9F3R: PDB entry 9F3R

13pf E254Q microtubule from recombinant human tubulin decorated with EB3. Determined by electron microscopy at 4.3 Å resolution. Released 19 Mar 2025.

Method: Electron microscopy
Resolution: 4.3 Å
Organism: Homo sapiens
Chains: 14
Atoms: 43,264
Mol. weight: 649.4 kDa
Ligands: MG, GTP
Released: 19 Mar 2025

Explore 9F3R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9F3R contains 299 α-helices and 236 β-strands across 14 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: 23 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	10-28	19
α-helix	49-51	3
β-strand	53-55	3	2
β-strand	61-63	3	2
β-strand	65-69	5	1
α-helix	73-80	8
β-strand	93-94	2	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-128	14
β-strand	132-138	7	1
α-helix	144-160	17
β-strand	165-169	5	1
β-strand	172	1	3
α-helix	173-174	2
α-helix	183-194	12
β-strand	200-202	3	1
β-strand	203	1	4
β-strand	205	1	3
α-helix	206-212	7
α-helix	213-217	5
α-helix	224-243	20
β-strand	248	1	4
α-helix	252-259	8
β-strand	269-273	5	4
α-helix	279-282	4
α-helix	288-296	9
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-321	10	4
α-helix	325-337	13
β-strand	343	1	4
β-strand	352-356	5	4
α-helix	359-361	3
β-strand	373-381	9	4
α-helix	384-399	16
α-helix	405-410	6
α-helix	415-436	22

Chain B: 23 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	5
α-helix	10-28	19
β-strand	30	1	6
β-strand	36	1	6
α-helix	42-45	4
β-strand	51-54	4	7
β-strand	58-61	4	7
β-strand	63-67	5	5
α-helix	71-78	8
α-helix	87-89	3
β-strand	91-92	2	5
α-helix	101-102	2
α-helix	103-107	5
α-helix	109-126	18
β-strand	130-138	9	5
α-helix	143-158	16
β-strand	163-169	7	5
α-helix	170-172	3
α-helix	182-195	14
β-strand	198-202	5	5
α-helix	205-213	9
α-helix	222-241	20
β-strand	246	1	8
α-helix	250-257	8
β-strand	265-266	2	5
β-strand	267-271	5	8
α-helix	277-279	3
α-helix	286-293	8
α-helix	296-298	3
α-helix	305-307	3
β-strand	310-317	8	8
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	8
β-strand	350-353	4	8
α-helix	357-358	2
β-strand	365-371	7	8
α-helix	374-391	18
α-helix	396-399	4
α-helix	405-426	22

Chain C: 25 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	21
α-helix	10-28	19
α-helix	49-51	3
β-strand	53-55	3	22
β-strand	61-63	3	22
β-strand	65-69	5	21
α-helix	72-80	9
β-strand	93-94	2	21
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-128	14
β-strand	134-138	5	21
α-helix	148-160	13
β-strand	165-172	8	21
α-helix	173-174	2
α-helix	183-194	12
β-strand	200-205	6	21
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-238	15
α-helix	240-243	4
β-strand	248	1	23
α-helix	252-258	7
β-strand	269-273	5	21
α-helix	279-281	3
α-helix	288-294	7
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-314	3	24
β-strand	317-321	5	23
α-helix	325-337	13
β-strand	343	1	24
β-strand	353-356	4	23
α-helix	359-361	3
α-helix	368-370	3
β-strand	373-374	2	23
β-strand	375-379	5	21
β-strand	380-381	2	24
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-410	6
α-helix	415-436	22

