Citations in PubMed

Primary Citation PubMed: 19914170 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 6

Citations in PubMed

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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