8RGH: Dynein-2 intermediate chain DYNC2I1
Structure of dynein-2 intermediate chain DYNC2I1 (WDR60) in complex with the dynein-2 heavy chain DYNC2H1. Determined by electron microscopy at 3.9 Å resolution. Released 20 Mar 2024.
- Method
- Electron microscopy
- Resolution
- 3.9 Å
- Organism
- Homo sapiens
- Chains
- 6
- Atoms
- 9,682
- Mol. weight
- 760.28 kDa
- Released
- 20 Mar 2024
Explore 8RGH in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8RGH contains 47 α-helices and 49 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 28 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 173-185 | 13 | |
| α-helix | 189-210 | 22 | |
| α-helix | 212-214 | 3 | |
| α-helix | 217-236 | 20 | |
| α-helix | 242-244 | 3 | |
| α-helix | 245-268 | 24 | |
| α-helix | 277-299 | 23 | |
| α-helix | 300-306 | 7 | |
| α-helix | 307-308 | 2 | |
| α-helix | 322-323 | 2 | |
| α-helix | 324-328 | 5 | |
| α-helix | 329-347 | 19 | |
| α-helix | 348-349 | 2 | |
| α-helix | 352-365 | 14 | |
| α-helix | 378-409 | 32 | |
| α-helix | 414-423 | 10 | |
| α-helix | 425-428 | 4 | |
| α-helix | 431-436 | 6 | |
| α-helix | 438-464 | 27 | |
| α-helix | 481-506 | 26 | |
| β-strand | 508 | 1 | 1 |
| β-strand | 510 | 1 | 1 |
| α-helix | 513-545 | 33 | |
| β-strand | 562-565 | 4 | 2 |
| β-strand | 570-573 | 4 | 2 |
| α-helix | 577-592 | 16 | |
| α-helix | 598-629 | 32 | |
| α-helix | 636-653 | 18 | |
| α-helix | 668-707 | 40 | |
| α-helix | 712-714 | 3 | |
| α-helix | 715-734 | 20 | |
| α-helix | 739-769 | 31 | |
Chain C: 12 helices, 34 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 579-584 | 6 | |
| α-helix | 586-610 | 25 | |
| β-strand | 629-632 | 4 | 3 |
| β-strand | 644-649 | 6 | 4 |
| β-strand | 656-661 | 6 | 4 |
| α-helix | 662-664 | 3 | |
| α-helix | 670-673 | 4 | |
| β-strand | 676-682 | 7 | 4 |
| β-strand | 691-695 | 5 | 4 |
| β-strand | 699-704 | 6 | 5 |
| β-strand | 711-716 | 6 | 5 |
| β-strand | 721-725 | 5 | 5 |
| β-strand | 735-738 | 4 | 6 |
| β-strand | 741-744 | 4 | 6 |
| β-strand | 746 | 1 | 4 |
| β-strand | 750-751 | 2 | 5 |
| α-helix | 752-754 | 3 | |
| β-strand | 765-771 | 7 | 7 |
| β-strand | 798-803 | 6 | 7 |
| β-strand | 808-815 | 8 | 7 |
