6F1T Motor Protein date Nov 23, 2017
title Cryo-Em Structure Of Two Dynein Tail Domains Bound To Dynact Bicdr1
authors L.Urnavicius, C.K.Lau, M.M.Elshenawy, E.Morales-Rios, C.Motz, A.Y A.P.Carter
compound source
Molecule: Arp1 Actin Related Protein 1 Homolog A
Chain: A, B, C, D, E, F, G, I
Other_details: Adp: Adenosine Diphosphate Ligand
Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Actin, Cytoplasmic 1
Chain: H
Synonym: Beta-Actin
Other_details: Atp: Adenosine Triphosphate

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Actin Related Protein 10 Homolog
Chain: J
Other_details: Adp: Adenosine Diphosphate

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Capping Protein (Actin Filament) Muscle Z-Line, A
Chain: K
Synonym: F-Actin Capping Protein Alpha 1 Subunit,F-Actin Ca Protein Subunit Alpha 1;

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: F-Actin Capping Protein Beta Subunit
Chain: L
Synonym: F-Actin-Capping Protein Subunit Beta,F-Actin-Cappi Subunit Beta Isoform 1;

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Dynactin Subunit 2
Chain: M

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Dynactin Subunit 2
Chain: N

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Dynactin Subunit 3
Chain: O, P

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Dynactin Subunit 2
Chain: Q, R

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Dynactin 6
Chain: U

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Dynactin Subunit 5
Chain: V

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Bicd Family-Like Cargo Adapter 1,Bicd Family-Like Adapter 1,Bicd Family-Like Cargo Adapter 1,Bicdr-1;
Chain: X
Synonym: Bicaudal D-Related Protein 1,Bicdr-1,Coiled-Coil D Containing Protein 64a,Bicaudal D-Related Protein 1,Bicdr-1 Coil Domain-Containing Protein 64a,Bicaudal D-Related Prote Bicdr-1,Coiled-Coil Domain-Containing Protein 64a;
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Bicdl1, Bicdr1, Ccdc64
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9

Molecule: Dynactin Subunit 4
Chain: Y

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Dynactin Subunit 1
Chain: Z

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Dynactin Subunit 2
Chain: a

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Dynactin Subunit 2
Chain: b

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Dynactin Subunit 2
Chain: c

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Dynactin Subunit 2
Chain: d

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823

Molecule: Cytoplasmic Dynein 1 Heavy Chain 1,Cytoplasmic Dy Heavy Chain 1,Cytoplasmic Dynein 1 Heavy Chain 1,Dynein Hea Cytoplasmic Dynein 1 Heavy Chain 1,Cytoplasmic Dynein 1 Hea 1,Cytoplasmic Dynein 1 Heavy Chain 1,Cytoplasmic Dynein 1 H 1,Dynein Heavy Chain,Cytoplasmic Dynein 1 Heavy Chain 1,Cyt Dynein 1 Heavy Chain 1;
Chain: e, f, m, n
Synonym: Cytoplasmic Dynein Heavy Chain 1,Dynein Heavy Chai Cytosolic,Cytoplasmic Dynein Heavy Chain 1,Dynein Heavy Cha Cytosolic,Cytoplasmic Dynein Heavy Chain 1,Dynein Heavy Cha Cytosolic,Cytoplasmic Dynein Heavy Chain 1,Dynein Heavy Cha Cytosolic,Cytoplasmic Dynein Heavy Chain 1,Dynein Heavy Cha Cytosolic,Cytoplasmic Dynein Heavy Chain 1,Dynein Heavy Cha Cytosolic,Cytoplasmic Dynein Heavy Chain 1,Dynein Heavy Cha Cytosolic,Cytoplasmic Dynein Heavy Chain 1,Dynein Heavy Cha Cytosolic,Cytoplasmic Dynein Heavy Chain 1,Dynein Heavy Cha Cytosolic;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dync1h1, Dhc1, Dnch1, Dncl, Dnecl, Dyhc, Kiaa0325
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9

