Citations in PubMed

Primary Citation PubMed: 12004076 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 12

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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Sequence and structural analysis of BTB domain proteins.

(2005) Genome Biol 6

PubMed: 16207353 | PubMedCentral: PMC1257465 | DOI: 10.1186/gb-2005-6-10-r82

Representative structures from the Protein Data Bank are labeled as follows: a 1buo :A and 1cs3 :A; b 1nex :a; c 1ldk :D, 1p22 :b, 1fqv :B, 1fs1 :B, 1fs2 :B; d 1hv2 :a; e 1vcb :B, 1lm8 :C, 1lqb :B; f ... a68 :_, 1eod :A, 1eoe :A, 1eof :A, 1t1d :A, 1exb :E (rat Kv1.1); g 1s1g :A; h 1r28 :A, 1r29 :A, 1r2b :A.

Publication Year: 2005


A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family.

(2009) PLoS Comput Biol 5

PubMed: 19478996 | PubMedCentral: PMC2682763 | DOI: 10.1371/journal.pcbi.1000393

The resulting ensemble consisted of 20 structures: 1XD3 chain B, 1BT0 chain A, 1EUV chain B, 1IYF, 1J8C, 1LM8 chain B, 1M94, 1NDD chain A, 1OQY, 1P1A, 1TGZ chain B, 1V5O, 1V5T, 1V86, 1WE6, 1WE7, 1WGD,... 1WGG, 1WH3, and 1WM3 chain A. To create the C-alpha distance difference matrix we used the 66 positions that aligned in all 20 structures, which were (using 1UBQ numbering): 1–7, 9–16, 18–34, 36–46, 48–55, 57–64, 66–72.

Publication Year: 2009


The mechanism of ubiquitination in the cullin-RING E3 ligase machinery: conformational control of substrate orientation.

(2009) PLoS Comput Biol 5

PubMed: 19798438 | PubMedCentral: PMC2741574 | DOI: 10.1371/journal.pcbi.1000527

(A) Superposition of Elongin C (purple, violet) and VHL-box/SOCS-box of pVHL (Cyan) (PDB code 1lm8) and SOCS2 (pink) (PDB code 2c9w).

Methods System setup The starting structures of the unbound and bound forms of nine proteins, Skp2, Fbw7, β-TrCP1, Cdc4, Fbs1, TIR1, pVHL, SOCS2, and SOCS4 were obtained from crystal structures (PDB codes: 2ast, 2ovq, 1p22, 1nex, 2e31, 2p1q, 1lm8, 2c9w, and 2ziv).

Publication Year: 2009


The structural impact of cancer-associated missense mutations in oncogenes and tumor suppressors.

(2011) Mol Cancer 10

PubMed: 21575214 | PubMedCentral: PMC3123651 | DOI: 10.1186/1476-4598-10-54

Table 1 Overview of genes Gene name Length (AA) Mut SNP PDB codes (sequence range) Oncogenes AKT1 478 6 5 1UNQ A (1-123), 3CQW A (144-480) BRAF 766 46 3 3D4Q A (433-726), 3NY5 A (153-237) EGFR 1210 22... 9 1YY9 A (25-642), 1XKK A (695-1022) GNAS 394 12 9 1AZS C (1-394) HRAS 189 19 0 4Q21 A (1-189) KIT 976 9 9 2EC8 A (1-519), 3G0E A (544-935) KRAS 188 85 1 3GFT A (1-164) MET 1408 24 30 2UZX B (25-740), 3DKC A (1049-1360) NRAS 189 9 1 3CON A (1-172) PIK3CA 1068 148 17 2RD0 A (1-1068) PTPN11 593 7 6 2SHP A (3-529) RET 1114 24 3 2IVS A (705-1013), 2X2U A (29-270) Tumor Suppressor Genes CDH1 882 17 3 2O72 A (155-367) CDKN2A 156 76 10 1BI7 B (1-156) FBXW7 707 34 4 2OVR B (263-707) MLH1 756 8 3 3NA3 A (1-347) MSH2 934 12 17 2O8B A (1-934) PTEN 403 93 2 1D5R A (8-353) RB1 928 7 9 2R7G A (380-787), 2QDJ A (52-355), 2AZE C (829-874) SMAD4 552 51 3 1DD1 A (285-552) STK11 433 30 1 2WTK C (43-347) TP53 393 826 17 2VUK A (94-312), 1AIE A (326-356) VHL 213 216 16 1LM8 V (54-213) WT1 449 9 3 2PRT A (318-438) Abbreviations: AA, amino acid, Mut, number of mutations, SNP, number of SNPs, PDB, Protein Data Bank Single nucleotide polymorphism dataset ( Snp ) As a control set, we extracted single nucleotide polymorphism (SNP) data for the 24 genes from version 131 of the common variation database dbSNP [ 17 ].

Publication Year: 2011


Targeting the von Hippel-Lindau E3 ubiquitin ligase using small molecules to disrupt the VHL/HIF-1? interaction.

