A knowledge-driven approach for crystallographic protein model completion

Joosten, Krista; Cohen, Serge; Emsley, Paul; Mooij, Wijnand T. M.; Lamzin, Victor S.; Perrakis, Anastassis

doi:10.1107/s0907444908001558

Cited by 24 publications

(25 citation statements)

References 20 publications

(26 reference statements)

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“…Molecular replacement was performed in PHASER [33] using the structure of MBP (pdb: 1hsj) as the search model. For MBP-TRIAP1, 5% of the reflections was omitted for cross-validation, density modification was performed with PARROT [34], and automated model building was carried out with ARPWARP [35]. TLS and NCS refinement was then carried out using REFMAC [36], and model building was carried out in COOT [37].…”

Section: Methodsmentioning

confidence: 99%

Structural insight into the TRIAP 1/ PRELI ‐like domain family of mitochondrial phospholipid transfer complexes

et al. 2015

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The composition of the mitochondrial membrane is important for its architecture and proper function. Mitochondria depend on a tightly regulated supply of phospholipid via intra-mitochondrial synthesis and by direct import from the endoplasmic reticulum. The Ups1/PRELI-like family together with its mitochondrial chaperones (TRIAP1/Mdm35) represent a unique heterodimeric lipid transfer system that is evolutionary conserved from yeast to man. Work presented here provides new atomic resolution insight into the function of a human member of this system. Crystal structures of free TRIAP1 and the TRIAP1–SLMO1 complex reveal how the PRELI domain is chaperoned during import into the intermembrane mitochondrial space. The structural resemblance of PRELI-like domain of SLMO1 with that of mammalian phoshatidylinositol transfer proteins (PITPs) suggest that they share similar lipid transfer mechanisms, in which access to a buried phospholipid-binding cavity is regulated by conformationally adaptable loops.

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Section: Methodsmentioning

confidence: 99%

Structural insight into the TRIAP 1/ PRELI ‐like domain family of mitochondrial phospholipid transfer complexes

et al. 2015

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“…The structure of intact hoefavidin was initially refined using the rigid body protocol in Refmac (Vagin et al, 2004;Winn et al, 2011), resulting in an R-value of 45.7% and R-free of 47.8%. The structure was further refined via the TLS & restrained refinement mode at a resolution range of 50.0-2.4 Å, and solvent molecules were added with ARP/wARP (Joosten et al, 2008), after several iterative cycles of refinement and extensive model building using Coot (Table 1) (Emsley et al, 2010). The remaining structures were solved by molecular replacement by a similar approach as that described above, using the refined structure of intact hoefavidin as the search model.…”

Section: Crystallization Data Collection and Structure Solutionmentioning

confidence: 99%

Hoefavidin: A dimeric bacterial avidin with a C-terminal binding tail

Avraham

Meir

Fish

et al. 2015

Journal of Structural Biology

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“…Sometimes for specific purposes, especially for exhaustive search as in Fitmunk [71] or Rapper [72], more complicated conformer libraries containing many curated conformations from representative structures are used. Additionally, some model building programs such as ARP/wARP [73], Buccaneer [74], and RESOLVE [75] use larger fragments of proteins to build the complete model.…”

Section: Data Resources Used Internally By Structural Biology Softwarementioning

confidence: 99%

Databases, Repositories, and Other Data Resources in Structural Biology

Zheng

Porebski

Grabowski

et al. 2017

Methods in Molecular Biology

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Structural biology, like many other areas of modern science, produces an enormous amount of primary, derived, and “meta” data with a high demand on data storage and manipulations. Primary data comes from various steps of sample preparation, diffraction experiments, and functional studies. These data are not only used to obtain tangible results, like macromolecular structural models, but also to enrich and guide our analysis and interpretation of existing biomedical studies. Herein we define several categories of data resources, (a) Archives, (b) Repositories, (c) “Databases” and (d) Advanced Information Systems, that can accommodate primary, derived, or reference data. Data resources may be used either as web portals or internally by structural biology software. To be useful, each resource must be maintained, curated, and be integrated with other resources. Ideally, the system of interconnected resources should evolve toward comprehensive “hubs” or Advanced Information Systems. Such systems, encompassing the PDB and UniProt, are indispensable not only for structural biology, but for many related fields of science. The categories of data resources described herein are applicable well beyond our usual scientific endeavors.

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A knowledge-driven approach for crystallographic protein model completion

Cited by 24 publications

References 20 publications

Structural insight into the TRIAP 1/ PRELI ‐like domain family of mitochondrial phospholipid transfer complexes

Structural insight into the TRIAP 1/ PRELI ‐like domain family of mitochondrial phospholipid transfer complexes

Hoefavidin: A dimeric bacterial avidin with a C-terminal binding tail

Databases, Repositories, and Other Data Resources in Structural Biology

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