Recent advances in the<i>CRANK</i>software suite for experimental phasing

Pannu, Navraj S.; Waterreus, Willem Jan; Skubák, Pavol; Sikharulidze, Irakli; Abrahams, Jan Pieter; Graaff, R. A. G. de

doi:10.1107/s0907444910052224

Cited by 95 publications

(78 citation statements)

References 67 publications

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“…All structures were solved by Se‐SAD phasing. For BaTIE and SaTIE‐TED, data were input into the Crank2 pipeline in the CCP4 suite, which also built the initial model . For EfmTIE86‐TED, data were input into autoSHARP by the i03 data processing pipeline, which outputs a poly‐Ala model.…”

Section: Methodsmentioning

confidence: 99%

A new structural class of bacterial thioester domains reveals a slipknot topology

2018

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An increasing number of surface‐associated proteins identified in Gram‐positive bacteria are characterized by intramolecular cross‐links in structurally conserved thioester, isopeptide, and ester domains (TIE proteins). Two classes of thioester domains (TEDs) have been predicted based on sequence with, to date, only representatives of Class I structurally characterized. Here, we present crystal structures of three Class II TEDs from Bacillus anthracis, vancomycin‐resistant Staphylococcus aureus, and vancomycin‐resistant Enterococcus faecium. These proteins are structurally distinct from Class I TEDs due to a β‐sandwich domain that is inserted into the conserved TED fold to form a slipknot structure. Further, the B. anthracis TED domain is presented in the context of a full‐length sortase‐anchored protein structure (BaTIE). This provides insight into the three‐dimensional arrangement of TIE proteins, which emerge as very abundant putative adhesins of Gram‐positive bacteria.

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Section: Methodsmentioning

confidence: 99%

A new structural class of bacterial thioester domains reveals a slipknot topology

2018

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“…The locations of the two selenium sites were identified using the program SHELX/C/D/E [58], with an occupancy of greater than 0.8. The initial phases were solved using the program CRANK [59] of the CCP4 program suite [60], resulting in an overall figure of merit (FOM) of 0.497 for the 30.0–2.0 Å resolution data. The phases were further improved by modifying the density using the program DM [61], resulting in an FOM of 0.76 for the 24.40–2.45 Å resolution data.…”

Section: Methodsmentioning

confidence: 99%

The Arginine Pairs and C-Termini of the Sso7c4 from Sulfolobus solfataricus Participate in Binding and Bending DNA

et al. 2017

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The Sso7c4 from Sulfolobus solfataricus forms a dimer, which is believed to function as a chromosomal protein involved in genomic DNA compaction and gene regulation. Here, we present the crystal structure of wild-type Sso7c4 at a high resolution of 1.63 Å, showing that the two basic C-termini are disordered. Based on the fluorescence polarization (FP) binding assay, two arginine pairs, R11/R22′ and R11′/R22, on the top surface participate in binding DNA. As shown in electron microscopy (EM) images, wild-type Sso7c4 compacts DNA through bridging and bending interactions, whereas the binding of C-terminally truncated proteins rigidifies and opens DNA molecules, and no compaction of the DNA occurs. Moreover, the FP, EM and fluorescence resonance energy transfer (FRET) data indicated that the two basic and flexible C-terminal arms of the Sso7c4 dimer play a crucial role in binding and bending DNA. Sso7c4 has been classified as a repressor-like protein because of its similarity to Escherichia coli Ecrep 6.8 and Ecrep 7.3 as well as Agrobacterium tumefaciens ACCR in amino acid sequence. Based on these data, we proposed a model of the Sso7c4-DNA complex using a curved DNA molecule in the catabolite activator protein-DNA complex. The DNA end-to-end distance measured with FRET upon wild-type Sso7c4 binding is almost equal to the distance measured in the model, which supports the fidelity of the proposed model. The FRET data also confirm the EM observation showing that the binding of wild-type Sso7c4 reduces the DNA length while the C-terminal truncation does not. A functional role for Sso7c4 in the organization of chromosomal DNA and/or the regulation of gene expression through bridging and bending interactions is suggested.

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“…The diffraction data, the sequence of the protein monomer, the f′ and f′′ values for the substructure atoms and the substructure as determined by SHELXC and SHELXD16, or AFRO9 and CRUNCH2 (ref. 17), were input to PHENIX and to CRANK’s stepwise and combined pipelines.…”

Section: Methodsmentioning

confidence: 99%

Automatic protein structure solution from weak X-ray data

2013

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Determining new protein structures from X-ray diffraction data at low resolution or with a weak anomalous signal is a difficult and often an impossible task. Here we propose a multivariate algorithm that simultaneously combines the structure determination steps. In tests on over 140 real data sets from the protein data bank, we show that this combined approach can automatically build models where current algorithms fail, including an anisotropically diffracting 3.88 Å RNA polymerase II data set. The method seamlessly automates the process, is ideal for non-specialists and provides a mathematical framework for successfully combining various sources of information in image processing.

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Recent advances in theCRANKsoftware suite for experimental phasing

Cited by 95 publications

References 67 publications

A new structural class of bacterial thioester domains reveals a slipknot topology

A new structural class of bacterial thioester domains reveals a slipknot topology

The Arginine Pairs and C-Termini of the Sso7c4 from Sulfolobus solfataricus Participate in Binding and Bending DNA

Automatic protein structure solution from weak X-ray data

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