6RFD: N-terminal DC repeat (NDC) of NDC-NDC chimera

Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence) bound to 14-protofilament GDP-microtubule. Determined by electron microscopy at 3.9 Å resolution. Released 13 May 2020.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Bos taurus, Homo sapiens
Chains: 5
Atoms: 14,407
Mol. weight: 206.18 kDa
Ligands: GDP, MG, GTP
Released: 13 May 2020

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

Secondary structure: helices and β-sheets

6RFD contains 97 α-helices and 79 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: 24 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	5-9	5	3
α-helix	10-26	17
α-helix	49-51	3
β-strand	53-55	3	4
β-strand	61-63	3	4
β-strand	65-68	4	3
α-helix	73-79	7
α-helix	89-91	3
β-strand	92-93	2	3
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-126	16
β-strand	134-138	5	3
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	3
α-helix	173-174	2
α-helix	183-194	12
β-strand	200-205	6	3
α-helix	206-215	10
α-helix	224-238	15
α-helix	240-243	4
β-strand	248	1	3
α-helix	252-259	8
β-strand	268-273	6	3
α-helix	288-296	9
α-helix	307-309	3
β-strand	312-314	3	3
β-strand	317-321	5	3
α-helix	325-337	13
β-strand	343	1	3
β-strand	353-356	4	3
α-helix	358-361	4
β-strand	373-381	9	3
α-helix	385-400	16
α-helix	406-409	4
α-helix	417-436	20
α-helix	438-439	2

Chain b: 23 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	11
α-helix	10-27	18
β-strand	30	1	12
β-strand	36	1	12
α-helix	47-49	3
β-strand	51-54	4	13
β-strand	58-61	4	13
β-strand	63-67	5	11
α-helix	73-78	6
β-strand	90-92	3	11
α-helix	101-102	2
α-helix	103-107	5
α-helix	108-110	3
α-helix	113-126	14
β-strand	130-136	7	11
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-166	4	11
β-strand	169-170	2	14
α-helix	171-172	2
α-helix	181-195	15
β-strand	198-200	3	11
β-strand	202-203	2	14
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-236	15
β-strand	246	1	11
α-helix	250-256	7
β-strand	265-271	7	11
α-helix	286-292	7
α-helix	296-298	3
β-strand	299	1	11
α-helix	305-307	3
β-strand	310-317	8	11
β-strand	318	1	15
α-helix	323-336	14
β-strand	341	1	11
β-strand	349-353	5	11
α-helix	356-358	3
β-strand	364	1	15
β-strand	365-371	7	11
α-helix	375-389	15
α-helix	396-399	4
α-helix	405-426	22

Chain B: 23 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	5
α-helix	10-27	18
β-strand	30	1	6
β-strand	36	1	6
α-helix	47-49	3
β-strand	51-54	4	7
β-strand	58-61	4	7
β-strand	63-67	5	5
α-helix	73-78	6
β-strand	90-92	3	5
α-helix	101-102	2
α-helix	103-107	5
α-helix	108-110	3
α-helix	113-126	14
β-strand	130-136	7	5
α-helix	143-147	5
α-helix	148-158	11
β-strand	163-166	4	5
β-strand	169-170	2	8
α-helix	171-172	2
α-helix	181-195	15
β-strand	198-200	3	5
β-strand	202-203	2	8
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-236	15
β-strand	246	1	9
α-helix	250-256	7
β-strand	265-266	2	5
β-strand	267-271	5	9
α-helix	286-292	7
α-helix	296-298	3
β-strand	299	1	9
α-helix	305-307	3
β-strand	310-317	8	9
β-strand	318	1	10
α-helix	323-336	14
β-strand	341	1	9
β-strand	349-353	5	9
α-helix	356-358	3
β-strand	364	1	10
β-strand	365-371	7	9
α-helix	375-389	15
α-helix	396-399	4
α-helix	405-426	22

Chain N: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	53-55	3	16
β-strand	56-59	4	17
α-helix	68-69	2
β-strand	70-72	3	16
α-helix	81-89	9
β-strand	103-106	4	17
β-strand	112	1	17
α-helix	116-118	3
β-strand	124-128	5	17

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	N	protein	99	Homo sapiens	O43602 (AlphaFold model)

Sequence of entity 1 (A, a), FASTA

>6RFD_1 Tubulin alpha-1B chain (chains A, a)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPDSFNTFFSETGAGKHVPRAVFVD
LEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQC
TGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSIL
TTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALN
VDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRH
GKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLA
KVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALE
KDYEEVGVDSVE

Sequence of entity 2 (B, b), FASTA

>6RFD_2 Tubulin beta-2B chain (chains B, b)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDAT

Sequence of entity 3 (N), FASTA

>6RFD_3 Neuronal migration protein doublecortin (chains N)
QALSNEKKAKKVRFYRNGDRYFKGIVYAVSSDRFRSFDALLADLTRSLSDNINLPQGVRY
IYTIDGSRKIGSMDELEEGESYVCSSDNFFKKVEYTKNV

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	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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