| β-strand | 830 | 1 | 5 |
| β-strand | 836-840 | 5 | 7 |
| β-strand | 844 | 1 | 7 |
| α-helix | 846-849 | 4 | |
| α-helix | 861-862 | 2 | |
| β-strand | 863-868 | 6 | 8 |
| β-strand | 875-880 | 6 | 8 |
| β-strand | 885-889 | 5 | 8 |
| β-strand | 899-900 | 2 | 8 |
| α-helix | 901-902 | 2 | |
| β-strand | 912-917 | 6 | 9 |
| β-strand | 924-929 | 6 | 9 |
| β-strand | 934-938 | 5 | 9 |
| β-strand | 946-948 | 3 | 9 |
| β-strand | 957-962 | 6 | 10 |
| β-strand | 969-974 | 6 | 10 |
| β-strand | 978-983 | 6 | 10 |
| β-strand | 987 | 1 | 10 |
| β-strand | 993-996 | 4 | 10 |
| α-helix | 1001 | 1 | |
| β-strand | 1002-1007 | 6 | 3 |
| β-strand | 1020-1025 | 6 | 3 |
| β-strand | 1030-1034 | 5 | 3 |
| α-helix | 1035-1036 | 2 | |
| α-helix | 1037-1040 | 4 | |
| α-helix | 1046-1056 | 11 | |
Chain D: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 105-128 | 24 | |
Chain E: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 320-338 | 19 | |
Chain G: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-12 | 9 | |
| β-strand | 17-24 | 8 | 11 |
| β-strand | 29-32 | 4 | 11 |
| α-helix | 36-60 | 25 | |
| β-strand | 66-73 | 8 | 11 |
| β-strand | 77-82 | 6 | 11 |
| β-strand | 86-92 | 7 | 11 |
Chain H: 3 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-12 | 9 | |
| β-strand | 17 | 1 | 11 |
| β-strand | 21-24 | 4 | 11 |
| β-strand | 29 | 1 | 11 |
| α-helix | 30-31 | 2 | |
| α-helix | 36-60 | 25 | |
| β-strand | 66-73 | 8 | 11 |
| β-strand | 77-82 | 6 | 11 |
| β-strand | 86-92 | 7 | 11 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Methylated-DNA--protein-cysteine methyltransferase,Cytoplasmic dynein 2 heavy chain 1 | A | protein | 4513 | Homo sapiens | P16455 (AlphaFold model), Q8NCM8 (AlphaFold model) |
| Cytoplasmic dynein 2 intermediate chain 1 | C | protein | 1066 | Homo sapiens | Q8WVS4 (AlphaFold model) |
| Cytoplasmic dynein 2 intermediate chain 2 | D | protein | 564 | Homo sapiens | Q96EX3 (AlphaFold model) |
| Cytoplasmic dynein 2 light intermediate chain 1 | E | protein | 351 | Homo sapiens | Q8TCX1 |
| Dynein light chain roadblock-type 1 | G, H | protein | 96 | Homo sapiens | Q9NP97 |
Sequence of entity 1 (A), FASTA
