Structure of PDB 8dzz Chain D

Receptor sequence

>8dzzD (length=2363) Species: 4932 (Saccharomyces cerevisiae)

QFYWLDLYGILGENLDIQNFLPLETSKFKSLSLKMIKSSLSTFLERQRRQ
FPRFYFLGNDDLLKIIGSGKHHDQVSKFMKKMFGSIESIIFFEDSITGVR
SVEGEVLNLNEKIELKDSIQAQEWLNILDTEIKLSVFTQFRDCLGQLKDG
TDIEVVVSKYIFQAILLSAQVMWTELVEKCLQTNEFSKYWKEVDMKIKGL
LDKLNKSSDNVKKKIEALLVEYLHFNNVIGQLKNCSTKEEARLLWAKVQK
FYQKNDTLDDLNSVFISQSGYLLQYKFEYIGIPERLIYTPLLLVGFATLT
DSLHQKYGGCFFGPAGTGKTETVKAFGQNLGRVVVVFNCDDSFDYQVLSR
LLVGITQIGAWGCFDEFNRLDEKVLSAVSANIQQIQNGLQVGKSHITLLE
EETPLSPHTAVFITLNPGYNGRSELPENLKKSFREFSMKSPQSGTIAEMI
LQIMGFEDSKSLASKIVHFLELLSSKCSSMNHYHFGLRTLKGVLRNCSPL
VSEFGEGEKTVVESLKRVILPSLGDTDELVFKDELSKIFDSNSKAIVQCL
KDAGQRSGFSMSEEFLKKCMQFYYMQKTQQALILVGKAGCGKTATWKTVI
DAMAIFDGHANVVYVIDTKVLTKESLYGSMLKATLEWRDGLFTSILRRVN
DDITGTFKNSRIWVVFDSDLDPEYVEAMNSVLDDNKILTLPNGERLPIPP
NFRILFETDNLDHTTPATITRCGLLWFSTDVCSISSKIDHLLNKSYEALF
ELDKLKDLISDSFDMASLTNIFTCSNDLVHILGVRTFNKLETAVQLAVHL
ISSYRQWFQNLDDKSLKDVITLLIKRSLLYALAGDSTGESQRAFIQTINT
YFGHDSQELSDYSTIVILSFSSFCSEIPSVSLEAHEVMRPDIVIPTIDTI
KHEKIFYDLLNSKRGIILCGPPGSGKTMIMNNALRNSSLYDVVGINFSKD
TTTEHILSALHRHTNYVTGLTLLPKSDIKNLVLFCDQINLPKLDKYGSQN
VVLFLRQLMEKQGFWKTPENKWVTIERIHIVGACNPPTDPGRIPMSERFT
RHAAILYLGYPSGKSLSQIYEIYYKAIFKLVPEFRSYTEPFARASVHLYN
ECKARYSTGLQSHYLFSPRELTRLVRGVYTAINTGPRQTLRSLIRLWAYE
AWRIFADRLVGVKEKNSFEQLLYETVDKYLPLGNISSTSLLFSGLLSLDF
KEVNKTDLVNFIEERFKTFCDEELEVPMVIHESMVDHILRIDRALKQVQG
HMMLIGASRTGKTILTRFVAWLNGLKIVQPKIHRHSNLSDFDMILKKAIS
DCSLKESRTCLIIDESNILETAFLERMNTLLANADIPDLFQGEEYDKLLN
NLRNKTRSLGLLLDTEQELYDWFVGEIAKNLHVVFTICDPTNNKSSAMIS
SPALFNRCIINWMGDWDTKTMSQVANNMVDVVPMEFTDFIVPEVNKELVF
TEPIQTIRDAVVNILIHFDRNFYQKMKVGVNPRSPGYFIDGLRALVKLVT
AKYQDLQENQRFVNVGLEKLNESVLKVNELNKTLSKKSTELTEKEKEARS
TLDKSKQKYSLLIRDVEAIKTEMSNVQANLDRSISLVKSLTFEKERWLNT
TKQFSKTSQELIGNCIISSIYETYFGHLNERERGDMLVILKRLLGKFAVK
YDVNYRFIDYLVTLDEKMKWLECGLDKNDYFLENMSIVMNSQDAVPFLLD
PSSHMITVISNYYGNKTVLLSFLEEGFVKRLENAVRFGSVVIIQDGEFFD
PIISRLISREFNHAGNRVTVEIGDHEVDVSGDFKLFIHSCDPSGDIPIFL
RSRVRLVHFVTNKESIETRIFDITLTEENAEMQRKREDLIKLNTEYRLKL
KNLEKRLLEELNNSQGNMLENDELMVTLNNLKKEAMNIEKKLSESEEFFP
QFDNLVEEYSIIGKHSVKIFSMLEKFGQFHWFYGISIGQFLSCFKRVFIK
TRVDEILWLLYQEVYCQFSTALDKKFKMIMAMTMFCLYKFDIESEQYKEA
VLTMIGVLSESSDGVPKLTNDDLRYLWDYVTTKSYISALNWFKNEFFVDE
WNIADVVANSENNYFTMASERDVDGTFKLIELAKASKESLKIIPLGSIEN
LNYAQEEISKSKIEGGWILLQNIQMSLSWVKTYLHKHVEETKAAEEHEKF
KMFMTCHLTGDKLPAPLLQRTDRVVYEDIPGILDTVKDLWGSQGVWSVYC
TFLLSWFHALITARTRLVPHGFSKKYYFNDCDFQFASVYLENVLATNSTN
NIPWAQVRDHIATIVYGGKIDEEKDLEVVAKLCAHVFCGSDNLQIVPGVR
IPQPLLQQSEEEERARLTAILSNTIEPADSLSSWLQLPRESILDYERLQA
KEVASSTEQLLQE

3D structure

• PDB: 8dzz Lis1 relieves cytoplasmic dynein-1 autoinhibition by acting as a molecular wedge.
• Chain: D
• Resolution: 4.1 Å

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	ATP	D	F2047 S2048 G2077 C2078 G2079 K2080 T2081 A2082 E2195 C2220 K2225 H2228 R2549	F559 S560 G589 C590 G591 K592 T593 A594 E707 C732 K737 H740 R1048
BS02	ATP	D	L1769 I1770 A1798 G1801 K1802 T1803 E1804 E1849 N1899 I1929 L1970 R1971 K1974 R2209	L286 I287 A315 G318 K319 T320 E321 E366 N416 I446 L487 R488 K491 R721
BS03	ADP	D	M2732 V2733 H2735 R2763 T2764 G2765 K2766 T2767 I2768 W2920 I2993 R3512	M1228 V1229 H1231 R1259 T1260 G1261 K1262 T1263 I1264 W1416 I1489 R1803
BS04	ATP	D	G2421 G2423 T2425 M2426 I2570 R2620 T2623	G923 G925 T927 M928 I1069 R1119 T1122

Gene Ontology

Molecular Function

• GO:0005524 ATP binding
• GO:0008569 minus-end-directed microtubule motor activity
• GO:0016887 ATP hydrolysis activity
• GO:0045505 dynein intermediate chain binding
• GO:0051959 dynein light intermediate chain binding

Biological Process

• GO:0007018 microtubule-based movement

Cellular Component

• GO:0030286 dynein complex

External links

• PDB: RCSB:8dzz, PDBe:8dzz, PDBj:8dzz
• PDBsum: 8dzz
• PubMed: 37620585
• UniProt: P36022|DYHC_YEAST Dynein heavy chain, cytoplasmic (Gene Name=DYN1)