3J6P: Dynein heavy chain, cytoplasmic

Pseudo-atomic model of dynein microtubule binding domain-tubulin complex based on a cryoEM map. Determined by electron microscopy at 8.2 Å resolution. Released 31 Dec 2014.

Method: Electron microscopy
Resolution: 8.2 Å
Organisms: Dictyostelium discoideum, Sus scrofa
Chains: 3
Atoms: 7,563
Mol. weight: 114.19 kDa
Ligands: TA1, GDP, GTP, MG
Released: 31 Dec 2014

Explore 3J6P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3J6P contains 52 α-helices and 31 β-strands across 3 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: 20 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-9	7	1
α-helix	11-28	18
β-strand	66-69	4	1
α-helix	72-80	9
β-strand	92-94	3	1
α-helix	103-107	5
α-helix	109-128	20
β-strand	132-140	9	1
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-172	8	1
α-helix	184-194	11
β-strand	200-205	6	1
α-helix	206-211	6
α-helix	212-217	6
α-helix	224-236	13
α-helix	237-241	5
α-helix	242-243	2
α-helix	252-259	8
β-strand	269-272	4	1
β-strand	277	1	2
α-helix	288-296	9
α-helix	298-300	3
β-strand	312-320	9	1
α-helix	325-338	14
β-strand	343	1	1
β-strand	351-356	6	1
α-helix	359-360	2
β-strand	368	1	2
β-strand	374-381	8	1
α-helix	384-401	18
α-helix	405-411	7
α-helix	415-435	21

Chain B: 24 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	3
β-strand	6-9	4	4
α-helix	10-28	19
β-strand	30	1	5
β-strand	36	1	5
α-helix	43-48	4
α-helix	49-51	3
β-strand	53-55	3	6
β-strand	61-63	3	6
β-strand	65-69	5	4
α-helix	72-80	9
α-helix	83-86	4
β-strand	92-94	3	4
α-helix	103-104	2
α-helix	105-110	6
α-helix	111-127	17
β-strand	134-135	2	3
β-strand	138-140	3	4
α-helix	145-149	5
α-helix	150-160	11
β-strand	165-166	2	3
β-strand	167-171	5	4
α-helix	172-174	3
α-helix	183-197	15
β-strand	200-204	5	4
α-helix	206-211	6
α-helix	212-216	5
α-helix	224-236	13
α-helix	237-241	5
α-helix	242-243	2
α-helix	252-259	8
β-strand	267-268	2	4
β-strand	271	1	4
α-helix	289-296	8
β-strand	312-320	9	4
α-helix	325-338	14
α-helix	340-343	4
β-strand	351-356	6	4
β-strand	374-381	8	4
α-helix	384-401	18
α-helix	406-410	5
α-helix	415-436	22

Chain D: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	3385-3393	9
α-helix	3399-3412	14
α-helix	3419-3426	8
α-helix	3429-3436	8
α-helix	3445-3453	9
α-helix	3464-3470	7
α-helix	3474-3481	8
α-helix	3484-3488	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Dynein heavy chain, cytoplasmic	D	protein	108	Dictyostelium discoideum	P34036
Tubulin alpha-1A chain	A	protein	451	Sus scrofa	P02550 (AlphaFold model)
Tubulin beta chain	B	protein	445	Sus scrofa	P02554 (AlphaFold model)

Sequence of entity 1 (D), FASTA

>3J6P_1 Dynein heavy chain, cytoplasmic (chains D)
TIKKKHLDEIKSLPKPPTPVKLAMEAVCLMLGGKKLEWADIRKKIMEPNFITSIINYDTK
KMMTPKIREAITKGYLEDPGFDYETVNRASKACGPLVKWATAQTYYSE

Sequence of entity 2 (A), FASTA

>3J6P_2 Tubulin alpha-1A chain (chains A)
MRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGGDDSFNTFFSETGAGK
HVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYARGHYTIGKEIIDLVLD
RIRKLADQCTGLQGFSVFHSFGGGTGSGFTSLLMERLSVDYGKKSKLEFSIYPAPQVSTA
VVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERPTYTNLNRLIGQIVSSITA
SLRFDGALNVDLTEFQTNLVPYPRGHFPLATYAPVISAEKAYHEQLSVAEITNACFEPAN
QMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRTIQFVDWCPTGFKVGINYEPP
TVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMYAKRAFVHWYVGEGMEEGEFSE
AREDMAALEKDYEEVGVDSVEGEGEEEGEEY

Sequence of entity 3 (B), FASTA

>3J6P_3 Tubulin beta chain (chains B)
MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPTGSYHGDSDLQLERINVYYNEAAGNKYV
PRAILVDLEPGTMDSVRSGPFGQIFRPDNFVFGQSGAGNNWAKGHYTEGAELVDSVLDVV
RKESESCDCLQGFQLTHSLGGGTGSGMGTLLISKIREEYPDRIMNTFSVVPSPKVSDTVV
EPYNATLSVHQLVENTDETYCIDNEALYDICFRTLKLTTPTYGDLNHLVSATMSGVTTCL
RFPGQLNADLRKLAVNMVPFPRLHFFMPGFAPLTSRGSQQYRALTVPELTQQMFDAKNMM
AACDPRHGRYLTVAAVFRGRMSMKEVDEQMLNVQNKNSSYFVEWIPNNVKTAVCDIPPRG
LKMSATFIGNSTAIQELFKRISEQFTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVS
EYQQYQDATADEQGEFEEEGEEDEA

Ligands and cofactors

ID	Name	Formula	Copies
TA1	Taxol	C47 H51 N O14	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	1
MG	Magnesium ion	Mg	1

Primary citation

A flipped ion pair at the dynein-microtubule interface is critical for dynein motility and ATPase activation. Uchimura, S., Fujii, T., Takazaki, H. et al. J Cell Biol (2015) 208:211-222. DOI 10.1083/jcb.201407039 · PubMed

Other PDB entries of the same protein (UniProt P34036), best resolution first:

27PT 2.2 Å, Dictyostelium discoideum cytoplasmic dynein motor domain in complex with ADP.Vi…
27PY 2.61 Å, Dictyostelium discoideum cytoplasmic dynein motor domain in the presence of ADP (ADP…
27QB 2.66 Å, Dictyostelium discoideum cytoplasmic dynein motor domain in the absence of nucleotide…
27QA 2.76 Å, Dictyostelium discoideum cytoplasmic dynein motor domain in the presence of ADP (Apo…
3VKG 2.81 Å, X-ray structure of an MTBD truncation mutant of dynein motor domain
27PZ 3.2 Å, Dictyostelium discoideum cytoplasmic dynein motor domain in the presence of ADP (ADP…
3VKH 3.8 Å, X-ray structure of a functional full-length dynein motor domain

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