>8RGH_1 Methylated-DNA--protein-cysteine methyltransferase,Cytoplasmic dynein 2 heavy chain 1 (chains A)
GDKDCEMKRTTLDSPLGKLELSGCEQGLHRIIFLGKGTSAADAVEVPAPAAVLGGPEPLM
QATAWLNAYFHQPEAIEEFPVPALHHPVFQQESFTRQVLWKLLKVVKFGEVISYSHLAAL
AGNPAATAAVKTALSGNPVPILIPCHRVVQGDLDVGGYEGGLAVKEWLLAHEGHRLGKPG
LGGSLEVLFQGPDYDIPTTLEVLFQGPANGTADVRKLFIFTTTQNYFGLMSELWDQPLLC
NCLEINNFLDDGNQMLLRVQRSDAGISFSNTIEFGDTKDKVLVFFKLRPEVITDENLHDN
ILVSSMLESPISSLYQAVRQVFAPMLLKDQEWSRNFDPKLQNLLSELEAGLGIVLRRSDT
NLTKLKFKEDDTRGILTPSDEFQFWIEQAHRGNKQISKERANYFKELFETIAREFYNLDS
LSLLEVVDLVETTQDVVDDVWRQTEHDHYPESRMLHLLDIIGGSFGRFVQKKLGTLNLWE
DPYYLVKESLKAGISICEQWVIVCNHLTGQVWQRYVPHPWKNEKYFPETLDKLGKRLEEV
LAIRTIHEKFLYFLPASEEKIICLTRVFEPFTGLNPVQYNPYTEPLWKAAVSQYEKIIAP
AEQKIAGKLKNYISEIQDSPQQLLQAFLKYKELVKRPTISKELMLERETLLARLVDSIKD
FRLDFENRCRGIPGDASGPLSGKNLSEVVNSIVWVRQLELKVDDTIKIAEALLSDLPGFR
CFHQSAKDLLDQLKLYEQEQFDDWSRDIQSGLSDSRSGLCIEASSRIMELDSNDGLLKVH
YSDRLVILLREVRQLSALGFVIPAKIQQVANIAQKFCKQAIILKQVAHFYNSIDQQMIQS
QRPMMLQSALAFEQIIKNSKAGSGGKSQITWDNPKELEGYIQKLQNAAERLATENRKLRK
WHTTFCEKVVVLMNIDLLRQQQRWKDGLQELRTGLATVEAQGFQASDMHAWKQHWNHQLY
KALEHQYQMGLEALNENLPEINIDLTYKQGRLQFRPPFEEIRAKYYREMKRFIGIPNQFK
GVGEAGDESIFSIMIDRNASGFLTIFSKAEDLFRRLSAVLHQHKEWIVIGQVDMEALVEK
HLFTVHDWEKNFKALKIKGKEVERLPSAVKVDCLNINCNPVKTVIDDLIQKLFDLLVLSL
KKSIQAHLHEIDTFVTEAMEVLTIMPQSVEEIGDANLQYSKLQERKPEILPLFQEAEDKN
RLLRTVAGGGLETISNLKAKWDKFELMMESHQLMIKDQIEVMKGNVKSRLQIYYQELEKF
KARWDQLKPGDDVIETGQHNTLDKSAKLIKEKKIEFDDLEVTRKKLVDDCHHFRLEEPNF
SLASSISKDIESCAQIWAFYEEFQQGFQEMANEDWITFRTKTYLFEEFLMNWHDRLRKVE
EHSVMTVKLQSEVDKYKIVIPILKYVRGEHLSPDHWLDLFRLLGLPRGTSLEKLLFGDLL
RVADTIVAKAADLKDLNSRAQGEVTIREALRELDLWGVGAVFTLIDYEDSQSRTMKLIKD
WKDIVNQVGDNRCLLQSLKDSPYYKGFEDKVSIWERKLAELDEYLQNLNHIQRKWVYLEP
IFGRGALPKEQTRFNRVDEDFRSIMTDIKKDNRVTTLTTHAGIRNSLLTILDQLQRCQRS
LNEFLEEKRSAFPRFYFIGDDDLLEILGQSTNPSVIQSHLKKLFAGINSVCFDEKSKHIT
AMKSLEGEVVPFKNKVPLSNNVETWLNDLALEMKKTLEQLLKECVTTGRSSQGAVDPSLF
PSQILCLAEQIKFTEDVENAIKDHSLHQIETQLVNKLEQYTNIDTSSEDPGNTESGILEL
KLKALILDIIHNIDVVKQLNQIQVHTTEDWAWKKQLRFYMKSDHTCCVQMVDSEFQYTYE
YQGNASKLVYTPLTDKCYLTLTQAMKMGLGGNPYGPAGTGKTESVKALGGLLGRQVLVFN
CDEGIDVKSMGRIFVGLVKCGAWGCFDEFNRLEESVLSAVSMQIQTIQDALKNHRTVCEL
LGKEVEVNSNSGIFITMNPAGKGYGGRQKLPDNLKQLFRPVAMSHPDNELIAEVILYSEG