Molecule: Cytoplasmic Dynein 1 Intermediate Chain 2
Chain: g, h, o, p
Synonym: Cytoplasmic Dynein Intermediate Chain 2,Dynein Int Chain 2,Cytosolic,Dh Ic-2;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dync1i2, Dnci2, Dncic2
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9

Molecule: Cytoplasmic Dynein 1 Light Intermediate Chain 2
Chain: I, j, q, r
Synonym: Dynein Light Intermediate Chain 2,Cytosolic,Lic-2,
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dync1li2, Dncli2, Lic2
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9

Molecule: Dynein Light Chain Roadblock-Type 1
Chain: k, l, s, t
Synonym: Bithoraxoid-Like Protein,Blp,Dynein Light Chain 2a Cytoplasmic,Dynein-Associated Protein Km23,Roadblock Domain Containing Protein 1;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Dynlrb1, Bith, Dncl2a, Dnlc2a, Robld1, Hspc162
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9

Molecule: Bicd Family-Like Cargo Adapter 1,Bicd Family-Like Adapter 1,Bicd Family-Like Cargo Adapter 1;
Chain: x
Synonym: Bicaudal D-Related Protein 1,Bicdr-1,Coiled-Coil D Containing Protein 64a,Bicaudal D-Related Protein 1,Bicdr-1 Coil Domain-Containing Protein 64a,Bicaudal D-Related Prote Bicdr-1,Coiled-Coil Domain-Containing Protein 64a;
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Bicdl1, Bicdr1, Ccdc64
Expression_system: Spodoptera Frugiperda
Expression_system_taxid: 7108
Expression_system_cell_line: Sf9

Molecule: Dynactin Subunit 1
Chain: z

Organism_scientific: Sus Scrofa
Organism_common: Pig
Organism_taxid: 9823
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 3.50 Å
Gene
Ontology
ChainFunctionProcessComponent
H
  • structural constituent of po...
  • synaptic vesicle endocytosis...

  • J
  • establishment of mitotic spi...
  • retrograde axonal transport ...

  • K


    L


    U


    V


    a, b


    f, e, n, m


    h, g, p, o


    k, t, s, l


    r, j, i, q


    Primary referenceCryo-EM shows how dynactin recruits two dyneins for faster movement., Urnavicius L, Lau CK, Elshenawy MM, Morales-Rios E, Motz C, Yildiz A, Carter AP, Nature. 2018 Feb 7;554(7691):202-206. doi: 10.1038/nature25462. PMID:29420470
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1732 Kb) [Save to disk]
  • Biological Unit Coordinates (6f1t.pdb1.gz) 1690 Kb
  • CSU: Contacts of Structural Units for 6F1T
  • Retrieve 6F1T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6F1T from S2C, [Save to disk]
  • View 6F1T in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 6F1T
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6f1t from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6f1t_K] [6f1t_o] [6f1t_t] [6f1t_m] [6f1t_x] [6f1t_A] [6f1t_s] [6f1t_q] [6f1t_e] [6f1t_F] [6f1t_O] [6f1t_r] [6f1t_J] [6f1t_P] [6f1t_X] [6f1t_I] [6f1t_d] [6f1t_c] [6f1t_Z] [6f1t_E] [6f1t_g] [6f1t_k] [6f1t_C] [6f1t_N] [6f1t_Y] [6f1t_j] [6f1t_H] [6f1t_V] [6f1t_z] [6f1t_b] [6f1t_l] [6f1t_p] [6f1t_f] [6f1t_U] [6f1t_a] [6f1t_L] [6f1t_B] [6f1t_n] [6f1t_R] [6f1t_D] [6f1t_i] [6f1t_Q] [6f1t_h] [6f1t_G] [6f1t_M]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6F1T
  • Community annotation for 6F1T at PDBWiki (http://pdbwiki.org)

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