9M1M: Tubulin-specific chaperone C

Name: PDB 9M1M: Cryo-EM structure of the TBC-DEC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
Published: 2025-10-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: chaperone

Cryo-EM structure of the TBC-DEC-Arl2-alpha-beta-tubulin complex with GDP-AlFx. Determined by electron microscopy at 2.21 Å resolution. Released 22 Oct 2025.

Method: Electron microscopy
Resolution: 2.21 Å
Organisms: Homo sapiens, Sus scrofa
Chains: 6
Atoms: 22,547
Mol. weight: 353.95 kDa
Ligands: GDP, AF3, MG, GTP
Released: 22 Oct 2025

Explore 9M1M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9M1M contains 154 α-helices and 108 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.

Chain a: 17 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	19
α-helix	11-28	18
α-helix	49-51	3
β-strand	53-55	3	20
β-strand	61-63	3	20
β-strand	65-68	4	19
α-helix	72-79	8
α-helix	89-91	3
β-strand	92-93	2	19
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-128	18
β-strand	132-133	2	19
β-strand	134	1	21
β-strand	135-138	4	19
α-helix	148-160	13
β-strand	165	1	21
β-strand	168	1	19
α-helix	183-193	11
β-strand	201	1	19
α-helix	206-215	10
α-helix	224-243	20
α-helix	253-258	6
β-strand	269-273	5	12
β-strand	277	1	22
α-helix	298-300	3
β-strand	301	1	12
β-strand	312	1	23
β-strand	315-321	7	12
α-helix	325-338	14
β-strand	343	1	23
β-strand	351-356	6	12
β-strand	368	1	22
β-strand	373-379	7	12
β-strand	381	1	23
α-helix	384-399	16
α-helix	406-409	4
α-helix	416-436	21

Chain b: 22 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	24
α-helix	10-28	19
β-strand	30	1	25
β-strand	36	1	25
α-helix	43-45	3
α-helix	47-49	3
β-strand	51-53	3	26
α-helix	55-57	3
β-strand	59-61	3	26
β-strand	65-66	2	24
α-helix	71-77	7
α-helix	87-89	3
β-strand	90-91	2	24
α-helix	101-102	2
α-helix	103-107	5
α-helix	108-124	17
β-strand	129-136	8	24
β-strand	138	1	27
α-helix	142-158	17
β-strand	163-166	4	24
β-strand	169-170	2	27
α-helix	181-194	14
β-strand	198-200	3	24
β-strand	202-203	2	27
α-helix	206-209	4
α-helix	210-214	5
α-helix	223-236	14
α-helix	238-241	4
α-helix	250-257	8
β-strand	265-266	2	24
β-strand	267-271	5	28
α-helix	286-293	8
α-helix	296-298	3
β-strand	299	1	28
β-strand	313-318	6	28
α-helix	323-333	11
β-strand	350	1	28
β-strand	364-369	6	28
α-helix	374-386	13
α-helix	396-399	4
α-helix	405-425	21

Chain C: 3 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	184-187	4	1
β-strand	193	1	1
β-strand	196	1	2
β-strand	205-212	8	1
β-strand	215-217	3	1
β-strand	218	1	2
β-strand	224-231	8	1
β-strand	234-236	3	1
β-strand	239	1	3
β-strand	243-247	5	1
β-strand	250	1	1
β-strand	253-254	2	1
β-strand	257	1	3
β-strand	260-264	5	1
β-strand	267-271	5	1
β-strand	278-282	5	1
β-strand	285-289	5	1
α-helix	300-306	7
β-strand	318-320	3	1
α-helix	329-330	2
β-strand	333-335	3	1
α-helix	336-337	2