FKDAKVLSRKLVAIFNLSRELLTPQQHYDWGLRALKTVLRGSGNLLRQLNKSGTTQNANE
SHIVVQALRLNTMSKFTFTDCTRFDALIKDVFPGIELKEVEYDELSAALKQVFEEANYEI
IPNQIKKALELYEQLCQRMGVVIVGPSGAGKSTLWRMLRAALCKTGKVVKQYTMNPKAMP
RYQLLGHIDMDTREWSDGVLTNSARQVVREPQDVSSWIICDGDIDPEWIESLNSVLDDNR
LLTMPSGERIQFGPNVNFVFETHDLSCASPATISRMGMIFLSDEETDLNSLIKSWLRNQP
AEYRNNLENWIGDYFEKALQWVLKQNDYVVETSLVGTVMNGLSHLHGCRDHDEFIINLIR
GLGGNLNMKSRLEFTKEVFHWARESPPDFHKPMDTYYDSTRGRLATYVLKKPEDLTADDF
SNGLTLPVIQTPDMQRGLDYFKPWLSSDTKQPFILVGPEGCGKGMLLRYAFSQLRSTQIA
TVHCSAQTTSRHLLQKLSQTCMVISTNTGRVYRPKDCERLVLYLKDINLPKLDKWGTSTL
VAFLQQVLTYQGFYDENLEWVGLENIQIVASMSAGGRLGRHKLTTRFTSIVRLCSIDYPE
REQLQTIYGAYLEPVLHKNLKNHSIWGSSSKIYLLAGSMVQVYEQVRAKFTVDDYSHYFF
TPCILTQWVLGLFRYDLEGGSSNHPLDYVLEIVAYEARRLFRDKIVGAKELHLFDIILTS
VFQGDWGSDILDNMSDSFYVTWGARHNSGARAAPGQPLPPHGKPLGKLNSTDLKDVIKKG
LIHYGRDNQNLDILLFHEVLEYMSRIDRVLSFPGGSLLLAGRSGVGRRTITSLVSHMHGA
VLFSPKISRGYELKQFKNDLKHVLQLAGIEAQQVVLLLEDYQFVHPTFLEMINSLLSSGE
VPGLYTLEELEPLLLPLKDQASQDGFFGPVFNYFTYRIQQNLHIVLIMDSANSNFMINCE
SNPALHKKCQVLWMEGWSNSSMKKIPEMLFSETGGGEKYNDKKRKEEKKKNSVDPDFLKS
FLLIHESCKAYGATPSQYMTFLHVYSAISSSKKKELLKRQSHLQAGVSKLNEAKALVDEL
NRKAGEQSVLLKTKQDEADAALQMITVSMQDASEQKTELERLKHRIAEEVVKIEERKNKI
DDELKEVQPLVNEAKLAVGNIKPESLSEIRSLRMPPDVIRDILEGVLRLMGIFDTSWVSM
KSFLAKRGVREDIATFDARNISKEIRESVEELLFKNKGSFDPKNAKRASTAAAPLAAWVK
ANIQYSHVLERIHPLETEQAGLESNLKKTEDRKRKLEELLNSVGQKVSELKEKFQSRTSE
AAKLEAEVSKAQETIKAAEVLINQLDREHKRWNAQVVEITEELATLPKRAQLAAAFITYL
SAAPESLRKTCLEEWTKSAGLEKFDLRRFLCTESEQLIWKSEGLPSDDLSIENALVILQS
RVCPFLIDPSSQATEWLKTHLKDSRLEVINQQDSNFITALELAVRFGKTLIIQEMDGVEP
VLYPLLRRDLVAQGPRYVVQIGDKIIDYNEEFRLFLSTRNPNPFIPPDAASIVTEVNFTT
TRSGLRGQLLALTIQHEKPDLEEQKTKLLQQEEDKKIQLAKLEESLLETLATSQGNILEN
KDLIESLNQTKASSALIQESLKESYKLQISLDQERDAYLPLAESASKMYFIISDLSKINN
MYRFSLAAFLRLFQRALQNKQDSENTEQRIQSLISSLQHMVYEYICRCLFKADQLMFALH
FVRGMHPELFQENEWDTFTGVVVGDMLRKADSQQKIRDQLPSWIDQERSWAVATLKIALP
SLYQTLCFEDAALWRTYYNNSMCEQEFPSILAKKVSLFQQILVVQVLRPDRLQSAMALFA
CKTLGLKEVSPLPLNLKRLYKETLEIEPILIIISPGADPSQELQELANAERSGECYHQVA
MGQGQADLAIQMLKECARNGDWLCLKNLHLVVSWLPVLEKELNTLQPKDTFRLWLTAEVH
PNFTPILLQSSLKITYESPPGLKKNLMRTYESWTPEQISKKDNTHRAHALFSLAWFHAAC
QERRNYIPQGWTKFYEFSLSDLRAGYNIIDRLFDGAKDVQWEFVHGLLENAIYGGRIDNY
