Biological Crystallography

 

Acta Cryst. (2010). D66, 223-232  [ doi:10.1107/S0907444909053979 ]

Direct inter-subdomain interactions switch between the closed and open forms of the Hsp70 nucleotide-binding domain in the nucleotide-free state

M. Shida, A. Arakawa, R. Ishii, S. Kishishita, T. Takagi, M. Kukimoto-Niino, S. Sugano, A. Tanaka, M. Shirouzu and S. Yokoyama

Synopsis: In this study, the crystal structures of the human Hsp70 nucleotide-binding domain (NBD) fragment were determined in the nucleotide-free state and in complex with adenosine 5'-(,-imido)triphosphate (AMPPNP).

PDB references: 2e88 and 2e8a

Online 12 February 2010

 

Acta Cryst. (2010). D66, 233-242  [ doi:10.1107/S0907444909054298 ]

Structure of the unbound form of HIV-1 subtype A protease: comparison with unbound forms of proteases from other HIV subtypes

A. H. Robbins, R. M. Coman, E. Bracho-Sanchez, M. A. Fernandez, C. T. Gilliland, M. Li, M. Agbandje-McKenna, A. Wlodawer, B. M. Dunn and R. McKenna

Synopsis: The crystal structure of the unbound form of HIV-1 subtype A protease has been determined to 1.7 Å resolution. A detailed structural analysis and comparison of the unbound subtype A, B and C protease structures is presented. The results showed that although no inhibitor is present in the active site, the subtype A protease has flaps in the closed position.

PDB reference: 3ixo

Online 12 February 2010

 

Acta Cryst. (2010). D66, 243-250  [ doi:10.1107/S0907444909055462 ]

Introduction of a leucine half-zipper engenders multiple high-quality crystals of a recalcitrant tRNA synthetase

M. Guo, R. Shapiro, P. Schimmel and X.-L. Yang

Synopsis: E. coli alanyl-tRNA synthetase is recalcitrant to crystallization. A group of leucine substitutions has transformed the protein.

Online 12 February 2010

 

Acta Cryst. (2010). D66, 251-257  [ doi:10.1107/S0907444909055693 ]

Coiled-coil conformation of a pentamidine-DNA complex

T. Moreno, J. Pous, J. A. Subirana and J. L. Campos

Synopsis: The oligonucleotide d(ATATATATAT) has been crystallized as a coiled coil in the presence of pentamidine. The drug sits in the minor groove of the duplex, but shows a new form of interaction with DNA as a cross-linking agent. The duplex contains both Watson-Crick and Hoogsteen base pairs.

PDB reference: 3ey0

NDB reference: DD0102

Online 12 February 2010

 

Acta Cryst. (2010). D66, 258-267  [ doi:10.1107/S0907444909055760 ]

pH-dependent structural changes in haemoglobin component V from the midge larva Propsilocerus akamusi (Orthocladiinae, Diptera)

T. Kuwada, T. Hasegawa, T. Takagi, I. Sato and F. Shishikura

Synopsis: The crystal structure of midge larval haemoglobin was determined at five different pH conditions. Comparison of these structures indicated that pH changes result in a swinging movement of the distal Arg residue and a partial shift of the F-helix C-terminus followed by haem tilting in this insect haemoglobin.

PDB references: 2zwj, 3a5a, 3a5b, 3a5g and 3a9m

Online 12 February 2010

 

Acta Cryst. (2010). D66, 268-275  [ doi:10.1107/S0907444910000314 ]

Rapid model building of -helices in electron-density maps

T. C. Terwilliger

Synopsis: A method for rapid model building of -helices at moderate resolution is presented.

Online 12 February 2010

 

Acta Cryst. (2010). D66, 276-284  [ doi:10.1107/S0907444910000302 ]

Rapid model building of -sheets in electron-density maps

T. C. Terwilliger

Synopsis: A method for rapid model building of -sheets at moderate resolution is presented.

Online 12 February 2010

 

Acta Cryst. (2010). D66, 285-294  [ doi:10.1107/S0907444910000272 ]

Rapid chain tracing of polypeptide backbones in electron-density maps

T. C. Terwilliger

Synopsis: A method for rapid chain tracing of polypeptide backbones at moderate resolution is presented.

Online 12 February 2010

 

Acta Cryst. (2010). D66, 295-303  [ doi:10.1107/S0907444910000879 ]

Structural insights into the assembly of the human and archaeal signal recognition particles

K. Wild, G. Bange, G. Bozkurt, B. Segnitz, A. Hendricks and I. Sinning

Synopsis: The structures of the human and a crenarchaeal SRP19-SRP RNA complex reveal general features of SRP S-domain organization and allow an update of the SRP-assembly paradigm.

PDB references: 3ktv and 3ktw

Online 12 February 2010

 

Acta Cryst. (2010). D66, 304-308  [ doi:10.1107/S0907444909051798 ]

Getting the best out of long-wavelength X-rays: de novo chlorine/sulfur SAD phasing of a structural protein from ATV

A. Goulet, G. Vestergaard, C. Felisberto-Rodrigues, V. Campanacci, R. A. Garrett, C. Cambillau and M. Ortiz-Lombardía

Synopsis: The solution of a structural protein from the Acidianus two-tailed virus using long-wavelength SAD phasing suggests a systematic approach for the solution of protein crystal structures by taking advantage of the anomalous signal of serendipitously associated chloride ions from the solvent.

PDB reference: 3faj

Online 12 February 2010

 

Acta Cryst. (2010). D66, 309-313  [ doi:10.1107/S0907444909053244 ]

Structure determination using poorly diffracting membrane-protein crystals: the H⁺-ATPase and Na⁺,K⁺-ATPase case history

B. P. Pedersen, J. P. Morth and P. Nissen

Synopsis: Procedures for heavy-atom site identification by molecular replacement at low resolution and for density modification by multi-crystal averaging using quasi-isomorphous diffraction data are presented. The procedures are based on the case history from the structure determination of H⁺-ATPase and Na⁺, K⁺-ATPase and have been successfully applied to the transporter Mhp1 to reveal general applicability.

Online 12 February 2010

 

Acta Cryst. (2010). D66, 314-318  [ doi:10.1107/S0907444909054535 ]

Accommodation of structural rearrangements in the huntingtin-interacting protein 1 coiled-coil domain

J. D. Wilbur, P. K. Hwang, F. M. Brodsky and R. J. Fletterick

Synopsis: Variable packing interaction related to the conformational flexibility within the huntingtin-interacting protein 1 coiled coil domain.

PDB reference: 3i00

Online 12 February 2010

 

Acta Cryst. (2010). D66, 319-323  [ doi:10.1107/S0907444909055504 ]

Deleting two C-terminal -helices is effective to crystallize the bacterial ABC transporter Escherichia coli MsbA complexed with AMP-PNP

K. Terakado, A. Kodan, H. Nakano, Y. Kimura, K. Ueda, T. Nakatsu and H. Kato

Synopsis: Deleting two C-terminal -helices of the MsbA molecule from E. coli improved its crystallizability and generated new crystal forms of the complex with adenosine 5'-(,-imido)triphosphate that had an outward-facing conformation.

Online 12 February 2010