BioNMR
NMR aggregator & online community since 2003
BioNMR    
Learn or help to learn NMR - get free NMR books!
 

Go Back   BioNMR > Educational resources > Journal club
Advanced Search



Jobs Groups Conferences Literature Pulse sequences Software forums Programs Sample preps Web resources BioNMR issues


Webservers
NMR processing:
MDD
NMR assignment:
Backbone:
Autoassign
MARS
UNIO Match
PINE
Side-chains:
UNIO ATNOS-Ascan
NOEs:
UNIO ATNOS-Candid
UNIO Candid
ASDP
Structure from NMR restraints:
Ab initio:
GeNMR
Cyana
XPLOR-NIH
ASDP
UNIO ATNOS-Candid
UNIO Candid
Fragment-based:
BMRB CS-Rosetta
Rosetta-NMR (Robetta)
Template-based:
GeNMR
I-TASSER
Refinement:
Amber
Structure from chemical shifts:
Fragment-based:
WeNMR CS-Rosetta
BMRB CS-Rosetta
Homology-based:
CS23D
Simshift
Torsion angles from chemical shifts:
Preditor
TALOS
Promega- Proline
Secondary structure from chemical shifts:
CSI (via RCI server)
TALOS
MICS caps, β-turns
d2D
PECAN
Flexibility from chemical shifts:
RCI
Interactions from chemical shifts:
HADDOCK
Chemical shifts re-referencing:
Shiftcor
UNIO Shiftinspector
LACS
CheckShift
RefDB
NMR model quality:
NOEs, other restraints:
PROSESS
PSVS
RPF scores
iCing
Chemical shifts:
PROSESS
CheShift2
Vasco
iCing
RDCs:
DC
Anisofit
Pseudocontact shifts:
Anisofit
Protein geomtery:
Resolution-by-Proxy
PROSESS
What-If
iCing
PSVS
MolProbity
SAVES2 or SAVES4
Vadar
Prosa
ProQ
MetaMQAPII
PSQS
Eval123D
STAN
Ramachandran Plot
Rampage
ERRAT
Verify_3D
Harmony
Quality Control Check
NMR spectrum prediction:
FANDAS
MestReS
V-NMR
Flexibility from structure:
Backbone S2
Methyl S2
B-factor
Molecular dynamics:
Gromacs
Amber
Antechamber
Chemical shifts prediction:
From structure:
Shiftx2
Sparta+
Camshift
CH3shift- Methyl
ArShift- Aromatic
ShiftS
Proshift
PPM
CheShift-2- Cα
From sequence:
Shifty
Camcoil
Poulsen_rc_CS
Disordered proteins:
MAXOCC
Format conversion & validation:
CCPN
From NMR-STAR 3.1
Validate NMR-STAR 3.1
NMR sample preparation:
Protein disorder:
DisMeta
Protein solubility:
camLILA
ccSOL
Camfold
camGroEL
Zyggregator
Isotope labeling:
UPLABEL
Solid-state NMR:
sedNMR


Reply
Thread Tools Search this Thread Rate Thread Display Modes
  #1  
Unread 11-19-2016, 08:35 PM
nmrlearner's Avatar
Senior Member
 
Join Date: Jan 2005
Posts: 23,137
Points: 193,617, Level: 100
Points: 193,617, Level: 100 Points: 193,617, Level: 100 Points: 193,617, Level: 100
Level up: 0%, 0 Points needed
Level up: 0% Level up: 0% Level up: 0%
Activity: 50.7%
Activity: 50.7% Activity: 50.7% Activity: 50.7%
Last Achievements
Award-Showcase
NMR Credits: 0
NMR Points: 193,617
Downloads: 0
Uploads: 0
Default NMR structure of the HIV-1 reverse transcriptase thumb subdomain

NMR structure of the HIV-1 reverse transcriptase thumb subdomain

Abstract

The solution NMR structure of the isolated thumb subdomain of HIV-1 reverse transcriptase (RT)Â*has been determined. A detailed comparison of the current structure with dozens of the highest resolution crystal structures of this domain in the context of the full-length enzyme reveals that the overall structures are very similar, with only two regions exhibiting local conformational differences. The C-terminal capping pattern of the αH helix is subtly different, and the loop connecting the αI and αJ helices in the p51 chain of the full-length p51/p66 heterodimeric RT differs from our NMR structure due to unique packing interactions in mature RT. Overall, our data show that the thumb subdomain folds independently and essentially the same in isolation as in its natural structural context.