FDLRVLQSYLKQFFNSSVIDVFNQRNKKSIFPYSVSLPQSCSILDYRAVIEKIPEDDKPS
FFGLPANIARSSQRMISSQVISQLRILGRSITAGSKFDREIWSNELSPVLNLWKKLNQNS
NLIHQKVPPPNDRQGSPILSFIILEQFNAIRLVQSVHQSLAALSKVIRGTTLLSSEVQKL
ASALLNQKCPLAWQSKWEGPEDPLQYLRGLVARALAIQNWVDKAEKQALLSETLDLSELF
HPDTFLNALRQETARAVGRSVDSLKFVASWKGRLQEAKLQIKISGLLLEGCSFDGNQLSE
NQLDSPSVSSVLPCFMGWIPQDACGPYSPDECISLPVYTSAERDRVVTNIDVPCGGNQDQ
WIQCGAALFLKNQ
Sequence of entity 2 (C), FASTA
>8RGH_2 Cytoplasmic dynein 2 intermediate chain 1 (chains C)
MEPGKRRTKDDTWKADDLRKHLWAIQSGGSKEERKHREKKLRKESEMDLPEHKEPRCRDP
DQDARSRDRVAEVHTAKESPRGERDRDRQRERRRDAKDREKEKLKEKHREAEKSHSRGKD
REKEKDRRARKEELRQTVAHHNLLGQETRDRQLLERAERKGRSVSKVRSEEKDEDSERGD
EDRERRYRERKLQYGDSKDNPLKYWLYKEEGERRHRKPREPDRDKKHREKSSTREKREKY
SKEKSNSFSDKGEERHKEKRHKEGFHFDDERHQSNVDRKEKSAKDEPRKREFQNGEHRNR
GASSKRDGTSSQHAENLVRNHGKDKDSRRKHGHEEGSSVWWKLDQRPGGEETVEIEKEET
DLENARADAYTASCEDDFEDYEDDFEVCDGDDDESSNEPESREKLEELPLAQKKEIQEIQ
RAINAENERIGELSLKLFQKRGRTEFEKEPRTDTNSSPSRASVCGIFVDFASASHRQKSR
TQALKQKMRSTKLLRLIDLDFSFTFSLLDLPPVNEYDMYIRNFGKKNTKQAYVQCNEDNV
ERDIQTEEIETREVWTQHPGESTVVSGGSEQRDTSDAVVMPKIDTPRLCSFLRAACQVMA
VLLEEDRLAAEPSWNLRAQDRALYFSDSSSQLNTSLPFLQNRKVSSLHTSRVQRQMVVSV
HDLPEKSFVPLLDSKYVLCVWDIWQPSGPQKVLICESQVTCCCLSPLKAFLLFAGTAHGS
VVVWDLREDSRLHYSVTLSDGFWTFRTATFSTDGILTSVNHRSPLQAVEPISTSVHKKQS
FVLSPFSTQEEMSGLSFHIASLDESGVLNVWVVVELPKADIAGSISDLGLMPGGRVKLVH
SALIQLGDSLSHKGNEFWGTTQTLNVKFLPSDPNHFIIGTDMGLISHGTRQDLRVAPKLF
KPQQHGIRPVKVNVIDFSPFGEPIFLAGCSDGSIRLHQLSSAFPLLQWDSSTDSHAVTGL
QWSPTRPAVFLVQDDTSNIYIWDLLQSDLGPVAKQQVSPNRLVAMAAVGEPEKAGGSFLA
LVLARASGSIDIQHLKRRWAAPEVDECNRLRLLLQEALWPEGKLHK
Sequence of entity 3 (D), FASTA
>8RGH_3 Cytoplasmic dynein 2 intermediate chain 2 (chains D)
MATRAQPGPLSQAGSAGVAALATVGVASGPGPGRPGPLQDETLGVASVPSQWRAVQGIRG
ETKSCQTASIATASASAQARNHVDAQVQTEAPVPVSVQPPSQYDIPRLAAFLRRVEAMVI
RELNKNWQSHAFDGFEVNWTEQQQMVSCLYTLGYPPAQAQGLHVTSISWNSTGSVVACAY
GRLDHGDWSTLKSFVCAWNLDRRDLRPQQPSAVVEVPSAVLCLAFHPTQPSHVAGGLYSG
EVLVWDLSRLEDPLLWRTGLTDDTHTDPVSQVVWLPEPGHSHRFQVLSVATDGKVLLWQG
IGVGQLQLTEGFALVMQQLPRSTKLKKHPRGETEVGATAVAFSSFDPRLFILGTEGGFPL
KCSLAAGEAALTRMPSSVPLRAPAQFTFSPHGGPIYSVSCSPFHRNLFLSAGTDGHVHLY
SMLQAPPLTSLQLSLKYLFAVRWSPVRPLVFAAASGKGDVQLFDLQKSSQKPTVLIKQTQ
