Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural snapshots of TRPV1 reveal mechanism of polymodal functionality.
Journal, issue, pages	Cell, Vol. 184, Issue 20, Page 5138-5150.e12, Year 2021
Publish date	Sep 30, 2021
Authors	Kaihua Zhang / David Julius / Yifan Cheng /
PubMed Abstract	Many transient receptor potential (TRP) channels respond to diverse stimuli and conditionally conduct small and large cations. Such functional plasticity is presumably enabled by a uniquely dynamic ...Many transient receptor potential (TRP) channels respond to diverse stimuli and conditionally conduct small and large cations. Such functional plasticity is presumably enabled by a uniquely dynamic ion selectivity filter that is regulated by physiological agents. What is currently missing is a "photo series" of intermediate structural states that directly address this hypothesis and reveal specific mechanisms behind such dynamic channel regulation. Here, we exploit cryoelectron microscopy (cryo-EM) to visualize conformational transitions of the capsaicin receptor, TRPV1, as a model to understand how dynamic transitions of the selectivity filter in response to algogenic agents, including protons, vanilloid agonists, and peptide toxins, permit permeation by small and large organic cations. These structures also reveal mechanisms governing ligand binding substates, as well as allosteric coupling between key sites that are proximal to the selectivity filter and cytoplasmic gate. These insights suggest a general framework for understanding how TRP channels function as polymodal signal integrators.
External links	Cell / PubMed:34496225 / PubMed Central
Methods	EM (single particle)
Resolution	2.6 - 3.89 Å
Structure data	23128 7l2h EMDB-23128, PDB-7l2h: Cryo-EM structure of unliganded full-length TRPV1 at neutral pH Method: EM (single particle) / Resolution: 2.63 Å 23129 7l2i EMDB-23129, PDB-7l2i: Cryo-EM structure of full-length TRPV1 at pH6a state Method: EM (single particle) / Resolution: 3.7 Å 23130 7l2j EMDB-23130, PDB-7l2j: Cryo-EM structure of full-length TRPV1 at pH6c state Method: EM (single particle) / Resolution: 3.66 Å 23131 7l2k EMDB-23131, PDB-7l2k: Cryo-EM structure of full-length TRPV1 at pH6b state Method: EM (single particle) / Resolution: 3.89 Å 23132 7l2l EMDB-23132, PDB-7l2l: Cryo-EM structure of RTX-bound full-length TRPV1 in O1 state Method: EM (single particle) / Resolution: 3.42 Å 23133 7l2m EMDB-23133, PDB-7l2m: Cryo-EM structure of DkTx/RTX-bound full-length TRPV1 Method: EM (single particle) / Resolution: 3.84 Å 23134 7l2n EMDB-23134, PDB-7l2n: Cryo-EM structure of RTX-bound full-length TRPV1 in C1 state Method: EM (single particle) / Resolution: 3.09 Å 23135 7l2o EMDB-23135, PDB-7l2o: Cryo-EM structure of RTX-bound full-length TRPV1 at pH 5.5 Method: EM (single particle) / Resolution: 3.64 Å 23136 7l2p EMDB-23136, PDB-7l2p: cryo-EM structure of unliganded minimal TRPV1 Method: EM (single particle) / Resolution: 2.6 Å 23138 7l2r EMDB-23138, PDB-7l2r: Cryo-EM structure of DkTx-bound minimal TRPV1 at the pre-open state Method: EM (single particle) / Resolution: 3.3 Å 23139 7l2s EMDB-23139, PDB-7l2s: cryo-EM structure of DkTx-bound minimal TRPV1 at the pre-bound state Method: EM (single particle) / Resolution: 2.71 Å 23140 7l2t EMDB-23140, PDB-7l2t: cryo-EM structure of DkTx-bound minimal TRPV1 in