Citations in PubMed

Primary Citation PubMed: 19914170 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 6

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Atomic-level modelling of the HIV capsid.

(2011) Nature 469

PubMed: 21248851 | PubMedCentral: PMC3075868 | DOI: 10.1038/nature09640

These distances are in close correspondence to the dimensions of two independently-determined CTD dimer structures, 2KOD 12 and 1A43 5 , and suggests a rationale for the seemingly disparate structures... of the dimers.

The capsid model was built by manual rigid-body docking of the high-resolution structures of the 5-fold symmetric NTD ring (PDB code 3P05), the 6-fold symmetric NTD ring (3H47), and 2-fold symmetric CTD dimers (2KOD and 1A43) into a geometric fullerene cone model.

Publication Year: 2011

Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings.

(2011) J Am Chem Soc 133

PubMed: 21466200 | PubMedCentral: PMC3080108 | DOI: 10.1021/ja111318m

( 14 ) Table 1 Structural Statistics Reported from the Application of the RosettaOligomers Pipeline on Ten Oligomers with Experimentally Determined Structures target name PDB ID/method size fold/inter... ace data used a Rosetta rmsd (Å) b RDC Q-factor c TolR 2JWK/NMR 74 × 2 αβ/αβ CS, RDC(1,261), SAXS d 1.2/1.5/0.6 0.4 ykuJ 2FFG/X-ray 80 × 2 αβ/α CS, RDC(2,59) 0.7/0.9/0.4 0.26/0.18 SeR13 2K1H/NMR e 86 × 2 αβ/β CS, RDC(2,53), NOE (32) 2.0/3.4/3.4 0.26/0.24 At5g22580 1RJJ/NMR 101 × 2 αβ/β CS, RDC(1,96) 2.2/2.2/1.7 0.4 HIV-I CCD 1BIS/X-ray 152 × 2 αβ/αβ CS, RDC(2,96) 1.0/1.3/0.7 0.30/0.32 yiiF 2K5J/NMR 44 × 2 αβ/αβ f CS, RDC(1,24) 0.9/1.0/0.5 0.05 KR150 3OBH/X-ray e 74 × 2 αβ/αβ f CS, RDC(1,56), NOE (67) 1.4/2.8/2.7 0.32 ATU0232 2K7I/NMR 64 × 2 αβ/αβ f CS, RDC(1,46) 2.2/2.5/2.1 0.24 CA dimer 2KOD/NMR 77 × 2 α/α CS, RDC(1,100) 1.3/1.4/1.2 0.1 P53 1C26/X-ray 31 × 4 αβ/αβ f CS only 0.7/1.1/0.3 N/A a RDC (number of alignment media, number of RDCs per medium per monomer).

( 28 ) The structure determined in solution fits well into the Cryo-EM density map and shows a semi-interleaved dimer interface in which the N-terminus of the CTD (residues 145−151 in the full-length protein) fit into a helical groove on the symmetric subunit, as confirmed by the observation of several intersubunit NOEs (PDB ID 2KOD ).

Publication Year: 2011

Protease cleavage leads to formation of mature trimer interface in HIV-1 capsid.

(2012) PLoS Pathog 8

PubMed: 22927821 | PubMedCentral: PMC3426514 | DOI: 10.1371/journal.ppat.1002886

(A–C) Docking of the CA-NTD (PDB 3h47) and CA-CTD (PDB 2kod) domain models, independently, into the CA region (gold) of the density map contoured at 1.22σ, enclosing 100% volume.

As a first approximation, we constructed a model for CA-SP1 by connecting the SP1 NMR structure model (PDB 1u57), determined in the presence of trifluoroethanol [45] , to the CA-CTD by superimposing the overlap region (LEEMMTACQG) from the CA-CTD (PDB 2kod) and the SP1 structures ( Fig. 2D , inset).

Rigid body fitting Pseudo-atomic models of CA hexamers were constructed by docking the following NTD and CTD domain models (PDB 3h47 for CA-NTD and PDB 2kod for CA-CTD) into the density map separately.

Molecular docking of a pseudo-atomic structure into the CA-SP1-NC density map For a detailed comparison of the CA structure in the CA and CA-SP1-NC assemblies, we docked atomic models of the CA-NTD (PDB 3h47) [19] and the solution CA-CTD dimer (PDB 2kod) [20] , separately, into the CA-SP1-NC density map using a correlation-based automated rigid-body fitting method [20] .

A pseudo-atomic model for CA-SP1was constructed by aligning the overlapping segment (LEEMMTACQG) from both CA-CTD structure (PDB 2kod) and SP1 structure (PDB 1u57) using the tool “MatchMaker" in Chimera.

Publication Year: 2012

The maturational refolding of the ?-hairpin motif of equine infectious anemia virus capsid protein extends its helix ?1 at capsid assembly locus.

(2013) J Biol Chem 288

PubMed: 23184932 | PubMedCentral: PMC3548464 | DOI: 10.1074/jbc.M112.425140

The side chain bonds of chemical shift mapped residues were colored blue in both hexamer ( A ) and dimer ( B ) models, which were generated using rigid body rotation of the refined EIAV-CA N and the o... iginal EIAV-CA C crystal coordinates onto the crystal structure of HIV-1-CA hexamer (PDB code 3GV2 )( 39 ) and the solution structure of HIV-1-CA C dimer (PDB code 2KOD )( 41 ), respectively.

Publication Year: 2013

Structure of a novel shoulder-to-shoulder p24 dimer in complex with the broad-spectrum antibody A10F9 and its implication in capsid assembly.

(2013) PLoS One 8

PubMed: 23620741 | PubMedCentral: PMC3631186 | DOI: 10.1371/journal.pone.0061314

The p24 CTD dimer solved by NMR displays a V-shape-like architecture ( Fig. 5C ) (PDBID: 2KOD), which is partly supported by the cryo-EM study of the HIV-1 CA tubular structure at 16 Å resolut... on and an electron density map derived from flattened 2D sheets formed by full-length p24 [11] .

Publication Year: 2013

Towards an integrative structural biology approach: combining Cryo-TEM, X-ray crystallography, and NMR.

(2014) J Struct Funct Genomics 15

PubMed: 24748171 | PubMedCentral: PMC4125826 | DOI: 10.1007/s10969-014-9179-9

These interactions were not previously seen in X-ray crystallographic studies [ 29 ] (EMDB Accession code: EMD-5136; Fitted PDB ID: 2KOD).

Publication Year: 2014