Crystallographic model quality at a glance

Urzhumtseva, Ludmila; Afonine, Pavel V.; Adams, Paul D.; Urzhumtsev, Alexandre

doi:10.1107/s0907444908044296

Cited by 98 publications

(87 citation statements)

References 18 publications

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“…These values are within the range of those for structures reported at a comparable resolution, as calculated by the Polygon subroutine (62,64) in the program PHENIX (Python-based Hierarchical Environment for Integrated Xtallography) (1). The quality of the refined structure was analyzed using the Coot (18) and MOLPROBITY (42) programs.…”

Section: Methodsmentioning

confidence: 99%

Structural Characterization of the Dual Glycan Binding Adeno-Associated Virus Serotype 6

Govindasamy

Gurda

et al. 2010

J Virol

122

137

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The three-dimensional structure of adeno-associated virus (AAV) serotype 6 (AAV6) was determined using cryo-electron microscopy and image reconstruction and using X-ray crystallography to 9.7-and 3.0-Å resolution, respectively. The AAV6 capsid contains a highly conserved, eight-stranded (␤B to ␤I) ␤-barrel core and large loop regions between the strands which form the capsid surface, as observed in other AAV structures. The loops show conformational variation compared to other AAVs, consistent with previous reports that amino acids in these loop regions are involved in differentiating AAV receptor binding, transduction efficiency, and antigenicity properties. Toward structure-function annotation of AAV6 with respect to its unique dual glycan receptor (heparan sulfate and sialic acid) utilization for cellular recognition, and its enhanced lung epithelial transduction compared to other AAVs, the capsid structure was compared to that of AAV1, which binds sialic acid and differs from AAV6 in only 6 out of 736 amino acids. Five of these residues are located at or close to the icosahedral 3-fold axis of the capsid, thereby identifying this region as imparting important functions, such as receptor attachment and transduction phenotype. Two of the five observed amino acids are located in the capsid interior, suggesting that differential AAV infection properties are also controlled by postentry intracellular events. Density ordered inside the capsid, under the 3-fold axis in a previously reported, conserved AAV DNA binding pocket, was modeled as a nucleotide and a base, further implicating this capsid region in AAV genome recognition and/or stabilization.

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Section: Methodsmentioning

confidence: 99%

Structural Characterization of the Dual Glycan Binding Adeno-Associated Virus Serotype 6

Govindasamy

Gurda

et al. 2010

J Virol

122

137

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“…The quality of the final model was validated using the comprehensive validation software from the PHENIX suite (43,44). PDB2PQR and APBS from the APBS plug-in in PyMOL were used to calculate and display the electrostatic potential of the protein solvent-accessible areas of ORF49 KSHV (45,46).…”

Section: Methodsmentioning

confidence: 99%

Structure of the Open Reading Frame 49 Protein Encoded by Kaposi's Sarcoma-Associated Herpesvirus

Hew

Veerappan

Sim

et al. 2017

J Virol

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Herpesviruses alternate between the latent and the lytic life cycle. Switching into the lytic life cycle is important for herpesviral replication and disease pathogenesis. Activation of a transcription factor replication and transcription activator (RTA) has been demonstrated to govern this switch in Kaposi's sarcomaassociated herpesvirus (KSHV). The protein encoded by open reading frame 49 from KSHV (ORF49 KSHV ) has been shown to upregulate lytic replication in KSHV by enhancing the activities of the RTA. We have solved the crystal structure of the ORF49 KSHV protein to a resolution of 2.4 Å. The ORF49 KSHV protein has a novel fold consisting of 12 alpha-helices bundled into two pseudodomains. Most notably are distinct charged patches on the protein surface, which are possible protein-protein interaction sites. Homologs of the ORF49 KSHV protein in the gammaherpesvirus subfamily have low sequence similarities. Conserved residues are mainly located in the hydrophobic regions, suggesting that they are more likely to play important structural roles than functional ones. Based on the identification and position of three sulfates binding to the positive areas, we performed some initial protein-DNA binding studies by analyzing the thermal stabilization of the protein in the presence of DNA. The ORF49 KSHV protein is stabilized in a dose-responsive manner by doublestranded oligonucleotides, suggesting actual DNA interaction and binding. Biolayer interferometry studies also demonstrated that the ORF49 KSHV protein binds these oligonucleotides. IMPORTANCE Kaposi's sarcoma-associated herpesvirus (KSHV) is a tumorigenic gammaherpesvirus that causes multiple cancers and lymphoproliferative diseases. The virus exists mainly in the quiescent latent life cycle, but when it is reactivated into the lytic life cycle, new viruses are produced and disease symptoms usually manifest. Several KSHV proteins play important roles in this reactivation, but their exact roles are still largely unknown. In this study, we report the crystal structure of the open reading frame 49 protein encoded by KSHV (ORF49 KSHV ). Possible regions for protein interaction that could harbor functional importance were found on the surface of the ORF49 KSHV protein. This led to the discovery of novel DNA binding properties of the ORF49 KSHV protein. Evolutionary conserved structural elements with the functional homologs of ORF49 KSHV were also established with the structure.