DESPVYCLEFNSQQTQLLAAGDAQGTVKVWQLSTEFTEQGPREAEDLDCLAAEVAAWSHP
QFEKGSAGSAAGSGAGWSHPQFEK
Sequence of entity 4 (E), FASTA
>8RGH_4 Cytoplasmic dynein 2 light intermediate chain 1 (chains E)
MPSETLWEIAKAEVEKRGINGSEGDGAEIAEKFVFFIGSKNGGKTTIILRCLDRDEPPKP
TLALEYTYGRRAKGHNTPKDIAHFWELGGGTSLLDLISIPITGDTLRTFSLVLVLDLSKP
NDLWPTMENLLQATKSHVDKVIMKLGKTNAKAVSEMRQKIWNNMPKDHPDHELIDPFPVP
LVIIGSKYDVFQDFESEKRKVICKTLRFVAHYYGASLMFTSKSEALLLKIRGVINQLAFG
IDKSKSICVDQNKPLFITAGLDSFGQIGSPPVPENDIGKLHAHSPMELWKKVYEKLFPPK
SINTLKDIKDPARDPQYAENEVDEMRIQKDLELEQYKRSSSKSWKQIELDS
Sequence of entity 5 (G, H), FASTA
>8RGH_5 Dynein light chain roadblock-type 1 (chains G, H)
MAEVEETLKRLQSQKGVQGIIVVNTEGIPIKSTMDNPTTTQYASLMHSFILKARSTVRDI
DPQNDLTFLRIRSKKNEIMVAPDKDYFLIVIQNPTE
Primary citation
Structure and tethering mechanism of dynein-2 intermediate chains in intraflagellar transport. Mukhopadhyay, A.G., Toropova, K., Daly, L. et al. EMBO J (2024) 43:1257-1272. DOI 10.1038/s44318-024-00060-1 · PubMed
Other PDB entries of the same protein (UniProt P16455 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 1QNT 1.9 Å, X-ray structure of human O6alkylguanine-DNA alkyltransferase
- 1EH6 2.0 Å, Human O6-alkylguanine-DNA alkyltransferase
- 1EH7 2.0 Å, Methylated human O6-alkylguanine-DNA alkyltransferase
- 9QF2 2.42 Å, Cryo-EM structure of the fully Coronin-1B-decorated actin filament in the ADP state.
- 1EH8 2.5 Å, Benzylated human O6-alkylguanine-DNA alkyltransferase
- 28OP 2.7 Å, Structure of the human inner kinetochore CCAN and CENP-C bound to DNA
- 9QEY 2.74 Å, Cryo-EM structure of the actin filament bound by a single Coronin-1B molecule.
- 9QFB 2.74 Å, Cryo-EM structure of the fully Coronin-1B-decorated actin filament in the ADP state.
- 9QFQ 2.76 Å, Cryo-EM structure of the cofilactin barbed end bound by AIP1
- 1YFH 3.01 Å, wt Human O6-Alkylguanine-DNA Alkyltransferase Bound To DNA Containing an Alkylated…
- 9DI0 3.1 Å, Cryo-EM structure of Kif18A bound to a microtubule
- 9QFE 3.12 Å, Cryo-EM structure of the actin filament hetero-decorated by Coronin-1 and Cofilin-1 on…
Browse structure collections
About this viewer
MolViewer shows 8RGH directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.