<i>BALBES</i>: a molecular-replacement pipeline

Long, Fei; Vagin, A.A.; Young, Paul G.; Murshudov, Garib N.

doi:10.1107/s0907444907050172

Cited by 702 publications

(650 citation statements)

References 30 publications

Supporting

Mentioning

639

Contrasting

Unclassified

Order By: Relevance

“…Data were collected at beamline ID29 (ESRF) and processed using Mosflm and Scala from the CCP4 suite 28 . The structure of E. coli FdhD was solved by molecular replacement using the structure given in the PDB entry 2PW9 as a searched model and the programme Balbes 29 . PDB entry 2PW9 depict the 3D structure of a formate dehydrogenase accessory protein from D. psychrophila (30% identity with E. coli FdhD over 246 residues).…”

Section: Methodsmentioning

confidence: 99%

Sulphur shuttling across a chaperone during molybdenum cofactor maturation

et al. 2015

View full text Add to dashboard Cite

Formate dehydrogenases (FDHs) are of interest as they are natural catalysts that sequester atmospheric CO 2 , generating reduced carbon compounds with possible uses as fuel. FDHs activity in Escherichia coli strictly requires the sulphurtransferase EcFdhD, which likely transfers sulphur from IscS to the molybdenum cofactor (Mo-bisPGD) of FDHs. Here we show that EcFdhD binds Mo-bisPGD in vivo and has submicromolar affinity for GDP-used as a surrogate of the molybdenum cofactor's nucleotide moieties. The crystal structure of EcFdhD in complex with GDP shows two symmetrical binding sites located on the same face of the dimer. These binding sites are connected via a tunnel-like cavity to the opposite face of the dimer where two dynamic loops, each harbouring two functionally important cysteine residues, are present. On the basis of structure-guided mutagenesis, we propose a model for the sulphuration mechanism of Mo-bisPGD where the sulphur atom shuttles across the chaperone dimer.

show abstract

Section: Methodsmentioning

confidence: 99%

Sulphur shuttling across a chaperone during molybdenum cofactor maturation

et al. 2015

View full text Add to dashboard Cite

show abstract

“…The structure was determined by the molecular replacement method with the program BALBES in the CCP4 suite [40], using the structure of CD69 (PDB ID: 3HUP) [32] as a search model. Rotation and translation functions were calculated using data from 50.0 to 2.5Å resolution.…”

Section: Structure Determination Of Llt1mentioning

confidence: 99%

Crystal structure of extracellular domain of human lectin‐like transcript 1 (LLT1), the ligand for natural killer receptor‐P1A

et al. 2015

View full text Add to dashboard Cite

Emerging evidence has revealed the pivotal roles of C-type lectin-like receptors (CTLRs) in the regulation of a wide range of immune responses. Human natural killer cell receptor-P1A (NKRP1A) is one of the CTLRs and recognizes another CTLR, lectin-like transcript 1 (LLT1) on target cells to control NK, NKT and Th17 cells. The structural basis for the NKRP1A-LLT1 interaction was limitedly understood. Here, we report the crystal structure of the ectodomain of LLT1. The plausible receptor-binding face of the C-type lectin-like domain is flat, and forms an extended β-sheet. The residues of this face are relatively conserved with another CTLR, keratinocyte-associated C-type lectin, which binds to the CTLR member, NKp65. A LLT1-NKRP1A complex model, prepared using the crystal structures of LLT1 and the keratinocyte-associated C-type lectin-NKp65 complex, reasonably satisfies the charge consistency and the conformational complementarity to explain a previous mutagenesis study. Furthermore, crystal packing and analytical ultracentrifugation revealed dimer formation, which supports a complex model. Our results provide structural insights for understanding the binding modes and signal transduction mechanisms, which are likely to be conserved in the CTLR family, and for further rational drug design towards regulating the LLT1 function.Keywords: Cell surface receptor r Crystal structure r C-type lectin-like receptor r Natural killer cell r Protein-protein interactions Additional supporting information may be found in the online version of this article at the publisher's web-site Correspondence: Prof. Katsumi Maenaka e-mail: maenaka@pharm.hokudai.ac.jp * Equal contribution.C 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.eji-journal.eu 1606 S. Kita et al. Eur. J. Immunol. 2015. 45: 1605-1613 Introduction Natural killer (NK) cells are a component of innate immunity, and display cytotoxic activities against tumor cells and virally infected cells [1,2]. The activities of NK cells are precisely regulated by activating and inhibitory signals, through diverse receptors on the cell surface [3][4][5]. These receptors are encoded in two genomic regions, the leukocyte receptor complex (chromosome 19 in human) [6] and the NK gene complex (chromosome 12 in human) [7,8]. The leukocyte receptor complex encodes the NK receptors of the immunoglobulin (Ig) superfamily, such as killer Ig-like receptors and leukocyte Ig-like receptors, whereas the NK gene complex region encodes the NK receptors of the C-type lectinlike receptors (CTLRs). The CTLRs are subdivided into two groups, according to their expression patterns. Killer cell lectin-like receptors (KLRs) are expressed in NK cells, and C-type lectin receptors (CLECs) are expressed in non-NK cells [9]. The ligands of KLRs are (1) major histocompatibility complex (MHC) class I molecules and relatives, and (2) CLECs. The former members include CD94, the NKG2 subfamily [10], and the Ly49 subfamily [11], and the latter members are the NK receptor-P1 (NKRP1) subfamily [12,13]. The NKRP1 su...

show abstract

“…Molecular replacement was performed using balbes 27 with AccA3 as the template sequence, and a structural solution was identified with a homodimer of AccA3 in the asymmetric unit, and no evidence of the AccD6 subunit.…”

Section: Methodsmentioning

confidence: 99%

Crystal structure of the essential biotin‐dependent carboxylase AccA3 from Mycobacterium tuberculosis

Bennett

Högbom

2017

FEBS Open Bio

View full text Add to dashboard Cite

Biotin‐dependent acetyl‐CoA carboxylases catalyze the committed step in type II fatty acid biosynthesis, the main route for production of membrane phospholipids in bacteria, and are considered a key target for antibacterial drug discovery. Here we describe the first structure of AccA3, an essential component of the acetyl‐CoA carboxylase system in Mycobacterium tuberculosis (MTb). The structure, sequence comparisons, and modeling of ligand‐bound states reveal that the ATP cosubstrate‐binding site shows distinct differences compared to other bacterial and eukaryotic biotin carboxylases, including all human homologs. This suggests the possibility to design MTb AccA3 subtype‐specific inhibitors. Database Coordinates and structure factors have been deposited in the Protein Data Bank with the accession number http://www.rcsb.org/pdb/search/structidSearch.do?structureId=5MLK.

show abstract

BALBES: a molecular-replacement pipeline

Abstract: The fully automated pipeline, BALBES, integrates a redesigned hierarchical database of protein structures with their domains and multimeric organization, and solves molecular-replacement problems using only input X-ray and sequence data.

Cited by 702 publications

References 30 publications

Sulphur shuttling across a chaperone during molybdenum cofactor maturation

Sulphur shuttling across a chaperone during molybdenum cofactor maturation

Crystal structure of extracellular domain of human lectin‐like transcript 1 (LLT1), the ligand for natural killer receptor‐P1A

Crystal structure of the essential biotin‐dependent carboxylase AccA3 from Mycobacterium tuberculosis

Contact Info

Product

Resources

About