6RF8: 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 13-protofilament GDP-microtubule. Determined by electron microscopy at 3.8 Å resolution. Released 15 Apr 2020.

Method: Electron microscopy
Resolution: 3.8 Å
Organisms: Homo sapiens, Bos taurus
Chains: 5
Atoms: 14,407
Mol. weight: 206.18 kDa
Ligands: GDP, GTP, MG
Released: 15 Apr 2020

Explore 6RF8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6RF8 contains 89 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: 22 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	6-9	4	18
α-helix	10-26	17
β-strand	53-55	3	19
β-strand	61-63	3	19
β-strand	65-68	4	18
α-helix	75-80	6
β-strand	92-93	2	18
α-helix	103-104	2
α-helix	105-109	5
α-helix	111-127	17
β-strand	134-138	5	18
α-helix	144	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	18
α-helix	173-174	2
α-helix	183-194	12
β-strand	200-205	6	18
α-helix	207-215	9
α-helix	224-238	15
α-helix	240-243	4
β-strand	248	1	18
α-helix	252-259	8
β-strand	269-273	5	18
α-helix	288-296	9
α-helix	307-309	3
β-strand	312	1	20
β-strand	317-321	5	18
α-helix	325-335	11
β-strand	343	1	20
β-strand	353-356	4	18
α-helix	358-361	4
β-strand	373-379	7	18
β-strand	381	1	20
α-helix	385-400	16
α-helix	406-409	4
α-helix	416-436	21
α-helix	438-439	2

Chains b and B: 21 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	3
α-helix	10-28	19
β-strand	30	1	4
β-strand	36	1	4
α-helix	47-49	3
β-strand	51-54	4	5
β-strand	58-61	4	5
β-strand	63-67	5	3
α-helix	73-78	6
β-strand	90-92	3	3
α-helix	101-102	2
α-helix	103-107	5
α-helix	108-126	19
β-strand	130-136	7	3
β-strand	138	1	6
α-helix	143-156	14
β-strand	163-166	4	3
β-strand	169-170	2	6
α-helix	171-172	2
α-helix	181-195	15
β-strand	198-200	3	3
β-strand	202-203	2	6
α-helix	204-209	6
α-helix	210-214	5
α-helix	222-236	15
β-strand	244-246	3	7
α-helix	250-256	7
β-strand	265-266	2	3
β-strand	268-271	4	7
α-helix	286-293	8
α-helix	296-298	3
α-helix	305-307	3
β-strand	310-317	8	7
β-strand	318	1	8
α-helix	323-335	13
β-strand	341	1	7
β-strand	349-354	6	7
α-helix	356-358	3
β-strand	364	1	8
β-strand	365-371	7	7
α-helix	375-389	15
α-helix	396-399	4
α-helix	405-424	20

Chain N: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	53-55	3	1
β-strand	57-59	3	2
α-helix	68-69	2
β-strand	70-72	3	1
α-helix	80-89	10
β-strand	103-106	4	2
β-strand	112	1	2
α-helix	116-118	3
β-strand	125-128	4	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Neuronal migration protein doublecortin	N	protein	99	Homo sapiens	O43602 (AlphaFold model)
Tubulin beta-2B chain	B, b	protein	429	Bos taurus	Q6B856 (AlphaFold model)
Tubulin alpha-1B chain	A, a	protein	432	Bos taurus	P81947 (AlphaFold model)

Sequence of entity 1 (N), FASTA

>6RF8_1 Neuronal migration protein doublecortin (chains N)
QALSNEKKAKKVRFYRNGDRYFKGIVYAVSSDRFRSFDALLADLTRSLSDNINLPQGVRY
IYTIDGSRKIGSMDELEEGESYVCSSDNFFKKVEYTKNV

Sequence of entity 2 (B, b), FASTA

>6RF8_2 Tubulin beta-2B chain (chains B, b)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDAT

Sequence of entity 3 (A, a), FASTA

>6RF8_3 Tubulin alpha-1B chain (chains A, a)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPDSFNTFFSETGAGKHVPRAVFVD
LEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLDRIRKLADQC
TGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTAVVEPYNSIL
TTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLISQIVSSITASLRFDGALN
VDLTEFQTNLVPYPRIHFPLATYAPVISAEKAYHEQLSVAEITNACFEPANQMVKCDPRH
GKYMACCLLYRGDVVPKDVNAAIATIKTKRSIQFVDWCPTGFKVGINYQPPTVVPGGDLA
KVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSEAREDMAALE
KDYEEVGVDSVE

Ligands and cofactors

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

Primary citation

A microtubule RELION-based pipeline for cryo-EM image processing. Cook, A.D., Manka, S.W., Wang, S. et al. J Struct Biol (2020) 209:107402-107402. DOI 10.1016/j.jsb.2019.10.004 · PubMed

Other PDB entries of the same protein (UniProt O43602 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5IO9 1.3 Å, X-ray structure of the N-terminal domain of human doublecortin
5IP4 1.81 Å, X-ray structure of the C-terminal domain of human doublecortin
5IKC 2.06 Å, X-RAY STRUCTURE OF THE N-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN in complex with FAB
2BQQ 2.2 Å, X-ray Structure of the N-terminal Domain of Human Doublecortin
6FNZ 2.23 Å, Crystal Structure of domain-swapped C-terminal domain of human doublecortin
5IOI 2.4 Å, X-ray structure of the N-terminal domain of human doublecortin
5IN7 2.48 Å, X-ray structure of the N-terminal domain of human doublecortin
6REV 3.8 Å, Cryo-EM structure of the N-terminal DC repeat (NDC) of human doublecortin (DCX) bound to…
6RFD 3.9 Å, Cryo-EM structure of the N-terminal DC repeat (NDC) of NDC-NDC chimera (human sequence)…
6RF2 4.2 Å, Cryo-EM structure of the C-terminal DC repeat (CDC) of human doublecortin (DCX) bound to…
2XRP 8.2 Å, Human Doublecortin N-DC Repeat (1MJD) and Mammalian Tubulin (1JFF and 3HKE) Docked into…
4ATU 8.3 Å, Human doublecortin N-DC repeat plus linker, and tubulin (2XRP) docked into an 8A cryo-EM…

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