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PDB ID Mentions in PubMed Central Article count: 2

Citations in PubMed

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PDB ID Mentions in PubMed Central

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Multimeric complexes among ankyrin-repeat and SOCS-box protein 9 (ASB9), ElonginBC, and Cullin 5: insights into the structure and assembly of ECS-type Cullin-RING E3 ubiquitin ligases.

(2013) Biochemistry 52

PubMed: 23837592 | PubMedCentral: PMC3756526 | DOI: 10.1021/bi400758h

(B) Crystal structures of the ASB9–EloBC ternary complex (PDB 3ZKJ) and Cullin 5 N-terminal domain (Cul5 NTD , PDB 2WZK).

34 The Cul5 NTD crystal structure (PDB 2WZK) was aligned with Cul1 NTD , and EloC of the ASB9–EloBC crystal structure (PDB 3ZKJ) was aligned with Skp1 of the Fbox Skp2 –Skp1–Cul1 NTD structure.

To construct the model, the ASB9–EloBC crystal structure (PDB 3ZKJ) was first superimposed as a rigid body on the template by aligning its EloC subunit with the Skp1 subunit of Fbox Skp2 –Skp1–Cul1 NTD .

34 The first α-helical bundle of the crystal structure of Cul5 NTD (PDB 2WZK) was aligned with the corresponding region of Cul1 NTD (sequence identity 29%, rmsd of all atoms 2.31 Å), whereas the EloC subunit of the ASB9–EloBC ternary-complex crystal structure (PDB 3ZKJ) was aligned with the homologous Skp1 subunit (sequence identity 38%, rmsd of all atoms 1.19 Å) to give the quaternary complex shown in Figure 4 A. Similar models of other ECS-type CRL quaternary complexes have previously been reported, including those for SOCS2–EloBC–Cul5, 47 RAR3–EloBC–Cul5, 44 HIV-1 Vif–EloBC–Cul5, 48 and VHL–EloBC–Cul2.

Publication Year: 2013


Molecular architecture of the ankyrin SOCS box family of Cul5-dependent E3 ubiquitin ligases.

(2013) J Mol Biol 425

PubMed: 23806657 | PubMedCentral: PMC3779351 | DOI: 10.1016/j.jmb.2013.06.015

Accession numbers The atomic coordinates and structure factors have been deposited in the PDB with the following accession numbers: PDB ID: 3ZKJ and PDB ID: 2WZK .

Table 1 Summary of data collection and refinement statistics ASB9–Elongin B/C Cul5 NTD native Cul5 NTD SeMet Data collection Space group P 2 1 22 1 P 2 1 2 1 2 1 P 2 1 2 1 2 1 Wavelength (Å) 0.980 0.980 0.980 Unit cell dimensions (Å): a , b , c (α = β = γ = 90°) 102.86, 110.74, 113.41 30.18, 64.50, 197.54 30.11, 64.35, 197.50 Resolution range (Å) 50.47–2.58 33.69–2.05 65.83–2.27 Number of unique reflections 41,297 (5914) 25,290 (3681) 18,727 (2657) R meas (%) 10.6 (83.9) 14.5 (80.9) 12.4 (46.7) 〈 I 〉/〈σ I *〉 10.7 (2.1) 7.4 (2.0) 13.6 (4.4) Completeness (%) 99.7 (99.7) 99.9 (100.0) 100.0 (99.9) Multiplicity 6.7 (6.3) 3.8 (3.9) 6.8 (6.8) Anomalous completeness (%) 99.9 (99.7) Anomalous multiplicity 3.7 (3.6) 

 Refinement Maximum resolution used (Å) 2.58 2.05 Number of reflections 39,120 25,227 R -factor (%) 22.9 19.0 Free R -factor (%) 26.5 22.4 r.m.s.d. bond lengths (Å) 0.014 0.008 r.m.s.d. bond angles (°) 1.520 0.940 PDB accession code 3ZKJ 2WZK Average B -factor (Å 2 )  Chain A 59.97 34.37  Chain B 89.76  Chain C 123.24  Chain D 68.45  Chain E 97.14  Chain F 89.11  Waters 58.52 43.97 Numbers in parentheses refer to the highest-resolution shell.

Publication Year: 2013