Chain D: 82 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	33-41	9
α-helix	42-45	4
α-helix	51-64	14
α-helix	65-67	3
α-helix	71-74	4
α-helix	75-89	15
α-helix	96-112	17
α-helix	115-118	4
α-helix	119-121	3
α-helix	126-128	3
α-helix	130-135	6
α-helix	136-138	3
α-helix	147-159	13
α-helix	167-171	5
α-helix	181-184	4
α-helix	185-196	12
α-helix	203-211	9
α-helix	218-223	6
α-helix	225-238	14
α-helix	244-262	19
α-helix	266-269	4
α-helix	270-272	3
α-helix	273-283	11
α-helix	291-305	15
α-helix	310-311	2
α-helix	357-365	9
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	452-454	3	4
β-strand	457-459	3	4
α-helix	461-472	12
α-helix	484-486	3
α-helix	490-500	11
α-helix	504-520	17
α-helix	527-533	7
α-helix	542-547	6
α-helix	549-554	6
α-helix	561-566	6
α-helix	567-571	5
α-helix	577-590	14
α-helix	591-593	3
α-helix	595-597	3
α-helix	598-602	5
α-helix	603-609	7
α-helix	615-639	25
α-helix	643-645	3
α-helix	649-654	6
α-helix	658-663	6
α-helix	672-688	17
α-helix	698-712	15
α-helix	714-716	3
α-helix	722-740	19
α-helix	750-763	14
α-helix	769-779	11
α-helix	785-787	3
α-helix	791-802	12
α-helix	813-829	17
β-strand	831	1	5
β-strand	840	1	5
α-helix	846-853	8
β-strand	862	1	6
β-strand	865	1	6
α-helix	868-887	20
α-helix	891-893	3
α-helix	896-909	14
α-helix	915-929	15
β-strand	932	1	7
β-strand	935	1	7
α-helix	936	1
α-helix	942-948	7
α-helix	951-954	4
α-helix	962-964	3
α-helix	966-969	4
α-helix	970-974	5
α-helix	976-990	15
α-helix	995-1009	15
α-helix	1016-1032	17
α-helix	1037-1053	17
α-helix	1066-1079	14
α-helix	1085-1097	13
α-helix	1098-1100	3
α-helix	1104-1117	14
α-helix	1122-1138	17
α-helix	1145-1147	3
α-helix	1151-1157	7
α-helix	1164-1178	15

Chain E: 23 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	5-6	2
β-strand	13-16	4	8
β-strand	19-28	10	8
β-strand	35-41	7	8
α-helix	44-46	3
β-strand	49	1	8
β-strand	52-53	2	9
β-strand	56-57	2	9
β-strand	67-70	4	8
β-strand	76	1	8
β-strand	79	1	10
α-helix	81-85	5
α-helix	86-90	5
β-strand	105-106	2	11
β-strand	109-110	2	11
β-strand	111-113	3	12
α-helix	116-123	8
α-helix	126-128	3
β-strand	132	1	13
β-strand	139	1	10
α-helix	147-151	5
β-strand	157-159	3	13
β-strand	167	1	14
α-helix	169-177	9
β-strand	183-185	3	13
β-strand	192	1	14
β-strand	208-210	3	13
α-helix	218-224	7
α-helix	225-227	3
β-strand	233-235	3	13
β-strand	256-258	3	13
α-helix	267-270	4
α-helix	271-273	3
β-strand	281-283	3	13
β-strand	311-313	3	13
α-helix	323-328	6
β-strand	336-338	3	13
α-helix	349-351	3
α-helix	352-361	10
β-strand	367-368	2	13
β-strand	372	1	13
α-helix	375-395	21
α-helix	409-414	6
α-helix	419-424	6
α-helix	427-429	3
α-helix	430-432	3
α-helix	441-443	3
β-strand	445-451	7	15
β-strand	461-466	6	15
β-strand	470	1	16
α-helix	471-482	12
α-helix	486-488	3
β-strand	490-495	6	15
β-strand	498-504	7	15
β-strand	511	1	16
β-strand	522-526	5	15

Chain G: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	3-14	12
β-strand	16-23	8	17
α-helix	29-37	9
β-strand	50-57	8	17
β-strand	60-67	8	17
α-helix	77-80	4
β-strand	86-92	7	17
α-helix	99-110	12
β-strand	119-125	7	17
α-helix	132-134	3
α-helix	135-141	7
β-strand	154-156	3	17
β-strand	158	1	18
β-strand	163	1	18
α-helix	165-177	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin-specific chaperone C	C	protein	346	Homo sapiens	Q15814 (AlphaFold model)
Tubulin-specific chaperone D	D	protein	1192	Homo sapiens	Q9BTW9 (AlphaFold model)
Tubulin-specific chaperone E	E	protein	527	Homo sapiens	Q15813 (AlphaFold model)
ADP-ribosylation factor-like protein 2	G	protein	184	Homo sapiens	P36404 (AlphaFold model)
Tubulin alpha-1B chain	a	protein	451	Sus scrofa	Q2XVP4
Tubulin beta chain	b	protein	444	Sus scrofa	Q767L7

