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The actinome of Dictyostelium discoideum in comparison to actins and actin-related proteins from other organisms.
(2008) PLoS One 3
PubMed: 18612387 | PubMedCentral: PMC2441452 | DOI: 10.1371/journal.pone.0002654
(A) The ribbon model of muscle actin (PDB ID: 1J6Z) shows the characteristic structure of four subdomains (1–4), the topology of the binding motifs, the wireframe of ADP, calcium ions (blue) a... d water molecules (red).
Publication Year: 2008
Identification of hot-spot residues in protein-protein interactions by computational docking.
(2008) BMC Bioinformatics 9
PubMed: 18939967 | PubMedCentral: PMC2579439 | DOI: 10.1186/1471-2105-9-447
Table 6 Additional dataset of complexes used in this work Complex a Res b Receptor Ligand Receptor PDB Res (Id) b Ligand PDB Res(Id) b Complex type c X-ray subunits 1CBW 2.60 Chymotrypsin BPTI 4CHA 1.... 8 4PTI 1.50 U/U 1PM9 1.70 IL-6R IL-6 1N26 2.40 1ALU 1.90 U/U N/A N/A KDR VEGF 2P2H 1.95 1VFP 2.50 U/U N/A N/A trkC Neurotrophin-3 1WWC 1.90 1NT3 2.40 U/U 2BTF 2.55 Rabbit actin Bovine profilin I 1J6Z 1.54 1PNE 2.00 U/U 1DVF 1.90 E5.2 D1.3 - - 1VFA 1.80 B/U N/A N/A sHIR Insulin 2DTG 3.80 2C8Q 1.95 U/U NMR subunits N/A N/A GPIIbIIIa Kistrin 1TYE 2.90 1N4Y NMR U/U N/A N/A bFGF FGFR1b 4FGF 1.60 1WVZ NMR U/U N/A N/A IGF-1R IGF-1 1IGR 2.60 2GF1 NMR U/U N/A N/A IGF-1bp IGF-1 1ZT3 1.80 2GF1 NMR U/U Homology-based modeled subunits N/A N/A E9 DNase Im2 1FSJ 1.80 1FR2 d (66%) U/M N/A N/A AChR Erabutoxin 2BG9 4.00 5EBX 2.00 cryo- EM/U N/A N/A AChR NmmI 2BG9 4.00 1V6P 0.87 cryo- EM/U 1Z92 2.80 IL-2 receptor IL-2 (human) 2B5I d (100%) 1M47 1.99 M/U N/A N/A IL-2 beta receptor(human) IL-2 (murine) 2B5I d (99%) 1M48 d (64%) M/M N/A N/A IL-2 alpha receptor(murine) IL-2 (murine) 1NWV d (22%) 1M48 d (64%) M/M N/A N/A IL-4/IL-4bp GammaC 1IAR 2.30 2B5I d (99%) U/M N/A N/A gp75 Neurotrophin-3 1LNL d (18%) 1NT3 2.40 M/U N/A N/A CD48 CD2 2DRU d (39%) 1CDC 2.00 M/U N/A N/A Calcineurin CaM 1AUI d (59%) 1LKJ NMR M/U 2D9Q 2.80 hG-CSFbp hG-CSF 2D9Q d (99%) 1RHG 2.20 M/U a PDB Code; N/A, Not Available; b Resolution in Å or (Id): sequence identity with template in case of model; c B, Bound; U, Unbound; M, Model; cryo-EM, cryoelectron microscopy structures classified as modeled structures because of the low resolution compared to crystallographic or NMR structures, d PDB code of the template structure used for modelling However, only a few of the 94 known hot-spots were detected, so the corresponding sensitivity ( S = 15%) was lower than that of the initial dataset ( S = 24%).
Differential binding of tropomyosin isoforms to actin modified with m-maleimidobenzoyl-N-hydroxysuccinimide ester and fluorescein-5-isothiocyanate.
(2009) Anal Biochem 394
PubMed: 19583962 | PubMedCentral: PMC2739935 | DOI: 10.1016/j.ab.2009.07.004
Molecular distance calculation The distance separating Lys and Cys residues in actin atomic structure was calculated by the PyMOL 0.99rc6 Open Source (DeLano Scientific, Palo Alto, CA, USA) using skel... tal actin (PDB accession number 1j6z).