partial open state Method: EM (single particle) / Resolution: 3.08 Å 23141 7l2u EMDB-23141, PDB-7l2u: cryo-EM structure of DkTx-bound minimal TRPV1 in open state Method: EM (single particle) / Resolution: 3.47 Å 23142 7l2v EMDB-23142, PDB-7l2v: cryo-EM structure of RTX-bound minimal TRPV1 with NMDG at state b Method: EM (single particle) / Resolution: 3.64 Å 23143 7l2w EMDB-23143, PDB-7l2w: cryo-EM structure of RTX-bound minimal TRPV1 with NMDG at state a Method: EM (single particle) / Resolution: 3.16 Å 23144 7l2x EMDB-23144, PDB-7l2x: cryo-EM structure of RTX-bound minimal TRPV1 with NMDG at state c Method: EM (single particle) / Resolution: 3.26 Å EMDB-23161: Cryo-EM structure of DkTx-bound minimal TRPV1 at the singly-bound state Method: EM (single particle) / Resolution: 3.03 Å 24083 7mz5 EMDB-24083, PDB-7mz5: Cryo-EM structure of RTX-bound full-length TRPV1 in C2 state Method: EM (single particle) / Resolution: 2.76 Å 24084 7mz6 EMDB-24084, PDB-7mz6: Cryo-EM structure of minimal TRPV1 with 1 perturbed PI Method: EM (single particle) / Resolution: 2.91 Å 24085 7mz7 EMDB-24085, PDB-7mz7: Cryo-EM structure of minimal TRPV1 with 4 partially bound RTX Method: EM (single particle) / Resolution: 3.35 Å 24086 7mz9 EMDB-24086, PDB-7mz9: Cryo-EM structure of minimal TRPV1 with 1 partially bound RTX Method: EM (single particle) / Resolution: 3.18 Å 24087 7mza EMDB-24087, PDB-7mza: Cryo-EM structure of minimal TRPV1 with 2 bound RTX in adjacent pockets Method: EM (single particle) / Resolution: 3.46 Å 24088 7mzb EMDB-24088, PDB-7mzb: Cryo-EM structure of minimal TRPV1 with 3 bound RTX and 1 perturbed PI Method: EM (single particle) / Resolution: 3.72 Å 24089 7mzc EMDB-24089, PDB-7mzc: Cryo-EM structure of minimal TRPV1 with RTX bound in C1 state Method: EM (single particle) / Resolution: 3.03 Å 24090 7mzd EMDB-24090, PDB-7mzd: Cryo-EM structure of minimal TRPV1 with RTX bound in C2 state Method: EM (single particle) / Resolution: 2.9 Å 24091 7mze EMDB-24091, PDB-7mze: Cryo-EM structure of minimal TRPV1 with 2 bound RTX in opposite pockets Method: EM (single particle) / Resolution: 3.42 Å
Chemicals	ChemComp-XJ7: (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1r,2R,3S,4S,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate ChemComp-XJD: (10R,13S)-16-amino-13-hydroxy-7,13-dioxo-8,12,14-trioxa-13lambda~5~-phosphahexadecan-10-yl tridecanoate ChemComp-NA: Unknown entry ChemComp-XJA: (2S)-1-(butanoyloxy)-3-{[(R)-hydroxy{[(1S,2R,3R,4R,5R,6S)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}propan-2-yl tridecanoate ChemComp-6EU: resiniferatoxin / toxinYM ChemComp-6IY: (10R,13S)-16-amino-13-hydroxy-7,13-dioxo-8,12,14-trioxa-13lambda~5~-phosphahexadecan-10-yl hexadecanoate ChemComp-65I: (9R,12R)-15-amino-12-hydroxy-6,12-dioxo-7,11,13-trioxa-12lambda~5~-phosphapentadecan-9-yl undecanoate ChemComp-HOH: WATER ChemComp-XKP: (11R,14S)-17-amino-14-hydroxy-8,14-dioxo-9,13,15-trioxa-14lambda~5~-phosphaheptadecan-11-yl decanoate ChemComp-XPS: 6-deoxy-6-(methylamino)-D-galactitol ChemComp-XPJ*: 1-deoxy-1-(methylamino)-D-allitol
Source	rattus norvegicus (Norway rat) Cyriopagopus schmidtiCyriopagopus schmidti (Chinese earth tiger) cyriopagopus schmidti (Chinese earth tiger)
Keywords	TRANSPORT PROTEIN / TRP channel / cryo-EM / nanodisc / full length / proton / vanilloid agonist / toxin / large cation / stoichiometry