12-June-2013

Small Angle Scattering Task Force

We are pleased to announce that the Report of the wwPDB Small-Angle Scattering Task Force, "Data Requirements for Biomolecular Modeling and the PDB Structure", has been published in the journal Structure (doi:10.1016/j.str.2013.04.020).

The first meeting of the Small Angle Scattering (SAS) Task Force (July 12-13, 2012) was sponsored by the wwPDB and held at the Center for Integrative Proteomics Research at Rutgers, The State University of New Jersey. The Task Force, chaired by Jill Trewhella, includes experts in SAS, crystallography, data archiving, and molecular modeling.

Recognizing the rapidly growing community of structural biology researchers that acquire and interpret SAS data in terms of increasingly sophisticated molecular models, the SAS Task Force made several recommendations. These include: development of a global repository for X-ray and neutron SAS data; creation of a standard dictionary of terms for data collection and for managing the SAS data repository; options for including SAS-derived shape and atomistic models along with specific information regarding the modeling protocol, uniqueness and uncertainty; development of criteria for assessment of data quality and accuracy. The Task Force also recommends that leaders from the various structural biology disciplines should jointly define what to archive in the PDB and what complementary archives might be needed, taking into account both scientific needs and funding.

This report by the wwPDB SAS Task Force follows recommendations recently published by wwPDB Validation Task Forces on X-ray and 3DEM. The report from the NMR Validation Task Force will be published shortly.

30-May-2013

Landmark HIV Capsid Structures Released in PDB

Two complete HIV-capsid structures, both of unprecedented size, are described in this week's issue of Nature and released in the Protein Data Bank (PDB; wwpdb.org). This represents a significant advance in the field of structural biology and a milestone for the PDB.

PDB entries 3J3Q and 3J3Y are models based on cryo-electron microscopy data and use of a molecular dynamics flexible-fitting method. They contain 1356 and 1176 protein chains, respectively, and over two million atoms each. The HIV-1 capsid is the protein envelope that encloses and protects the RNA genome of the virus. An important subject of study, the full capsid has been a difficult target for structural characterization due to its extremely large size and morphological variability.

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22-May-2013

Deposition and Release of PDB Entries Containing Large Structures