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“…Occasionally, MAD and MAD phase combined maps were consulted. Evaluation of the model was done using POLY-GON [50], with results where most of the refinement quality criteria were better than the average. The secondary structure elements were identified with an aid of PROCHECK [51].…”

Section: Refinement and Final Structural Modelmentioning

confidence: 99%

Structure of a thermophilic F₁‐ATPase inhibited by an ε‐subunit: deeper insight into the ε‐inhibition mechanism

et al. 2015

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F 1 -ATPase (F 1 ) is the catalytic sector in F o F 1 -ATP synthase that is responsible for ATP production in living cells. In catalysis, its three catalytic b-subunits undergo nucleotide occupancy-dependent and concerted open-close conformational changes that are accompanied by rotation of the c-subunit. Bacterial and chloroplast F 1 are inhibited by their own e-subunit. In the einhibited Escherichia coli F 1 structure, the e-subunit stabilizes the overall conformation (half-closed, closed, open) of the b-subunits by inserting its C-terminal helix into the a 3 b 3 cavity. The structure of e-inhibited thermophilic F 1 is similar to that of E. coli F 1 , showing a similar conformation of the e-subunit, but the thermophilic e-subunit stabilizes another unique overall conformation (open, closed, open) of the b-subunits. The e-C-terminal helix 2 and hook are conserved between the two structures in interactions with target residues and in their positions. Rest of the e-C-terminal domains are in quite different conformations and positions, and have different modes of interaction with targets. This region is thought to serve e-inhibition differently. For inhibition, the e-subunit contacts the second catches of some of the b-and a-subunits, the N-and C-terminal helices, and some of the Rossmann fold segments. Those contacts, as a whole, lead to positioning of those b-and a-second catches in e-inhibition-specific positions, and prevent rotation of the c-subunit. Some of the structural features are observed even in IF 1 inhibition in mitochondrial F 1 .

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Crystallographic model quality at a glance

Cited by 98 publications

References 18 publications

Structural Characterization of the Dual Glycan Binding Adeno-Associated Virus Serotype 6

Structural Characterization of the Dual Glycan Binding Adeno-Associated Virus Serotype 6

Structure of the Open Reading Frame 49 Protein Encoded by Kaposi's Sarcoma-Associated Herpesvirus

Structure of a thermophilic F₁‐ATPase inhibited by an ε‐subunit: deeper insight into the ε‐inhibition mechanism

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Crystallographic model quality at a glance

Cited by 98 publications

References 18 publications

Structural Characterization of the Dual Glycan Binding Adeno-Associated Virus Serotype 6

Structural Characterization of the Dual Glycan Binding Adeno-Associated Virus Serotype 6

Structure of the Open Reading Frame 49 Protein Encoded by Kaposi's Sarcoma-Associated Herpesvirus

Structure of a thermophilic F1‐ATPase inhibited by an ε‐subunit: deeper insight into the ε‐inhibition mechanism

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Structure of a thermophilic F₁‐ATPase inhibited by an ε‐subunit: deeper insight into the ε‐inhibition mechanism