6F1Y: PDB entry 6F1Y

Dynein light intermediate chain region of the dynein tail/dynactin/BICDR1 complex. Determined by electron microscopy at 3.4 Å resolution. Released 17 Jan 2018.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,316
Mol. weight: 71.62 kDa
Released: 17 Jan 2018

Explore 6F1Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6F1Y contains 21 α-helices and 9 β-strands across 2 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 f: 10 helices, 0 β-strands

Element	Residues	Length
α-helix	781-796	16
α-helix	801-821	21
α-helix	830-862	33
α-helix	871-890	20
α-helix	896-925	30
α-helix	973-1000	28
α-helix	1001-1005	5
α-helix	1036-1052	17
α-helix	1076-1095	20
α-helix	1111-1136	26

Chain j: 11 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	39-45	7
β-strand	55-60	6	1
α-helix	67-74	8
β-strand	89-93	5	1
β-strand	102-106	5	1
β-strand	108-109	2	1
α-helix	116-120	5
β-strand	131-135	5	1
α-helix	142-163	22
α-helix	169-181	13
β-strand	227-230	4	1
α-helix	237-243	7
α-helix	248-265	18
β-strand	269-270	2	1
α-helix	280-288	9
β-strand	301	1	1
β-strand	309-310	2	1
α-helix	319-323	5
α-helix	336-339	4
α-helix	362-370	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytoplasmic dynein 1 heavy chain 1,Dynein heavy chain	f	protein	328	Homo sapiens	Q14204
Cytoplasmic dynein 1 light intermediate chain 2	j	protein	337	Homo sapiens	O43237 (AlphaFold model)

Sequence of entity 1 (f), FASTA

>6F1Y_1 Cytoplasmic dynein 1 heavy chain 1,Dynein heavy chain (chains f)
SLIESVRTYERTCEKVEERNTISLLVAGLKKEVQALIAEGIALVWESYKLDPYVQRLAET
VFNFQEKVDDLLIIEEKIDLEVRSLETCMYDHKTFSEILNRVQKAVDDLNLHSYSNLPIW
VNKLDMEIERILGVRLQAGLRAWTQVLLXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXLEESYSAVMGIVSEVEQYVKVXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXXXX

Sequence of entity 2 (j), FASTA

>6F1Y_2 Cytoplasmic dynein 1 light intermediate chain 2 (chains j)
SSILSEVSTRARSKLPSGKNILVFGEDGSGKTTLMTKLQGAEHGKKGRGLEYLYLSVHDE
DRDDHTRCNVWILDGDLYHKGLLKFAVSAESLPETLVIFVADMSRPWTVMESLQKWASVL
REHIDKMKIPPEKMRELERKFVKDFQDYMEPEEGCQGSPQRRGPLTSGSDEENVALPLGD
NVLTHNLGIPVLVVCTKCDAVSVLEKEHDYRDEHLDFIQSHLRRFCLQYGAALIYTSVKE
EKNLDLLYKYIVHKTYGFHFTTPALVVEKDAVFIPAGWDNEKKIAILHENFTTVKPEDAY
EDFIVKPPVRKLVHDKELAAEDEQVFLMKQQSLLAKQ

Primary citation

Cryo-EM shows how dynactin recruits two dyneins for faster movement. Urnavicius, L., Lau, C.K., Elshenawy, M.M. et al. Nature (2018) 554:202-206. DOI 10.1038/nature25462 · PubMed

Other PDB entries of the same protein (UniProt Q14204), best resolution first:

5OWO 1.79 Å, Human cytoplasmic Dynein N-Terminus dimerization domain at 1.8 Angstrom resolution
9BLZ 2.2 Å, State-1(phi motor) of full-length human dynein-1 in 5mM ATP
9BMR 2.6 Å, State-1 of motor domain from full-length human phi dynein-1 in 5 mM ADP
9DH5 2.6 Å, State-1 of the motor domain from full-length human dynein-1 in 5mM AMPPNP with 5mM Mg2+
9E0X 2.7 Å, Cryo-EM structure of Phi dynein
9E10 2.71 Å, Dimeric motor domains from phi dynein-1 under Lis1 condition
9BM0 2.8 Å, State-2 of motor domain from full-length human dynein-1 in 5mM ATP
9BMF 2.8 Å, State-1(phi motor) of full-length human dynein-1 in 5mM ATPVi
9BMH 2.8 Å, State-4 of motor domain from full-length human dynein-1 in 5mM ATPVi
9BN3 2.8 Å, The alpha registry-locked dynein motor domain mutant in 5mM ATP condition, class1
9BM2 2.82 Å, State-4 of motor domain from full-length human dynein-1 in 5 mM ATP
9BMG 2.86 Å, State-2 of full-length human dynein-1 in 5mM ATPVi

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