8FDU

Engineered human dynein motor domain in the microtubule-unbound state with LIS1 complex in the buffer containing ATP-Vi (local refined on AAA3-AAA5 and LIS1)


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
APF12777e8fduA6 A: alpha arraysX: Histone-likeH: Histone-relatedT: AAA+ ATPase lid domainF: PF12777ECOD (1.6)
APF12780e8fduA5 A: alpha arraysX: Histone-likeH: Histone-relatedT: AAA+ ATPase lid domainF: PF12780ECOD (1.6)
APF12781e8fduA7 A: alpha arraysX: Histone-likeH: Histone-relatedT: AAA+ ATPase lid domainF: PF12781ECOD (1.6)
APF22597e8fduA4 A: alpha arraysX: Histone-likeH: Histone-relatedT: AAA+ ATPase lid domainF: PF22597ECOD (1.6)
APF12775e8fduA2 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: PF12775ECOD (1.6)
APF12780e8fduA1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: PF12780ECOD (1.6)
APF12781e8fduA3 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: PF12781ECOD (1.6)
BPF00400e8fduB1 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 7-bladedF: PF00400ECOD (1.6)
CPF00400e8fduC1 A: beta duplicates or obligate multimersX: beta-propeller-likeH: beta-propellerT: 7-bladedF: PF00400ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF22597Dynein heavy chain, ATPase lid domain (DYN_lid)Dynein heavy chain, ATPase lid domainDyneins are microtubule-based AAA(+) motor complexes that power ciliary beating, cell division, cell migration and intracellular transport and comprise cytoplasmic and axonemal isoforms. They consist of a motor domain that contains a ring-shaped head ...Dyneins are microtubule-based AAA(+) motor complexes that power ciliary beating, cell division, cell migration and intracellular transport and comprise cytoplasmic and axonemal isoforms. They consist of a motor domain that contains a ring-shaped head with six AAA-domains, a coiled-coil stalk with a microtubule binding domain (MTBD) and a linker [1-5] This entry represents the lid domain found at the C-terminal of the third AAA+ ATPase domain in dyneins [1-5].
Domain
PF12775P-loop containing dynein motor region (AAA_7)P-loop containing dynein motor regionThis domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliophathies. Dyneins share a conserved motor domain that couples cycles of ATP hydr ...This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliophathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities (AAA1-AAA6). This is the third nucleotide binding sites in the dynein motor. However, AAA3 has lost the catalytic residues necessary for ATP hydrolysis (the Walker B glutamate, the arginine finger, sensor-I and sensor-II motifs) [1].
Domain
PF12781ATP-binding dynein motor region (AAA_9)ATP-binding dynein motor regionThis domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydro ...This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities (AAA1-AAA6). This is the fifth AAA+ domain subdomain AAA5S. Structural analysis reveal that it is the coiled-coil buttress interface. The relative movement of AAA5S together with the stalk (AAA4S), is coupled to rearrangements in the AAA+ ring. Closure of the AAA1 site and the rigid body movement of AAA2-AAA4 force the AAA4/AAA5 interface to close and the AAA6L subdomain to rotate towards the ring centre. The AAA5S subdomain rotates as a unit together with AAA6L, and this movement pulls the buttress relative to the stalk [1].
Domain
PF12780P-loop containing dynein motor region D4 (AAA_8)P-loop containing dynein motor region D4The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures describ ...The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This particular family is the D4 ATP-binding region of the motor [1].
Domain
PF12777Microtubule-binding stalk of dynein motor (MT)Microtubule-binding stalk of dynein motorthe 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures describ ...the 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules, of which four correspond to the ATP binding sites with P-loop signatures described previously, and two are modules in which the P loop has been lost in evolution. This family is the region between D4 and D5 and is the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component [1].
Domain
B, C
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
Cytoplasmic dynein 1 heavy chain 1,Serine--tRNA ligase
B, C
Platelet-activating factor acetylhydrolase IB subunit beta,Platelet-activating factor acetylhydrolase IB subunit beta,human LIS1 protein with a SNAP tag

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR045864Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)Homologous Superfamily
IPR042103Serine-tRNA synthetase, type1, N-terminal domain superfamilyHomologous Superfamily
IPR002317Serine-tRNA ligase, type1Family
IPR015866Serine-tRNA synthetase, type1, N-terminalDomain
IPR006195Aminoacyl-tRNA synthetase, class IIDomain
IPR002314Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)Domain
IPR010978Class I and II aminoacyl-tRNA synthetase, tRNA-binding armHomologous Superfamily
IPR033729Serine-tRNA ligase catalytic core domainDomain
IPR026983Dynein heavy chainFamily
IPR013602Dynein heavy chain, linkerDomain
IPR041658Dynein heavy chain AAA lid domainDomain
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
IPR042222Dynein heavy chain, domain 2, N-terminalHomologous Superfamily
IPR043160Dynein heavy chain, C-terminal domain, barrel regionHomologous Superfamily
IPR035706Dynein heavy chain, ATP-binding dynein motor regionDomain
IPR041228Dynein heavy chain, C-terminal domainDomain
IPR003593AAA+ ATPase domainDomain
IPR041466Dynein heavy chain, AAA 5 extension domainDomain
IPR042228Dynein heavy chain, linker, subdomain 3Homologous Superfamily
IPR035699Dynein heavy chain, hydrolytic ATP-binding dynein motor regionDomain
IPR042219Dynein heavy chain AAA lid domain superfamilyHomologous Superfamily
IPR024743Dynein heavy chain, coiled coil stalkDomain
IPR013594Dynein heavy chain, tailDomain
IPR043157Dynein heavy chain, AAA1 domain, small subdomainHomologous Superfamily
IPR004273Dynein heavy chain region D6 P-loop domainDomain
IPR024317Dynein heavy chain, AAA module D4Domain
B, C
IPR019775WD40 repeat, conserved siteConserved Site
B, C
IPR006594LIS1 homology motifConserved Site
B, C
IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
B, C
IPR020472G-protein beta WD-40 repeatRepeat
B, C
IPR037190LIS1, N-terminalHomologous Superfamily
B, C
IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
B, C
IPR001680WD40 repeatRepeat
B, C
IPR017252Dynein regulator LIS1Family