Structure of PDB 5nug Chain B

Receptor sequence

>5nugB (length=2920) Species: 9606 (Homo sapiens)

AIVKDVLLVAQGEMALEEFLKQIREVWNTYELDLVNYQNKCRLIRGWDDL
FNKVKEHINSVSAMKLSPYYKVFEEDALSWEDKLNRIMALFDVWIDVQRR
WVYLEGIFTGSADIKHLLPVETQRFQSISTEFLALMKKVSKSPLVMDVLN
IQGVQRSLERLADLLGKIQKALGEYLERERSSFPRFYFVGDEDLLEIIGN
SKNVAKLQKHFKKMFAGVSSIILNEDNSVVLGISSREGEEVMFKTPVSIT
EHPKINEWLTLVEKEMRVTLAKLLAESVTEVEIFGKATSIDPNTYITWID
KYQAQLVVLSAQIAWSENVETALSSAAPLHSVLSNVEVTLNVLADSVLME
QPPLRRRKLEHLITELVHQRDVTRSLIKSKIDNAKSFEWLSQMRFYFDPK
QTDVLQQLSIQMANAKFNYGFEYLGVQDKLVQTPLTDRCYLTMTQALEAR
LGGSPFGPAGTGKTESVKALGHQLGRFVLVFNCDETFDFQAMGRIFVGLC
QVGAWGCFDEFNRLEERMLSAVSQQVQCIQEALREHSNPITCELLNKQVK
VSPDMAIFITMNPGYAGRSNLPDNLKKLFRSLAMTKPDRQLIAQVMLYSQ
GFRTAEVLANKIVPFFKLCDEQLSSQSHYDFGLRALKSVLVSAGNVKRER
IQKIKREAENLPEQEILIQSVCETMVPKLVAEDIPLLFSLLSDVFPGVQY
HRGEMTALREELKKVCQEMYLTYGDGEEVGGMWVEKVLQLYQITQINHGL
MMVGPSGSGKSMAWRVLLKALERLEGVEGVAHIIDPKAISKDHLYGTLDP
NTREWTDGLFTHVLRKIIDSVRGELQKRQWIVFDGDVDPEWVENLNSVLD
DNKLLTLPNGERLSLPPNVRIMFEVQDLKYATLATVSRCGMVWFSEDVLS
TDMIFNNFLARLRSIPLDEASPMLQIQRDAATIMQPYFTSNGLVTKALEH
AFQLEHIMDLTRLRCLGSLFSMLHQACRNVAQYNANHPDFPMQIEQLERY
IQRYLVYAILWSLSGDSRLKMRAELGEYIRRITTVPLPTAPNIPIIDYEV
SISGEWSPWQAKVPQIEVETHKVAAPDVVVPTLDTVRHEALLYTWLAEHK
PLVLCGPPGSGKTMTLFSALRALPDMEVVGLNFSSATTPELLLKTFDHYC
EYRRTPNGVVLAPVQLGKWLVLFCDEINLPDMDKYGTQRVISFIRQMVEH
GGFYRTSDQTWVKLERIQFVGACNPPTDPGRKPLSHRFLRHVPVVYVDYP
GPASLTQIYGTFNRAMLRLIPSLRTYAEPLTAAMVEFYTMSQERFTQDTQ
PHYIYSPREMTRWVRGIFEALRPLETLPVEGLIRIWAHEALRLFQDRLVE
DEERRWTDENIDTVALKHFPNIDREKAMSRPILYSNWLSKDYIPVDQEEL
RDYVKARLKVFYEEELDVPLVLFNEVLDHVLRIDRIFRQPQGHLLLIGVS
GAGKTTLSRFVAWMNGLSVYQIKVHRKYTGEDFDEDLRTVLRRSGCKNEK
IAFIMDESNVLDSGFLERMNTLLANGEVPGLFEGDEYATLMTQCKEGAQK
EGLMLDSHEELYKWFTSQVIRNLHVVFTMNPSSEGLKDRAATSPALFNRC
VLNWFGDWSTEALYQVGKEFTSKMDLEKPNYIVPDYMPVVYDKLPQPPSH
REAIVNSCVFVHQTLHQANARLAKRGGRTMAITPRHYLDFINHYANLFHE
KRSELEEQQMHLNVGLRKIKETVDQVEELRRDLRIKSQELEVKNAAANDK
LKKMVKDQQEAEKKQMIRDLEASIARYKEEYAVLISEAQAIKADLAAVEA
KVNRSTALLKSLSAERERWEKTSETFKNQMSTIAGDCLLSAAFIAYAGYF
DQQMRQNLFTTWSHHLQQANIQFRTDIARTEYLSNADERLRWQASSLPAD
DLCTENAIMLKRFNRYPLIIDPSGQATEFIMNEYKDRKITRTSFLDDAFR
KNLESALRFGNPLLVQDVESYDPVLNPVLNREVRRTGGRVLITLGDQDID
LSPSFVIFLSTRDPTVEFPPDLCSRVTFVNFTVTRSSLQSQCLNEVLKAE
RPDVDEKRSDLLKLQGEFQLRLRQLEKSLLQALNEVKGRILDDDTIITTL
ENLKREAAEVTRKVEETDIVMQEVETVSQQYLPLSTACSSIYFTMESLKQ
IHFLYQYSLQFFLDIYHNVLYENPNLVTDHTQRLSIITKDLFQVAFNRVA
RGMLHQDHITFAMLLARIKLKGTGEPTYDAEFQHFLRGNEIVLSAGSTPR
IQGLTVEQAEAVVRLSCLPAFKDLIAKVQADEQFGIWLDSSSPEQTVPYL
WTPATPIGQAIHRLLLIQAFRPDRLLAMAHMFVSTNLGESFMSIMEQPLD
LTHIVGTEVKPNTPVLMCSVPGYDASGHVEDLAAEQNTQITSIAIGSAEG
FNQADKAINTAVKSGRWVMLKNVHLAPGWLMQLEKKLHSLQPHACFRLFL
TMEINPKVPVNLLRAGRIFVFEPPPGVKANMLRTFSSIPVSRICKSPNER
ARLYFLLAWFHAIIQERLRYAPLGWSKKYEFGESDLRSACDTVDTWLDDT
AKGRQNISPDKIPWSALKTLMAQSIYGGRVDNEFDQRLLNTFLERLFTTR
SFDSEFKLACKVDGHKDIQMPDGIRREEFVQWVELLPDTQTPSWLGLPNN
AERVLLTTQGVDMISKMLKMQMLETLHTTASNWLHLIPQTLSHLKRTENI
KDPLFRFFEREVKMGAKLLQDVRQDLADVVQVCEGKKKQTNYLRTLINEL
VKGILPRSWSHYTVPAGMTVIQWVSDFSERIKQLQNISLAAASKELKNIH
VCLGGLFVPEAYITATRQYVAQANSWSLEELCLEVNVSFGVTGLKLQGAT
CNNNKLSLSNAISTALPLTQLRWVKQSVVTLPVYLNFTRADLIFTVDFEI
ATKEDPRSFYERGVAVLCTE

