6RF2: C-terminal DC repeat (CDC) of human doublecortin

Cryo-EM structure of the C-terminal DC repeat (CDC) of human doublecortin (DCX) bound to 13-protofilament GDP.Pi-microtubule. Determined by electron microscopy at 4.2 Å resolution. Released 13 May 2020.

Method: Electron microscopy
Resolution: 4.2 Å
Organisms: Bos taurus, Homo sapiens
Chains: 5
Atoms: 14,328
Mol. weight: 204.83 kDa
Ligands: GDP, PO4, MG, GTP
Released: 13 May 2020

Explore 6RF2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6RF2 contains 87 α-helices and 82 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.

Chains a and A: 19 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	1
β-strand	6-9	4	2
α-helix	11-27	17
β-strand	53-55	3	3
β-strand	61-63	3	3
β-strand	65-68	4	2
α-helix	73-80	8
β-strand	92-93	2	2
α-helix	104-107	4
α-helix	115-127	13
β-strand	132-134	3	1
β-strand	137-138	2	2
β-strand	140	1	2
α-helix	145-160	16
β-strand	165	1	1
β-strand	168-172	5	2
α-helix	173-174	2
α-helix	183-197	15
β-strand	201-205	5	2
α-helix	206-215	10
α-helix	224-238	15
α-helix	240-243	4
β-strand	248	1	2
α-helix	252-258	7
β-strand	262	1	4
β-strand	265	1	4
β-strand	269-273	5	2
α-helix	290-296	7
α-helix	298-300	3
α-helix	307-309	3
β-strand	312-321	10	2
α-helix	325-335	11
β-strand	343	1	2
β-strand	351-356	6	2
α-helix	359-361	3
β-strand	373-381	9	2
α-helix	385-400	16
α-helix	406-409	4
α-helix	417-436	20

Chains b and B: 23 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	9
α-helix	11-26	16
α-helix	47-49	3
β-strand	51-53	3	10
α-helix	55-57	3
β-strand	59-61	3	10
β-strand	63-67	5	9
α-helix	74-77	4
β-strand	90-92	3	9
α-helix	103-107	5
α-helix	109-112	4
α-helix	114-126	13
β-strand	130-136	7	9
α-helix	143-158	16
β-strand	163-167	5	9
β-strand	169-170	2	11
α-helix	171-172	2
α-helix	181-195	15
β-strand	198-200	3	9
β-strand	202-203	2	11
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-236	15
β-strand	246	1	12
α-helix	252-255	4
β-strand	265-266	2	9
β-strand	267-271	5	12
α-helix	279-281	3
α-helix	286-293	8
β-strand	299	1	12
β-strand	310-318	9	12
α-helix	323-336	14
α-helix	338-340	3
β-strand	341	1	12
β-strand	349-353	5	12
α-helix	357-358	2
β-strand	364-371	8	12
α-helix	372-374	3
α-helix	375-389	15
α-helix	399-401	3
α-helix	405-424	20

Chain C: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	180-181	2	17
β-strand	183-185	3	18
β-strand	198-199	2	17
α-helix	207-213	7
α-helix	215-217	3
β-strand	228-229	2	18
β-strand	236	1	18
α-helix	240-242	3
β-strand	248-251	4	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Tubulin alpha-1B chain	A, a	protein	432	Bos taurus	P81947 (AlphaFold model)
Tubulin beta-2B chain	B, b	protein	429	Bos taurus	Q6B856 (AlphaFold model)
Neuronal migration protein doublecortin	C	protein	87	Homo sapiens	O43602 (AlphaFold model)

Sequence of entity 1 (A, a), FASTA

>6RF2_1 Tubulin alpha-1B chain (chains A, a)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPDSFNTFFSETGAGKHVPRAVFVD
LEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQC
TGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSIL
TTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALN
VDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRH
GKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLA
KVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALE
KDYEEVGVDSVE

Sequence of entity 2 (B, b), FASTA

>6RF2_2 Tubulin beta-2B chain (chains B, b)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDAT

Sequence of entity 3 (C), FASTA

>6RF2_3 Neuronal migration protein doublecortin (chains C)
RPKLVTIIRSGVKPRKAVRVLLNKKTAHSFEQVLTDITEAIKLETGVVKKLYTLDGKQVT
CLHDFFGDDDVFIACGPEKFRYAQDDF

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
PO4	Phosphate ion	O4 P	2
MG	Magnesium ion	Mg	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2

Primary citation

Pseudo-repeats in doublecortin make distinct mechanistic contributions to microtubule regulation. Manka, S.W., Moores, C.A. EMBO Rep (2020) 21:e51534-e51534. DOI 10.15252/embr.202051534 · PubMed

Other PDB entries of the same protein (UniProt P81947 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6S8K 1.52 Å, Structure, Thermodynamics, and Kinetics of Plinabulin Binding to two Tubulin Isotypes
8QL2 1.7 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
6ZWB 1.75 Å, Z-SBTub3 photoswitch bound to tubulin-DARPin D1 complex
4I4T 1.8 Å, Crystal structure of tubulin-RB3-TTL-Zampanolide complex
5IYZ 1.8 Å, Tubulin-MMAE complex
5NQU 1.8 Å, Tubulin Darpin cryo structure
7YZ3 1.8 Å, Molecular snapshots of drug release from tubulin: Apo state
8QEA 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
8QL3 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
8QL4 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
8QL5 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…
8QL6 1.8 Å, Ultrafast structural transitions in an azobenzene photoswitch at near-atomic resolution:…

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