3JAR: GDP-microtubule co-polymerized with EB3

Cryo-EM structure of GDP-microtubule co-polymerized with EB3. Determined by electron microscopy at 3.4 Å resolution. Released 12 Aug 2015.

Method: Electron microscopy
Resolution: 3.4 Å
Organisms: Sus scrofa, Homo sapiens
Chains: 14
Atoms: 43,024
Mol. weight: 652.35 kDa
Ligands: GDP, MG, GTP
Released: 12 Aug 2015

Explore 3JAR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3JAR contains 336 α-helices and 192 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.

Chains A, C, E, J, K and L: 28 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-9	6	25
α-helix	10-28	19
α-helix	48-51	4
β-strand	53-55	3	26
β-strand	61-63	3	26
β-strand	65-69	5	25
α-helix	73-80	8
α-helix	89-91	3
β-strand	92-94	3	25
α-helix	103-107	5
α-helix	111-113	3
α-helix	115-127	13
β-strand	134-140	7	25
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	25
α-helix	173-174	2
α-helix	183-194	12
α-helix	195-197	3
β-strand	200-205	6	25
α-helix	206-217	12
α-helix	224-243	20
β-strand	246-248	3	25
α-helix	253-259	7
β-strand	269-273	5	25
α-helix	278-281	4
α-helix	288-296	9
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-321	10	25
α-helix	325-337	13
β-strand	343	1	25
β-strand	351-356	6	25
α-helix	359-361	3
α-helix	369-370	2
β-strand	373-381	9	25
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-410	6
α-helix	415-436	22
α-helix	438-440	3

Chains B, D, F, G, H and I: 25 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	27
α-helix	10-27	18
β-strand	30	1	28
β-strand	36	1	28
α-helix	42-47	4
α-helix	49-51	3
β-strand	53-56	4	29
β-strand	60-63	4	29
β-strand	65-69	5	27
α-helix	73-80	8
α-helix	84-86	3
α-helix	89-91	3
β-strand	92-94	3	27
α-helix	103-107	5
α-helix	110-128	19
β-strand	132-140	9	27
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	27
α-helix	173-174	2
α-helix	183-197	15
β-strand	200-205	6	27
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-243	20
β-strand	246-248	3	30
α-helix	252-259	8
β-strand	267-268	2	27
β-strand	269-273	5	30
α-helix	288-296	9
β-strand	301	1	30
α-helix	307-309	3
β-strand	312-321	10	30
α-helix	325-338	14
α-helix	340-342	3
β-strand	343	1	30
β-strand	351-356	6	30
α-helix	359-360	2
β-strand	373-381	9	30
α-helix	382-384	3
α-helix	385-399	15
α-helix	405-409	5
α-helix	415-437	23

Chains M and N: 9 helices, 0 β-strands

Element	Residues	Length
α-helix	17-28	12
α-helix	35-40	6
α-helix	42-51	10
α-helix	58-60	3
α-helix	68-85	18
α-helix	89-91	3
α-helix	93-97	5
α-helix	101-118	18
α-helix	126-130	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A, C, E, J, K, L	protein	451	Sus scrofa	Q2XVP4 (AlphaFold model)
Tubulin beta chain	B, D, F, G, H, I	protein	445	Sus scrofa	P02554 (AlphaFold model)
Microtubule-associated protein RP/EB family member 3	M, N	protein	203	Homo sapiens	Q9UPY8 (AlphaFold model)

Sequence of entity 1 (A, C, E, J, K, L), FASTA

>3JAR_1 Tubulin alpha-1B chain (chains A, C, E, J, K, L)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 2 (B, D, F, G, H, I), FASTA

>3JAR_2 Tubulin beta chain (chains B, D, F, G, H, I)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEGEEDEA

Sequence of entity 3 (M, N), FASTA

>3JAR_3 Microtubule-associated protein RP/EB family member 3 (chains M, N)
SNAMAVNVYSTSVTSENLSRHDMLAWVNDSLHLNYTKIEQLCSGAAYCQFMDMLFPGCVH
LRKVKFQAKLEHEYIHNFKVLQAAFKKMGVDKIIPVEKLVKGKFQDNFEFIQWFKKFFDA
NYDGKDYNPLLARQGQDVAPPPNPGDQIFNKSKKLIGTAVPQRTSPTGPKNMQTSGRLSN
VAPPCILRKNPPSARNGGHETDA

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	6
MG	Magnesium ion	Mg	6
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	6

Primary citation

Mechanistic Origin of Microtubule Dynamic Instability and Its Modulation by EB Proteins. Zhang, R., Alushin, G.M., Brown, A. et al. Cell (2015) 162:849-859. DOI 10.1016/j.cell.2015.07.012 · PubMed

Other PDB entries of the same protein (UniProt Q2XVP4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9U6A 1.92 Å, Tubulin-DARPin D1 in complex with a flavone
5EZY 2.05 Å, Crystal structure of T2R-TTL-taccalonolide AJ complex
5YL2 2.09 Å, Crystal structure of T2R-TTL-Y28 complex
7TTF 2.1 Å, Tubulin-RB3_SLD in complex with compound 12k
5XKG 2.2 Å, Crystal structure of T2R-TTL-CH1 complex
7L05 2.21 Å, Complex of novel maytansinoid M24 bound to T2R-TTL (two tubulin alpha/beta heterodimers,…
9M1M 2.21 Å, Cryo-EM structure of the TBC-DEC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
5JQG 2.24 Å, An apo tubulin-RB-TTL complex structure used for side-by-side comparison
9M1N 2.24 Å, Cryo-EM structure of the TBC-DC-Arl2-alpha-beta-tubulin complex with GDP-AlFx
5XKH 2.25 Å, Crystal structure of T2R-TTL-CF1 complex
7TTD 2.27 Å, Tubulin-RB3_SLD in complex with compound 12e
5JCB 2.3 Å, Microtubule depolymerizing agent podophyllotoxin derivative YJTSF1

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