(2012) J Am Chem Soc 134

PubMed: 22369643 | PubMedCentral: PMC3448299 | DOI: 10.1021/ja209924v

Figure 3 The 2.9 Å cocrystal structure of 15 (white carbons) bound to VHL, indicating that its binding mimics that of the HIF-1α peptide (yellow carbons, PDB 1LM8 ( 21 )).

Publication Year: 2012


Structure-based prediction of protein-protein interactions on a genome-wide scale.

(2012) Nature 490

PubMed: 23023127 | PubMedCentral: PMC3482288 | DOI: 10.1038/nature11503

The structures of the PH domain of PKD1 and the GNE domain of EF1δ (shown in green and purple) are homology models from ModBase; the structure of a C1 domain of PKCε (yellow) is a homo... ogy model from SkyBase; the structure of VHL (cyan) is from PDB (1lm8 V chain).

Publication Year: 2012


Three novel germ-line VHL mutations in Hungarian von Hippel-Lindau patients, including a nonsense mutation in a fifteen-year-old boy with renal cell carcinoma.

(2013) BMC Med Genet 14

PubMed: 23298237 | PubMedCentral: PMC3556325 | DOI: 10.1186/1471-2350-14-3

For molecular modeling, starting geometries for the model complexes of VHL-, Elongin C- and HIF-1α proteins [ 13 ] were obtained from the RCSB protein data bank (pdb ID: 1LM8).

Publication Year: 2013


P.Arg82Leu von Hippel-Lindau (VHL) gene mutation among three members of a family with familial bilateral pheochromocytoma in India: molecular analysis and in silico characterization.

(2013) PLoS One 8

PubMed: 23626751 | PubMedCentral: PMC3633967 | DOI: 10.1371/journal.pone.0061908

To gain, new mechanistic insight into the structural effect, we mapped the mutation on to 3D structure (PDB ID 1LM8).

The structure of the VHL protein (PDB ID 1LM8) contains two primary functional domains: the α-domain (155–192 aa), and the β-domain (63–154 and 193–204 aa) [19] .

For molecular dynamics study, native and mutant structures were generated based on the crystal structure (PDB ID 1LM8) of VHL protein by using Swiss PDB Viewer [20] .

Publication Year: 2013


Structural insights into the folding defects of oncogenic pVHL lead to correction of its function in vitro.

(2013) PLoS One 8

PubMed: 23840444 | PubMedCentral: PMC3688787 | DOI: 10.1371/journal.pone.0066333

The aromatic tetrahedron in WT and mutant pVHL proteins (based on PDB code:1lm8), comprising F76, W117, F119 and F136.

Crystal structure of pVHL (gray)(PDB ID code 1lm8) showing the N78, Y98, F119 and F136 residues (red).

Superimposition of the mutant pVHL structures on the structure of the WT pVHL (blue) (PDB code 1LM8) shown as spheres.

Results Modeling of Wild Type and Mutant pVHL Reveals an "Aromatic Tetrahedron" in its Core The crystal structure of human pVHL complexed with Elongin C and B (PDB code 1LM8) [32] was chosen for in silico evaluation of structural aspects of the wild type pVHL.

Experimental Procedures In Silico Analysis The VHL protein sequence was retrieved from UniProt and the VHL protein structure was obtained from The Protein Data bank (PDB code: 1LM8) [32] , [59] .

Publication Year: 2013


Diagnostic genetics at a distance: von hippel-lindau disease and a novel mutation.

(2013) Genet Res Int 2013

PubMed: 24062953 | PubMedCentral: PMC3767047 | DOI: 10.1155/2013/189196

pVHL30 comprises a seven-stranded β -sandwich, termed the β domain (amino acids 71–78, 84–89, 95–97, 105–112, 116–121, 129-130, and 147–... 5), together with a three helix cluster termed the α domain (amino acids 158–169, 183–189 and 194–206); see http://www.rcsb.org/pdb/explore/explore.do?structureId=1LM8 ) The β domain provides a binding site for hydroxyproline peptide-containing ligands.

Publication Year: 2013


Computational and experimental characterization of dVHL establish a Drosophila model of VHL syndrome.

(2014) PLoS One 9

PubMed: 25310726 | PubMedCentral: PMC4195687 | DOI: 10.1371/journal.pone.0109864

Superimposition of the resultant dVHL model structure on the crystal structure of pVHL19 (PDB ID: 1LM8) shows that the overall domain structure of pVHL19 is conserved in dVHL ( Figure 2A ).

( A ) Superposition of the structure of pVHL (red) (PDB ID: 1lm8) and the dVHL model structure (blue).

( B ) Superposition of the structure of pVHL (PDB ID: 1lm8) and the dVHL model structure, showing evolutionary conservation scores as calculated by ConSurf.

( A ) Hydrophobicity of pVHL (PDB ID: 1LM8) shown with its binding partner human Elongin C. ( B ) Hydrophobicity of the dVHL model structure superimposed with human Elongin C (from PDB ID: 1LM8).

The FFAS03 fold recognition server identified the structure of human pVHL19 (PDB ID 1LM8) as the best template with a significance score of –77.3 [45] .

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4515828

Indeed, pVHL-N was not solved in the x-ray structure (PDB code 1LM8), suggesting a different structural organization of the region when compared to the rest of the protein.

Publication Year: 2015