5IJ9: Tubulin alpha-1B chain

Cryo EM density of microtubule assembled from human TUBB3-D417H mutant. Determined by electron microscopy at 3.7 Å resolution. Released 20 Apr 2016.

Method: Electron microscopy
Resolution: 3.7 Å
Organism: Homo sapiens
Chains: 2
Atoms: 6,783
Mol. weight: 97.49 kDa
Ligands: GTP, MG, GDP
Released: 20 Apr 2016

Explore 5IJ9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5IJ9 contains 52 α-helices and 38 β-strands across 2 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: 28 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	10-27	18
β-strand	31	1	2
β-strand	35	1	2
α-helix	47-49	3
β-strand	53-55	3	3
β-strand	61-63	3	3
β-strand	65-69	5	1
α-helix	73-80	8
α-helix	82-85	4
β-strand	92-94	3	1
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-113	3
α-helix	115-127	13
β-strand	132-140	9	1
α-helix	144	1
α-helix	145-149	5
α-helix	150-161	12
β-strand	165-171	7	1
α-helix	172-174	3
α-helix	183-195	13
β-strand	200-204	5	1
α-helix	206-212	7
α-helix	213-217	5
α-helix	224-243	20
β-strand	248	1	1
α-helix	252-259	8
β-strand	262	1	4
β-strand	265	1	4
α-helix	268	1
β-strand	269-273	5	1
α-helix	280-283	4
α-helix	288-295	8
α-helix	298-300	3
β-strand	301	1	1
α-helix	307-309	3
β-strand	312	1	5
β-strand	315-321	7	1
α-helix	325-337	13
β-strand	343	1	5
β-strand	351-355	5	1
α-helix	361-363	3
α-helix	369-370	2
β-strand	373-379	7	1
α-helix	383-400	18
α-helix	405-410	6
α-helix	415-436	22

Chain B: 24 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	6
α-helix	12-27	16
β-strand	30	1	7
β-strand	36	1	7
α-helix	41-44	4
α-helix	47-49	3
β-strand	51-53	3	8
β-strand	59-61	3	8
β-strand	63-67	5	6
α-helix	70-78	9
α-helix	80-83	4
α-helix	87-89	3
β-strand	90-92	3	6
α-helix	101-102	2
α-helix	103-108	6
α-helix	110-125	16
β-strand	129-138	10	6
α-helix	142	1
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-169	7	6
α-helix	181-195	15
β-strand	198-202	5	6
α-helix	204-213	10
α-helix	222-241	20
β-strand	244-245	2	9
α-helix	250-257	8
β-strand	265-266	2	6
β-strand	267-271	5	9
α-helix	279-281	3
α-helix	286-293	8
α-helix	296-298	3
β-strand	310	1	10
β-strand	312-319	8	9
α-helix	323-336	14
β-strand	341	1	10
β-strand	349-354	6	9
α-helix	357-358	2
β-strand	363-370	8	9
α-helix	373-390	18
α-helix	395-400	6
α-helix	405-424	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A	protein	437	Homo sapiens	P68363 (AlphaFold model)
Tubulin beta-3 chain	B	protein	426	Homo sapiens	Q13509 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5IJ9_1 Tubulin alpha-1B chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGV

Sequence of entity 2 (B), FASTA

>5IJ9_2 Tubulin beta-3 chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPSGNYVGDSDLQLERISVYYNEASSHKYV
PRAILVDLEPGTMDSVRSGAFGHLFRPDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKECENCDCLQGFQLTHSLGGGTGSGMGTLLISKVREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSIHQLVENTDETYCIDNEALYDICFRTLKLATPTYGDLNHLVSATMSGVTTSL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTARGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVATVFRGRMSMKEVDEQMLAIQSKNSSYFVEWIPNNVKVAVCDIPPRG
LKMSSTFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNHLVS
EYQQYQ

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1

Primary citation

Mutations in Human Tubulin Proximal to the Kinesin-Binding Site Alter Dynamic Instability at Microtubule Plus- and Minus-Ends. Ti, S.C., Pamula, M.C., Howes, S.C. et al. Dev Cell (2016) 37:72-84. DOI 10.1016/j.devcel.2016.03.003 · PubMed

Other PDB entries of the same protein (UniProt P68363 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6S8L 1.8 Å, Structure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin Isotypes
6J8O 1.85 Å, Structure of a hypothetical protease
7PJF 1.86 Å, Inhibiting parasite proliferation using a rationally designed anti-tubulin agent
6J4V 2.1 Å, Structural basis of tubulin detyrosination by vasohibins-SVBP enzyme complex and…
8VT7 2.66 Å, Structure of the gamma tubulin ring complex nucleated microtubule protofilament.
7Z6S 2.9 Å, MATCAP bound to a human 14 protofilament microtubule
8V2J 2.9 Å, Structure of alpha1B and betaI/IVb microtubule bound to GDP
9COC 2.9 Å, Two protofilament structure of alpha1B and betaI/IVb microtubule bound to GDP
9BP6 3.1 Å, Structure of alpha1B and betaI/IVb microtubule bound to GMPCPP
9CMM 3.1 Å, Two protofilament structure of alpha1B and betaI/IVb microtubule bound to GMPCPP
7LXB 3.26 Å, HeLa-tubulin in complex with cryptophycin 52
9HQ4 3.28 Å, TTLL11 bound to microtubule

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