Actin subdomains 1 to 4 are indicated in panel D. Actin structure was plotted with the aid of PyMOL based on skeletal actin coordinates (PDB accession number 1j6z).
Publication Year: 2009
Structural polymorphism in F-actin.
(2010) Nat Struct Mol Biol 17
PubMed: 20935633 | PubMedCentral: PMC2988880 | DOI: 10.1038/nsmb.1930
In the second model the SD2 of actin (residues 34–69) was replaced with that from the crystal structure where the DB-loop is a helix (pdb entry: 1j6z), while in the last two models the D-loop ... residues 37–53), or the whole SD2 (residues 34–69) were removed.
Publication Year: 2010
Thermodynamic stability of histone H3 is a necessary but not sufficient driving force for its evolutionary conservation.
(2011) PLoS Comput Biol 7
PubMed: 21253558 | PubMedCentral: PMC3017104 | DOI: 10.1371/journal.pcbi.1001042
Further, when we performed similar analysis on all buried positions of actin (PDB ID 1J6Z) and tubulin (PDB ID 1Z5V), we observe statistically significant correlation between evolutionary and Medusa e... tropies ( Table 3 ).
Publication Year: 2011
Evolutionarily divergent, unstable filamentous actin is essential for gliding motility in apicomplexan parasites.
(2011) PLoS Pathog 7
PubMed: 21998582 | PubMedCentral: PMC3188518 | DOI: 10.1371/journal.ppat.1002280
Parasite actin homology models and alignment Homology models for TgACTI, PfACTI, and PfACTII sequences were built on the ADP-actin crystal structure (1J6Z)  using Modeller  .
Spatial localisation of actin filaments across developmental stages of the malaria parasite.
(2012) PLoS One 7
PubMed: 22389687 | PubMedCentral: PMC3289632 | DOI: 10.1371/journal.pone.0032188
B ) Surface representation of the structures of rabbit G-actin (PDB:1J6Z; A) and a protomer in rabbit F-actin (PDB:3G37; B) showing anti-Gly 245 epitope.
Publication Year: 2012
Subdomain location of mutations in cardiac actin correlate with type of functional change.
PubMed: 22590617 | PubMedCentral: PMC3348139 | DOI: 10.1371/journal.pone.0036821
Coordinate data for ATP-bound TMR-actin (1J6Z)  were visualized using PyMol  .
The protein structure of actin (PDB 1J6Z)  showing the locations of mutations related to HCM (in green spacefilling) or DCM (in red spacefilling) and bound ATP (sticks) visualized using PyMol  .
Complex intramolecular mechanics of G-actin--an elastic network study.
PubMed: 23077498 | PubMedCentral: PMC3471905 | DOI: 10.1371/journal.pone.0045859
As a reference state for the construction of the elastic network, the uncomplexed G-actin in the ADP-bound state (PDB ID: 1J6Z) was used  .
As the reference conformation, the ADP-bound state (PDB ID: 1J6Z) was always taken.
Spontaneous structural changes in actin regulate G-F transformation.
PubMed: 23144776 | PubMedCentral: PMC3489878 | DOI: 10.1371/journal.pone.0045864
When calculating the average over both states, the average distance between the labeled residues was 4.4 nm (average FRET efficiency = 0.7, Materials and Methods ), which is close to t... e value of the G-actin crystal structure (PDB ID: 1J6Z)  .
Structural dynamics of troponin I during Ca2+-activation of cardiac thin filaments: a multi-site Förster resonance energy transfer study.
PubMed: 23227172 | PubMedCentral: PMC3515578 | DOI: 10.1371/journal.pone.0050420
To assess the effect of the limited distribution of acceptor dipole orientation expected from the high anisotropy value, we used the high resolution structure of TMR-G-actin  (PDB: 1J6Z) and a pub... ished EM model of skeletal thin filament  to estimate the angle θ of the acceptor (TMR) probe on actin with regards to the filament axis.
A mechanism for actin filament severing by malaria parasite actin depolymerizing factor 1 via a low affinity binding interface.
(2014) J Biol Chem 289
PubMed: 24371134 | PubMedCentral: PMC3924271 | DOI: 10.1074/jbc.M113.523365
Given the nature of the EDC cross-links, manual validation of the high-resolution spectra permitted mapping of salt bridge interactions between the actin and PfADF1 crystal structures (PDB codes 1J6Z ... nd 3Q2B ) with near residue resolution ( 18 , 32 ).
