OCA Atlas for 6F1T

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

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 Microscopy

resolution

3.50 Å

ligand

ADP, ATP

enzyme

Gene
Ontology

Chain	Function	Process	Component
H	structural constituent of po...
J		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 reference

Cryo-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

LPC: Ligand-Protein Contacts for 6F1T

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

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

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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