Sequence of entity 1 (C), FASTA

>9M1M_1 Tubulin-specific chaperone C (chains C)
MESVSCSAAAVRTGDMESQRDLSLVPERLQRREQERQLEVERRKQKRQNQEVEKENSHFF
VATFVRERAAVEELLERAESVERLEEAASRLQGLQKLINDSVFFLAAYDLRQGQEALARL
QAALAERRRGLQPKKRFAFKTRGKDAASSTKVDAAPGIPPAVESIQDSPLPKKAEGDLGP
SWVCGFSNLESQVLEKRASELHQRDVLLTELSNCTVRLYGNPNTLRLTKAHSCKLLCGPV
STSVFLEDCSDCVLAVACQQLRIHSTKDTRIFLQVTSRAIVEDCSGIQFAPYTWSYPEID
KDFESSGLDRSKNNWNDVDDFNWLARDMASPNWSILPEEERNIQWD

Sequence of entity 2 (D), FASTA

>9M1M_2 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 3 (E), FASTA

>9M1M_3 Tubulin-specific chaperone E (chains E)
MSDTLTADVIGRRVEVNGEHATVRFAGVVPPVAGPWLGVEWDNPERGKHDGSHEGTVYFK
CRHPTGGSFIRPNKVNFGTDFLTAIKNRYVLEDGPEEDRKEQIVTIGNKPVETIGFDSIM
KQQSQLSKLQEVSLRNCAVSCAGEKGGVAEACPNIRKVDLSKNLLSSWDEVIHIADQLRH
LEVLNVSENKLKFPSGSVLTGTLSVLKVLVLNQTGITWAEVLRCVAGCPGLEELYLESNN
IFISERPTDVLQTVKLLDLSSNQLIDENQLYLIAHLPRLEQLILSDTGISSLHFPDAGIG
CKTSMFPSLKYLVVNDNQISQWSFFNELEKLPSLRALSCLRNPLTKEDKEAETARLLIIA
SIGQLKTLNKCEILPEERRRAELDYRKAFGNEWKQAGGHKDPEKNRLSEEFLTAHPRYQF
LCLKYGAPEDWELKTQQPLMLKNQLLTLKIKYPHQLDQKVLEKQLPGSMTIQKVKGLLSR
LLKVPVSDLLLSYESPKKPGREIELENDLKSLQFYSVENGDCLLVRW

Sequence of entity 4 (G), FASTA

>9M1M_4 ADP-ribosylation factor-like protein 2 (chains G)
MGLLTILKKMKQKERELRLLMLGLDNAGKTTILKKFNGEDIDTISPTLGFNIKTLEHRGF
KLNIWDVGGQKSLRSYWRNYFESTDGLIWVVDSADRQRMQDCQRELQSLLVEERLAGATL
LIFANKQDLPGALSSNAIREVLELDSIRSHHWCIQGCSAVTGENLLPGIDWLLDDISSRI
FTAD

Sequence of entity 5 (a), FASTA

>9M1M_5 Tubulin alpha-1B chain (chains a)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 6 (b), FASTA

>9M1M_6 Tubulin beta chain (chains b)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGTYHGDSDLQLDRISVYYNEATGGKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKEAESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQVFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMAVTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAEEEEDFGEEAEEEA

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
AF3	Aluminum fluoride	Al F3	1
MG	Magnesium ion	Mg	3
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2

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 Q15814 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9M1N 2.24 Å, Cryo-EM structure of the TBC-DC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
2L3L The solution structure of the N-terminal domain of human Tubulin Binding Cofactor C…
2YUH Solution structure of the C-terminal region in human tubulin folding cofactor C

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