3D structure

• PDB: 5nug Cryo-EM Reveals How Human Cytoplasmic Dynein Is Auto-inhibited and Activated.
• Chain: B
• Resolution: 3.8 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	ADP	B	L1879 G1911 T1913 E1914 I2049 L2090 R2091 R2358	L430 G462 T464 E465 I592 L633 R634 R888
BS02	ATP	B	L2191 T2192 W2203 S2226 G2227 G2229 K2230 S2231 L2369 M2373 N2377 R2726 R2729	L721 T722 W733 S756 G757 G759 K760 S761 L899 M903 N907 R1237 R1240
BS03	MG	B	S2231 E2344	S761 E874
BS04	ADP	B	P2597 G2598 S2599 G2600 K2601 T2602 M2603 P2739 I2747 P2796 R2797 T2800	P1108 G1109 S1110 G1111 K1112 T1113 M1114 P1250 I1258 P1307 R1308 T1311
BS05	ADP	B	V2907 L2909 V2910 S2939 G2940 A2941 G2942 K2943 T2944 T2945 W3097 R3174 L3177	V1418 L1420 V1421 S1450 G1451 A1452 G1453 K1454 T1455 T1456 W1608 R1685 L1688

Gene Ontology

Molecular Function

• GO:0003723 RNA binding
• GO:0005515 protein binding
• 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
• GO:0007052 mitotic spindle organization
• GO:0007097 nuclear migration
• GO:0008090 retrograde axonal transport
• GO:0031122 cytoplasmic microtubule organization
• GO:0032388 positive regulation of intracellular transport
• GO:0033962 P-body assembly
• GO:0034063 stress granule assembly
• GO:0051293 establishment of spindle localization
• GO:0051301 cell division
• GO:0060236 regulation of mitotic spindle organization
• GO:0090235 regulation of metaphase plate congression
• GO:0120162 positive regulation of cold-induced thermogenesis
• GO:1905832 positive regulation of spindle assembly

Cellular Component

• GO:0005576 extracellular region
• GO:0005737 cytoplasm
• GO:0005813 centrosome
• GO:0005829 cytosol
• GO:0005856 cytoskeleton
• GO:0005868 cytoplasmic dynein complex
• GO:0005874 microtubule
• GO:0005881 cytoplasmic microtubule
• GO:0005938 cell cortex
• GO:0016020 membrane
• GO:0030175 filopodium
• GO:0030286 dynein complex
• GO:0035578 azurophil granule lumen
• GO:0070062 extracellular exosome
• GO:1904115 axon cytoplasm

External links

• PDB: RCSB:5nug, PDBe:5nug, PDBj:5nug
• PDBsum: 5nug
• PubMed: 28602352
• UniProt: Q14204|DYHC1_HUMAN Cytoplasmic dynein 1 heavy chain 1 (Gene Name=DYNC1H1)