVEPVLDLVTIQNPKDHEAWETRYMLLLWLSVTCLIPFDFSRLDGNLLTQPGQ
ARMSIMDRILQIAESYLIVSDKARDAAAVLVSRFITRPDVKQSKMAEFLDWSLCNLARSS
FQTMQGVITMDGTLQALAQIFKHGKREDCLPYAATVLRCLDGCRLPESNQTLLRKLGVKL
VQRLGLTFLKPKVAAWRYQRGCRSLAANLQLLTQGQSEQKPLILTEDDDEDDDVPEGVER
VIEQLLVGLKDKDTVVRWSAAKGIGRMAGRLPRALADDVVGSVLDCFSFQETDKAWHGGC
LALAELGRRGLLLPSRLVDVVAVILKALTYDEKRGACSVGTNVRDAACYVCWAFARAYEP
QELKPFVTAISSALVIAAVFDRDINCRRAASAAFQENVGRQGTFPHGIDILTTADYFAVG
NRSNCFLVISVFIAGFPEYTQPMIDHLVTMKISHWDGVIRELAARALHNLAQQAPEFSAT
QVFPRLLSMTLSPDLHMRHGSILACAEVAYALYKLAAQENRPVTDHLDEQAVQGLKQIHQ
QLYDRQLYRGLGGQLMRQAVCVLIEKLSLSKMPFRGDTVIDGWQWLINDTLRHLHLISSH
SRQQMKDAAVSALAALCSEYYMKEPGEADPAIQEELITQYLAELRNPEEMTRCGFSLALG
ALPGFLLKGRLQQVLTGLRAVTHTSPEDVSFAESRRDGLKAIARICQTVGVKAGAPDEAV
CGENVSQIYCALLGCMDDYTTDSRGDVGTWVRKAAMTSLMDLTLLLARSQPELIEAHTCE
RIMCCVAQQASEKIDRFRAHAASVFLTLLHFDSPPIPHVPHRGELEKLFPRSDVASVNWS
APSQAFPRITQLLGLPTYRYHVLLGLVVSLGGLTESTIRHSTQSLFEYMKGIQSDPQALG
SFSGTLLQIFEDNLLNERVSVPLLKTLDHVLTHGCFDIFTTEEDHPFAVKLLALCKKEIK
NSKDIQKLLSGIAVFCEMVQFPGDVRRQALLQLCLLLCHRFPLIRKTTASQVYETLLTYS
DVVGADVLDEVVTVLSDTAWDAELAVVREQRNRLCDLLGVPRPQLVPQPGAC

Sequence of entity 2 (G), FASTA

>9M1L_2 ADP-ribosylation factor-like protein 2 (chains G)
MGLLTILKKMKQKERELRLLMLGLDNAGKTTILKKFNGEDIDTISPTLGFNIKTLEHRGF
KLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADRQRMQDCQRELQSLLVEERLAGATL
LIFANKQDLPGALSSNAIREVLELDSIRSHHWCIQGCSAVTGENLLPGIDWLLDDISSRI
FTAD

Sequence of entity 3 (E), FASTA

>9M1L_3 Tubulin-specific chaperone E (chains E)
MSDTLTADVIGRRVEVNGEHATVRFAGVVPPVAGPWLGVEWDNPERGKHDGSHEGTVYFK
CRHPTGGSFIRPNKVNFGTDFLTAIKNRYVLEDGPEEDRKEQIVTIGNKPVETIGFDSIM
KQQSQLSKLQEVSLRNCAVSCAGEKGGVAEACPNIRKVDLSKNLLSSWDEVIHIADQLRH
LEVLNVSENKLKFPSGSVLTGTLSVLKVLVLNQTGITWAEVLRCVAGCPGLEELYLESNN
IFISERPTDVLQTVKLLDLSSNQLIDENQLYLIAHLPRLEQLILSDTGISSLHFPDAGIG
CKTSMFPSLKYLVVNDNQISQWSFFNELEKLPSLRALSCLRNPLTKEDKEAETARLLIIA
SIGQLKTLNKCEILPEERRRAELDYRKAFGNEWKQAGGHKDPEKNRLSEEFLTAHPRYQF
LCLKYGAPEDWELKTQQPLMLKNQLLTLKIKYPHQLDQKVLEKQLPGSMTIQKVKGLLSR
LLKVPVSDLLLSYESPKKPGREIELENDLKSLQFYSVENGDCLLVRW

Sequence of entity 4 (a), FASTA

>9M1L_4 Tubulin alpha-1B chain (chains a)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 5 (b), FASTA

>9M1L_5 Tubulin beta chain (chains b)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQVFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMAVTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAEEEEDFGEEAEEEA

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	3

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:

9M1J 2.14 Å, Cryo-EM structure of the TBC-DE-Arl2-beta-tubulin complex
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

Browse structure collections

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