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	The mechanochemical cycle of reactive full-length human dynein 1.
Journal, issue, pages	Nat Struct Mol Biol, Year 2025
Publish date	Apr 22, 2025
Authors	Pengxin Chai / Jun Yang / Indigo C Geohring / Steven M Markus / Yue Wang / Kai Zhang /
PubMed Abstract	Dynein-driven cargo transport has a pivotal role in diverse cellular activities, central to which is dynein's mechanochemical cycle. Here, we performed a systematic cryo-electron microscopic ...Dynein-driven cargo transport has a pivotal role in diverse cellular activities, central to which is dynein's mechanochemical cycle. Here, we performed a systematic cryo-electron microscopic investigation of the conformational landscape of full-length human dynein 1 in reaction, in various nucleotide conditions, on and off microtubules. Our approach reveals over 40 high-resolution structures, categorized into eight states, providing a dynamic and comprehensive view of dynein throughout its mechanochemical cycle. The described intermediate states reveal mechanistic insights into dynein function, including a 'backdoor' phosphate release model that coordinates linker straightening, how microtubule binding enhances adenosine triphosphatase activity through a two-way communication mechanism and the crosstalk mechanism between AAA1 and the regulatory AAA3 site. Our findings also lead to a revised model for the force-generating powerstroke and reveal means by which dynein exhibits unidirectional stepping. These results improve our understanding of dynein and provide a more complete model of its mechanochemical cycle.
External links	Nat Struct Mol Biol / PubMed:40263469
Methods	EM (single particle)
Resolution	2.2 - 8.0 Å
Structure data	44681 9bly EMDB-44681, PDB-9bly: Composite structure of full-length human dynein-1 in phi-particle conformation Method: EM (single particle) / Resolution: 3.5 Å 44682 9blz EMDB-44682, PDB-9blz: State-1(phi motor) of full-length human dynein-1 in 5mM ATP Method: EM (single particle) / Resolution: 2.2 Å 44683 9bm0 EMDB-44683, PDB-9bm0: State-2 of motor domain from full-length human dynein-1 in 5mM ATP Method: EM (single particle) / Resolution: 2.8 Å 44684 9bm1 EMDB-44684, PDB-9bm1: State-3 of motor domain from full-length human dynein-1 in 5mM ATP Method: EM (single particle) / Resolution: 3.02 Å 44685 9bm2 EMDB-44685, PDB-9bm2: State-4 of motor domain from full-length human dynein-1 in 5 mM ATP Method: EM (single particle) / Resolution: 2.82 Å 44686 9bm3 EMDB-44686, PDB-9bm3: State-5a of motor domain from full-length human dynein-1 in 5 mM ATP Method: EM (single particle) / Resolution: 3.49 Å 44687 9bm4 EMDB-44687, PDB-9bm4: State-5b of motor domain from full-length human dynein-1 in 5 mM ATP Method: EM (single particle) / Resolution: 3.48 Å 44688 9bm5 EMDB-44688, PDB-9bm5: State-6 of motor domain from full-length human dynein-1 in 5 mM ATP Method: EM (single particle) / Resolution: 3.5 Å 44689 9bm6 EMDB-44689, PDB-9bm6: State-7a of motor domain from full-length human dynein-1 in 5 mM ATP Method: EM (single particle) / Resolution: 3.22 Å 44690 9bm7 EMDB-44690, PDB-9bm7: State-7b of motor domain from full-length human dynein-1 in 5 mM ATP Method: EM (single particle) / Resolution: 3.58 Å 44691 9bm8 EMDB-44691, PDB-9bm8: State-7c of motor domain from full-length human dynein-1 in 5 mM ATP Method: EM (single particle) / Resolution: 3.22 Å 44693 9bma EMDB-44693, PDB-9bma: Motor domain from full-length human dynein-1 bound to microtubules in apo condition Method: EM (single particle) / Resolution: 3.2 Å 44694 9bmb EMDB-44694, PDB-9bmb: Post-1 motor domain from full-length human dynein-1 bound to microtubules in 5mM ADP condition Method: EM (single particle) / Resolution: 3.6 Å 44695 9bmc EMDB-44695, PDB-9bmc: Post-2 motor domain from full-length human dynein-1 bound to microtubules in 5mM ADP condition Method: EM (single particle) / Resolution: 3.5 Å 44696 9bmd EMDB-44696, PDB-9bmd: Motor domain from full-length human dynein-1 bound to microtubules in 5mM AMPPNP condition Method: EM (single particle) / Resolution: 2.9 Å 44697 9bmf EMDB-44697, PDB-9bmf: State-1(phi motor) of full-length human dynein-1 in 5mM ATPVi Method: EM (single particle) / Resolution: 2.8 Å 44698 9bmg EMDB-44698, PDB-9bmg: State-2 of full-length human dynein-1 in 5mM ATPVi Method: EM (single particle) / Resolution: 2.86 Å 44699 9bmh EMDB-44699, PDB-9bmh: State-4 of motor domain from full-length human dynein-1 in 5mM ATPVi Method: EM (single particle) / Resolution: 2.8 Å 44701 9bmj EMDB-44701, PDB-9bmj: State-1 of the motor domain from full-length human dynein-1 in 5mM AMPPNP Method: EM (single particle) / Resolution: 3.1 Å 44702 9bml EMDB-44702, PDB-9bml: State-2 of the motor