XL-MS determined cross-linked peptide interfaces and the crystal structures of rabbit actin (PDB code 1J6Z ), PfADF1 (PDB code 3Q2B ), and HsCOF1 (PDB code 1Q8X ) were used to reconstruct the monomeric actin-ADF/cofilin structural models using the built in rotation and translation functions within PyMol (Delano Scientific LLC).
TABLE 1 Summary of G-actin-PfADF1 peptides detected Actin peptide Uniprot ID: P68135 PfADF1 peptide Uniprot ID: Q81467 Site of cross-link Cross-link agent Δ m / z error ppm Peptide-(327–335) (IKIIAPPER) Peptide-(81–86) (ESSNSR) PfADF1.E81 EDC 0.707 Actin.K328 Peptide-(327–335) (IKIIAPPER) Peptide-(101–122) IEGVNVLTSVIESAQDVADL PfADF1.D117/D120 EDC 0.759 Actin.K328 Peptide-(211–238) (DIKEKLCYVALDFENEMATAASSSSLEK) Peptide-(81–86) (ESSNSR) Actin.K215 SDA −2.963 Peptide-(51–61) (DSYVGDEAQSK) Peptide-(96–101) (QAILKK) PfADF1.K100 SDA −1.630 Peptide-(327–335) (IKIIAPPER) Peptide-(101–122) (IEGVNVLTSVIESAQDVADL) Actin.K328 SDA −0.347 Combining EDC and sulfo-SDA cross-links enabled us to model the G-actin-PfADF1 interaction using their two crystal structures (PDB codes 1J6Z and 3Q2B ) ( 18 , 32 ) ( Fig. 2 E ).
Publication Year: 2014
Bacterial actin MreB forms antiparallel double filaments.
(2014) Elife 3
PubMed: 24843005 | PubMedCentral: PMC4051119 | DOI: 10.7554/eLife.02634
PDB codes: ParM_AMPPNP: 4A61; PaRM_AMMPNP_ParR: 4A62; Actin-ADP_Rhodamine: 1J6Z ; F-actin-ADP:2ZWH.
Conserved and host-specific features of influenza virion architecture.
(2014) Nat Commun 5
PubMed: 25226414 | PubMedCentral: PMC4167602 | DOI: 10.1038/ncomms5816
Membrane co-ordinates were from Tieleman et al. (1996) 68 , the RNP structure was adapted from Hutchinson et al. (2013) 69 and the structure of NEP was modelled using Quark 70 ; other protein co-ordin... tes used were from the Protein Data Bank, with accession codes 1RU7 (HA), 3BEQ (NA), 3LBW (M2), 1EA3 (M1), 2GX9 and 2ZKO (NS1), 1J6Z (ACTB), 1UBI (UBB), 4HNA (TUBB), 2BTF (PFN1), 1Q8G (CFL1), 4HKC (YWHAZ), 1ZJH (PKM), 1WYM (TAGLN2), 3TH5 (RAC1), 4HMY (ARF1), 3T06 (RHOA), 2KB0 (CDC42), 3KOM (PPIA), 4H5N (HSPA8) and 3GPD (GAPDH).
PubMed ID is not available.
Published in 2015
ATP state, PDB entry 1nwk (Graceffa & Dominguez, 2003 ▶ ; grey); ADP state, PDB entry 1j6z (Otterbein et al. , 2001 ▶ ; magenta).
Publication Year: 2015
Comparison between an actin monomer (initial fit; PDB code 1j6z ; Otterbein et al. , 2001 ▸ ) rigidly fitted in an actin monomer density map (segmented from 6.6 Å resolution ac... in filament; EMD code 5168; Fujii et al. , 2010 ▸ ) and the final model resulting from flexible fitting in the same map (final fit; PDB code 3mfp ; Fujii et al. , 2010 ▸ ).
Example 2: Actin We also compared, using the segment-based assessment of a single fit, two models: (i) the published model of the F-actin subunit (PDB code 3mfp ) refined in the 6.6 Å resolution map of actin filament (EMD code 5168; Fujii et al. , 2010 ▸ ) and (ii) the crystal structure of a unbound G-actin monomer in the ADP state (PDB code 1j6z ; Otterbein et al. , 2001 ▸ ), which was used as a starting model.
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