Chain D: 24 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	25
α-helix	10-28	19
β-strand	30	1	26
β-strand	35	1	27
β-strand	36	1	26
β-strand	53	1	28
α-helix	55-57	3
β-strand	58	1	27
β-strand	59	1	28
β-strand	63-67	5	25
α-helix	71-77	7
α-helix	87-89	3
β-strand	90-92	3	25
α-helix	102	1
α-helix	103-107	5
α-helix	108-126	19
β-strand	130-136	7	25
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-166	4	25
β-strand	169	1	29
α-helix	182-192	11
β-strand	198-200	3	25
β-strand	202	1	29
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-241	20
β-strand	246	1	30
α-helix	250-257	8
β-strand	265-266	2	25
β-strand	267-271	5	30
α-helix	277-279	3
α-helix	286-294	9
α-helix	296-298	3
α-helix	305-307	3
β-strand	310-317	8	30
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	30
β-strand	349-353	5	30
α-helix	357-358	2
β-strand	365-371	7	30
α-helix	375-390	16
α-helix	395-397	3
α-helix	405-427	23

Chain E: 24 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	40
α-helix	10-27	18
α-helix	49-51	3
β-strand	53-55	3	41
β-strand	61-63	3	41
β-strand	65-69	5	40
α-helix	73-80	8
β-strand	93-94	2	40
α-helix	105-109	5
α-helix	112-128	17
β-strand	132-138	7	40
α-helix	148-160	13
β-strand	165-172	8	40
α-helix	173-174	2
α-helix	183-194	12
α-helix	195-197	3
β-strand	200-205	6	40
α-helix	206-215	10
α-helix	224-238	15
α-helix	240-243	4
β-strand	248	1	42
α-helix	252-258	7
β-strand	269	1	40
β-strand	272-273	2	42
α-helix	279-281	3
α-helix	288-295	8
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-314	3	43
β-strand	319-321	3	42
α-helix	325-337	13
β-strand	343	1	43
β-strand	355-356	2	42
α-helix	359-361	3
α-helix	369-370	2
β-strand	373-376	4	42
β-strand	379	1	40
β-strand	380-381	2	43
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-409	5
α-helix	415-436	22

Chain F: 24 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	44
α-helix	10-28	19
β-strand	30	1	45
β-strand	35	1	46
β-strand	36	1	45
α-helix	43-46	4
β-strand	51-53	3	47
α-helix	55-57	3
β-strand	58	1	46
β-strand	59-61	3	47
β-strand	63-67	5	44
α-helix	71-78	8
α-helix	87-89	3
β-strand	91-92	2	44
α-helix	102-105	4
α-helix	109-126	18
β-strand	130-136	7	44
α-helix	143-147	5
α-helix	148-158	11
β-strand	165-166	2	44
β-strand	169	1	48
α-helix	182-192	11
β-strand	198-200	3	44
β-strand	202	1	48
α-helix	205-209	5
α-helix	210-214	5
α-helix	222-241	20
β-strand	246	1	49
α-helix	250-257	8
β-strand	265-266	2	44
β-strand	267	1	49
β-strand	270-271	2	49
α-helix	277-279	3
α-helix	286-293	8
α-helix	296-298	3
α-helix	305-307	3
β-strand	310-317	8	49
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	49
β-strand	349-353	5	49
α-helix	357-358	2
β-strand	365-371	7	49
α-helix	374-390	17
α-helix	395-397	3
α-helix	405-423	19

Chain G: 21 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	9
α-helix	10-27	18
α-helix	49-51	3
β-strand	53-55	3	10
β-strand	61-63	3	10
β-strand	65-69	5	9
α-helix	73-79	7
β-strand	93-94	2	9
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-128	14
β-strand	132-138	7	9
α-helix	148-160	13
β-strand	165-169	5	9
β-strand	172	1	11
α-helix	173-174	2
α-helix	183-194	12
β-strand	200-202	3	9
β-strand	203	1	12
β-strand	205	1	11
α-helix	206-215	10
α-helix	224-238	15
α-helix	240-243	4
β-strand	248	1	13
α-helix	252-259	8
β-strand	269-273	5	12
α-helix	288-295	8
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-314	3	14
β-strand	317-321	5	12
α-helix	325-337	13
β-strand	343	1	14
β-strand	355	1	13
β-strand	373-379	7	12
β-strand	380-381	2	14
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-409	5
α-helix	415-436	22