domain from full-length human dynein-1 in 5mM AMPPNP Method: EM (single particle) / Resolution: 3.3 Å 44703 9bmm EMDB-44703, PDB-9bmm: State-4 of the motor domain from full-length human dynein-1 in 5mM AMPPNP Method: EM (single particle) / Resolution: 3.1 Å 44704 9bmn EMDB-44704, PDB-9bmn: State-5 of motor domain from full-length human dynein-1 in 5mM AMPPNP Method: EM (single particle) / Resolution: 3.8 Å 44705 9bmo EMDB-44705, PDB-9bmo: State-6 of motor domain from full-length human dynein-1 in 5mM AMPPNP Method: EM (single particle) / Resolution: 3.6 Å 44706 9bmp EMDB-44706, PDB-9bmp: State-7 of the motor domain from full-length human dynein-1 in 5mM AMPPNP Method: EM (single particle) / Resolution: 3.5 Å 44708 9bmr EMDB-44708, PDB-9bmr: State-1 of motor domain from full-length human phi dynein-1 in 5 mM ADP Method: EM (single particle) / Resolution: 2.6 Å 44709 9bms EMDB-44709, PDB-9bms: State-2 of motor domain from full-length human dynein-1 in 5 mM ADP Method: EM (single particle) / Resolution: 3.04 Å 44710 9bmt EMDB-44710, PDB-9bmt: State-5 of motor domain from full-length human dynein-1 in 5 mM ADP Method: EM (single particle) / Resolution: 3.7 Å 44711 9bmu EMDB-44711, PDB-9bmu: State-6 of motor domain from full-length human dynein-1 in 5 mM ADP Method: EM (single particle) / Resolution: 3.7 Å 44712 9bmv EMDB-44712, PDB-9bmv: State-7a-post1 of motor domain from full-length human dynein-1 in 5 mM ADP Method: EM (single particle) / Resolution: 3.7 Å 44713 9bmw EMDB-44713, PDB-9bmw: State-7b-post2 of motor domain from full-length human dynein-1 in 5 mM ADP Method: EM (single particle) / Resolution: 3.3 Å 44715 9bmy EMDB-44715, PDB-9bmy: State-1 of motor domain from full-length human dynein-1 in apo condition Method: EM (single particle) / Resolution: 2.86 Å 44716 9bmz EMDB-44716, PDB-9bmz: State-2 of motor domain from full-length human dynein-1 in apo condition Method: EM (single particle) / Resolution: 2.97 Å 44717 9bn0 EMDB-44717, PDB-9bn0: State-7 of motor domain from full-length human dynein-1 in apo condition Method: EM (single particle) / Resolution: 3.6 Å 44718 9bn1 EMDB-44718, PDB-9bn1: State-8 of motor domain from full-length human dynein-1 in apo condition Method: EM (single particle) / Resolution: 3.8 Å 44720 9bn3 EMDB-44720, PDB-9bn3: The alpha registry-locked dynein motor domain mutant in 5mM ATP condition, class1 Method: EM (single particle) / Resolution: 2.8 Å 44721 9bn4 EMDB-44721, PDB-9bn4: The alpha registry-locked dynein motor domain mutant in 5mM ATP condition, class2 Method: EM (single particle) / Resolution: 2.9 Å 44722 9bn5 EMDB-44722, PDB-9bn5: The alpha registry-locked dynein motor domain mutant in 5mM ATPVi condition, class1 Method: EM (single particle) / Resolution: 3.3 Å 44723 9bn6 EMDB-44723, PDB-9bn6: The alpha registry-locked dynein motor domain mutant in 5mM ATPVi condition, class2 Method: EM (single particle) / Resolution: 3.4 Å EMDB-46647: Raw consensus map of phi-particle dynein-1 Method: EM (single particle) / Resolution: 8.0 Å EMDB-46648: Focused refinement map of tail region in phi-particle dynein-1 Method: EM (single particle) / Resolution: 4.5 Å EMDB-46650: Focused refinement map of motor domain region in phi-particle dynein-1 Method: EM (single particle) / Resolution: 2.6 Å 46856 9dh5 EMDB-46856, PDB-9dh5: State-1 of the motor domain from full-length human dynein-1 in 5mM AMPPNP with 5mM Mg2+ Method: EM (single particle) / Resolution: 2.6 Å 46857 9dh6 EMDB-46857, PDB-9dh6: State-2 of the motor domain from full-length human dynein-1 in 5mM AMPPNP with 5mM Mg2+ Method: EM (single particle) / Resolution: 3.4 Å 46858 9dh7 EMDB-46858, PDB-9dh7: State-4 of the motor domain from full-length human dynein-1 in 5mM AMPPNP with 5mM Mg2+ Method: EM (single particle) / Resolution: 3.4 Å 46859 9dh8 EMDB-46859, PDB-9dh8: State-5 of the motor domain from full-length human dynein-1 in 5mM AMPPNP with 5mM Mg2+ Method: EM (single particle) / Resolution: 3.5 Å 46860 9dh9 EMDB-46860, PDB-9dh9: State-7-Post-2 of the motor domain from full-length human dynein-1 in 5mM AMPPNP with 5mM Mg2+ Method: EM (single particle) / Resolution: 3.4 Å 46861 9dha EMDB-46861, PDB-9dha: State-7-Post-1 of the motor domain from full-length human dynein-1 in 5mM AMPPNP with 5mM Mg2+ Method: EM (single particle) / Resolution: 3.6 Å
Chemicals	ChemComp-ADP: ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying moleculeYM ChemComp-ATP: ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying moleculeYM ChemComp-MG: Unknown entry ChemComp-HOH: WATER ChemComp-ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogueYM ChemComp-AOV: ADP ORTHOVANADATE / energy-carrying molecule analogueYM
Source	homo sapiens (human)
Keywords	MOTOR PROTEIN / dynein-1 / phi-particle