Source: Journal of Biomolecular NMR
Reply With Quote


Did you find this post helpful? Yes | No

Reply
Similar Threads
Thread Thread Starter Forum Replies Last Post
[NMR paper] NMR characterization of HIV-1 reverse transcriptase binding to various non-nucleoside reverse transcriptase inhibitors with different activities.
NMR characterization of HIV-1 reverse transcriptase binding to various non-nucleoside reverse transcriptase inhibitors with different activities. http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.nature.com-images-lo_npg.gif http://www.bionmr.com//www.ncbi.nlm.nih.gov/corehtml/query/egifs/https:--www.ncbi.nlm.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles NMR characterization of HIV-1 reverse transcriptase binding to various non-nucleoside reverse transcriptase inhibitors with different activities. Sci Rep. 2015;5:15806 ...
nmrlearner Journal club 0 09-24-2016 05:20 PM
[NMR paper] Conformational plasticity of the NNRTI-binding pocket in HIV-1 reverse transcriptase - A fluorine NMR study.
Conformational plasticity of the NNRTI-binding pocket in HIV-1 reverse transcriptase - A fluorine NMR study. Related Articles Conformational plasticity of the NNRTI-binding pocket in HIV-1 reverse transcriptase - A fluorine NMR study. Biochemistry. 2016 May 10; Authors: Sharaf NG, Ishima R, Gronenborn AM Abstract HIV-1 reverse transcriptase (RT) is a major drug target in the treatment of HIV-1 infection. RT inhibitors currently in use include non-nucleoside, allosteric RT inhibitors (NNRTIs), which bind to a hydrophobic pocket,...
nmrlearner Journal club 0 05-11-2016 08:04 PM
[NMR paper] NMR Characterization and Membrane Interactions of the Loop Region of Kindlin-3 F1 Subdomain.
NMR Characterization and Membrane Interactions of the Loop Region of Kindlin-3 F1 Subdomain. Related Articles NMR Characterization and Membrane Interactions of the Loop Region of Kindlin-3 F1 Subdomain. PLoS One. 2016;11(4):e0153501 Authors: Chua GL, Tan SM, Bhattacharjya S Abstract Kindlins-1,2 and 3 are FERM domain-containing cytosolic proteins involved in the activation and regulation of integrin-mediated cell adhesion. Apart from binding to integrin ? cytosolic tails, kindlins and the well characterized integrin-activator...
nmrlearner Journal club 0 04-22-2016 08:45 PM
[NMR paper] Application of Site-Specific Spin Labeling for NMR Detecting Inhibitor-Induced Conformational Change of HIV-1 Reverse Transcriptase.
Application of Site-Specific Spin Labeling for NMR Detecting Inhibitor-Induced Conformational Change of HIV-1 Reverse Transcriptase. Related Articles Application of Site-Specific Spin Labeling for NMR Detecting Inhibitor-Induced Conformational Change of HIV-1 Reverse Transcriptase. ChemMedChem. 2016 Jan 25; Authors: Seetaha S, Yagi-Utsumi M, Yamaguchi T, Ishii K, Hannongbua S, Choowongkomon K, Kato K Abstract Paramagnetism-assisted nuclear magnetic resonance (NMR) techniques can provide long-range structural information...
nmrlearner Journal club 0 01-26-2016 03:40 PM
[NMR paper] NMR assignments of the N-terminal domain of Ogataea polymorpha telomerase reverse transcriptase.
NMR assignments of the N-terminal domain of Ogataea polymorpha telomerase reverse transcriptase. Related Articles NMR assignments of the N-terminal domain of Ogataea polymorpha telomerase reverse transcriptase. Biomol NMR Assign. 2015 Dec 31; Authors: Polshakov VI, Petrova OA, Parfenova YY, Efimov SV, Klochkov VV, Zvereva MI, Dontsova OA Abstract Telomerase is a ribonucleoprotein enzyme that adds telomeric DNA fragments to the ends of chromosomes. This enzyme is the focus of substantial attention, both because its structure and...
nmrlearner Journal club 0 01-03-2016 01:25 AM
[NMR paper] Refining the overall structure and subdomain orientation of ribosomal protein S4 delt
Refining the overall structure and subdomain orientation of ribosomal protein S4 delta41 with dipolar couplings measured by NMR in uniaxial liquid crystalline phases. Related Articles Refining the overall structure and subdomain orientation of ribosomal protein S4 delta41 with dipolar couplings measured by NMR in uniaxial liquid crystalline phases. J Mol Biol. 1999 Sep 17;292(2):375-87 Authors: Markus MA, Gerstner RB, Draper DE, Torchia DA Prokaryotic protein S4 initiates assembly of the small ribosomal subunit by binding to 16 S rRNA....
nmrlearner Journal club 0 11-18-2010 08:31 PM
[NMR paper] Dissection of the basic subdomain of the c-Jun oncoprotein: a structural analysis of
Dissection of the basic subdomain of the c-Jun oncoprotein: a structural analysis of two peptide fragments by CD, Fourier-transform infrared and NMR. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles Dissection of the basic subdomain of the c-Jun oncoprotein: a structural analysis of two peptide fragments by CD, Fourier-transform infrared and NMR. Eur J Biochem. 1996 Feb 1;235(3):699-712 Authors: Krebs D, Dahmani B, Monnot M, Mauffret O,...
nmrlearner Journal club 0 08-22-2010 02:27 PM
[NMR paper] The basic subdomain of the c-Jun oncoprotein. A joint CD, Fourier-transform infrared
The basic subdomain of the c-Jun oncoprotein. A joint CD, Fourier-transform infrared and NMR study. http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles The basic subdomain of the c-Jun oncoprotein. A joint CD, Fourier-transform infrared and NMR study. Eur J Biochem. 1995 Jul 15;231(2):370-80 Authors: Krebs D, Dahmani B, el Antri S, Monnot M, Convert O, Mauffret O, Troalen F, Fermandjian S The structural properties of the basic...
nmrlearner Journal club 0 08-22-2010 03:50 AM


Thread Tools Search this Thread
Search this Thread:

Advanced Search
Display Modes Rate This Thread
Rate This Thread:

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is On
Trackbacks are Off
Pingbacks are Off
Refbacks are Off



BioNMR advertisements to pay for website hosting and domain registration. Nobody does it for us.



Powered by vBulletin® Version 3.7.3
Copyright ©2000 - 2024, Jelsoft Enterprises Ltd.
Copyright, BioNMR.com, 2003-2013
Search Engine Friendly URLs by vBSEO 3.6.0

All times are GMT. The time now is 12:12 PM.


Map