Chain I: 22 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	31
α-helix	10-27	18
α-helix	49-51	3
β-strand	53-55	3	32
β-strand	61-63	3	32
β-strand	65-69	5	31
α-helix	75-80	6
β-strand	93-94	2	31
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-128	14
β-strand	132-138	7	31
α-helix	148-160	13
β-strand	165-172	8	31
α-helix	173-174	2
α-helix	183-193	11
β-strand	200-205	6	31
α-helix	206-215	10
α-helix	224-238	15
β-strand	248	1	33
α-helix	252-259	8
β-strand	269-273	5	31
α-helix	288-295	8
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-314	3	34
β-strand	317-321	5	31
α-helix	327-336	10
β-strand	343	1	34
β-strand	355	1	33
α-helix	362-363	2
β-strand	373-379	7	31
β-strand	380-381	2	34
α-helix	382-384	3
α-helix	385-400	16
α-helix	405-409	5
α-helix	415-436	22

6 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Microtubule-associated protein RP/EB family member 3	S, T	protein	131	Homo sapiens	Q9UPY8 (AlphaFold model)
Detyrosinated tubulin alpha-1B chain	A, C, E, G, I, K	protein	453	Homo sapiens	P68363 (AlphaFold model)
Tubulin beta-3 chain	B, D, F, N, P, R	protein	456	Homo sapiens	Q13509 (AlphaFold model)

Sequence of entity 1 (S, T), FASTA

>9F3R_1 Microtubule-associated protein RP/EB family member 3 (chains S, T)
MAVNVYSTSVTSENLSRHDMLAWVNDSLHLNYTKIEQLCSGAAYCQFMDMLFPGCVHLRK
VKFQAKLEHEYIHNFKVLQAAFKKMGVDKIIPVEKLVKGKFQDNFEFIQWFKKFFDANYD
GKDYNPLLARQ

Sequence of entity 2 (A, C, E, G, I, K), FASTA

>9F3R_2 Detyrosinated tubulin alpha-1B chain (chains A, C, E, G, I, K)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIHHHHHHGGGHHHFNTFDS
FNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHY
TIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLE
FSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLN
RLISQIVSSITASLRFDGALNVDLTQFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSV
AEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCP
TGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWY
VGEGMEEGEFSEAREDMAALEKDYEEVGVDSVE

Sequence of entity 3 (B, D, F, N, P, R), FASTA

>9F3R_3 Tubulin beta-3 chain (chains B, D, F, N, P, R)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPSGNYVGDSDLQLERISVYYNEASSHKYV
PRAILVDLEPGTMDSVRSGAFGHLFRPDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKECENCDCLQGFQLTHSLGGGTGSGMGTLLISKVREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSIHQLVENTDETYCIDNEALYDICFRTLKLATPTYGDLNHLVSATMSGVTTSL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTARGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVATVFRGRMSMKEVDEQMLAIQSKNSSYFVEWIPNNVKVAVCDIPPRG
LKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATAEEEGEMYEDDEEESEAQGPKENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	12
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	12

Primary citation

Hydrolysis-deficient mosaic microtubules as faithful mimics of the GTP cap. Estevez-Gallego, J., Blum, T.B., Ruhnow, F. et al. Nat Commun (2025) 16:2396-2396. DOI 10.1038/s41467-025-57555-6 · PubMed

Other PDB entries of the same protein (UniProt Q9UPY8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3CO1 1.4 Å, Crystal structure of microtubule binding domain of human EB3
3TQ7 2.3 Å, EB1c/EB3c heterodimer in complex with the CAP-Gly domain of P150glued
3JAK 3.3 Å, Cryo-EM structure of GTPgammaS-microtubule co-polymerized with EB3 (merged dataset with…
3JAR 3.4 Å, Cryo-EM structure of GDP-microtubule co-polymerized with EB3
3JAL 3.5 Å, Cryo-EM structure of GMPCPP-microtubule co-polymerized with EB3
7SJ9 3.8 Å, 13pf E254A microtubule from recombinant human tubulin decorated with EB3
9F3S 4.2 Å, 13pf mosaic 20%E254Q - 80% E254N microtubule from recombinant human tubulin decorated…
1WYO Solution structure of the CH domain of human microtubule-associated protein RP/EB family…

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