8RGG: Dynein-2 intermediate chain DYNC2I2
Structure of dynein-2 intermediate chain DYNC2I2 (WDR34) in complex with dynein-2 heavy chain DYNC2H1. Determined by electron microscopy at 4.0 Å resolution. Released 20 Mar 2024.
- Method
- Electron microscopy
- Resolution
- 4.0 Å
- Organism
- Homo sapiens
- Chains
- 7
- Atoms
- 7,679
- Mol. weight
- 741.36 kDa
- Released
- 20 Mar 2024
Explore 8RGG in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8RGG contains 37 α-helices and 65 β-strands across 7 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 B: 15 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 396-410 | 15 | |
| α-helix | 414-423 | 10 | |
| α-helix | 425-429 | 5 | |
| α-helix | 431-436 | 6 | |
| α-helix | 438-462 | 25 | |
| α-helix | 466 | 1 | |
| α-helix | 481-507 | 27 | |
| α-helix | 511-547 | 37 | |
| α-helix | 549-551 | 3 | |
| β-strand | 562-565 | 4 | 1 |
| β-strand | 570-573 | 4 | 1 |
| α-helix | 577-592 | 16 | |
| α-helix | 594-597 | 4 | |
| α-helix | 598-630 | 33 | |
| α-helix | 633-635 | 3 | |
| α-helix | 636-652 | 17 | |
| α-helix | 669-692 | 24 | |
Chain C: 2 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 552-558 | 7 | 2 |
| β-strand | 566-568 | 3 | 2 |
| α-helix | 579-584 | 6 | |
| α-helix | 586-610 | 25 | |
Chain D: 12 helices, 42 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 82-88 | 7 | 2 |
| α-helix | 89-95 | 7 | |
| α-helix | 100-102 | 3 | |
| α-helix | 105-128 | 24 | |
| β-strand | 147 | 1 | 3 |
| β-strand | 152-153 | 2 | 3 |
| α-helix | 155-159 | 5 | |
| β-strand | 164 | 1 | 4 |
| β-strand | 168-169 | 2 | 4 |
| β-strand | 175-180 | 6 | 4 |
| β-strand | 193-199 | 7 | 4 |
| β-strand | 206 | 1 | 5 |
| β-strand | 209 | 1 | 5 |
| β-strand | 212-216 | 5 | 4 |
| β-strand | 220 | 1 | 6 |
| β-strand | 224-225 | 2 | 7 |
| β-strand | 232-236 | 5 | 7 |
| β-strand | 237 | 1 | 6 |
| β-strand | 242-246 | 5 | 7 |
| β-strand | 254-257 | 4 | 7 |
| α-helix | 268 | 1 | |
| β-strand | 269-276 | 8 | 8 |
| α-helix | 277 | 1 | |
| β-strand | 284-290 | 7 | 8 |
| β-strand | 294-300 | 7 | 8 |
| β-strand | 306-313 | 8 | 8 |
| β-strand | 315 | 1 | 9 |
| β-strand | 334 | 1 | 9 |
| α-helix | 335-336 | 2 | |
| β-strand | 337 | 1 | 10 |
| β-strand | 341-342 | 2 | 11 |
| β-strand | 350-352 | 3 | 11 |
| β-strand | 354 | 1 | 10 |
| β-strand | 360-362 | 3 | 11 |
| β-strand | 369 | 1 | 8 |
| β-strand | 381 | 1 | 8 |
| β-strand | 384-387 | 4 | 11 |
| α-helix | 388-391 | 4 | |
| β-strand | 395-400 | 6 | 12 |
| β-strand | 407-412 | 6 | 12 |
| β-strand | 416-421 | 6 | 12 |
| β-strand | 429-432 | 4 | 12 |
| β-strand | 438-443 | 6 | 13 |
| β-strand | 450-455 | 6 | 13 |
| β-strand | 459-464 | 6 | 13 |
| β-strand | 474-477 | 4 | 13 |
| β-strand | 485 | 1 | 3 |
| β-strand | 489-490 | 2 | 3 |
| β-strand | 497-502 | 6 | 3 |
| β-strand | 506-511 | 6 | 3 |
| α-helix | 512-513 | 2 | |
| α-helix | 514-517 | 4 | |
| α-helix | 519-520 | 2 | |
| α-helix | 523-533 | 11 | |
Chain G: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-12 | 9 | |
| β-strand | 17-23 | 7 | 14 |
| β-strand | 29-32 | 4 | 14 |
| α-helix | 36-60 | 25 | |
| β-strand | 66-73 | 8 | 14 |
| β-strand | 77-83 | 7 | 14 |
| β-strand | 86-92 | 7 | 14 |
Chain H: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-12 | 9 | |
| β-strand | 17-24 | 8 | 14 |
| β-strand | 29 | 1 | 14 |
| α-helix | 36-60 | 25 | |
| β-strand | 66-73 | 8 | 14 |
| β-strand | 77-82 | 6 | 14 |
| β-strand | 86-92 | 7 | 14 |
Chain I: 2 helices, 4 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-13 | 8 | 2 |
| α-helix | 15-31 | 17 | |
| α-helix | 35-49 | 15 | |
| β-strand | 54-69 | 16 | 2 |
| β-strand | 72-78 | 7 | 2 |
| β-strand | 81-87 | 7 | 2 |
Chain J: 2 helices, 5 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 6-7 | 2 | 2 |
| β-strand | 12-13 | 2 | 2 |
| α-helix | 15-31 | 17 | |
| α-helix | 35-49 | 15 | |
| β-strand | 54-68 | 15 | 2 |
| β-strand | 72-78 | 7 | 2 |
| β-strand | 81-87 | 7 | 2 |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Methylated-DNA--protein-cysteine methyltransferase,Cytoplasmic dynein 2 heavy chain 1 | B | 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) |
| Dynein light chain roadblock-type 1 | G, H | protein | 96 | Homo sapiens | Q9NP97 |
| Dynein light chain 1, cytoplasmic | I, J | protein | 89 | Homo sapiens | P63167 |
Sequence of entity 1 (B), FASTA
>8RGG_1 Methylated-DNA--protein-cysteine methyltransferase,Cytoplasmic dynein 2 heavy chain 1 (chains B)
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
>8RGG_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
>8RGG_3 Cytoplasmic dynein 2 intermediate chain 2 (chains D)
MATRAQPGPLSQAGSAGVAALATVGVASGPGPGRPGPLQDETLGVASVPSQWRAVQGIRG
ETKSCQTASIATASASAQARNHVDAQVQTEAPVPVSVQPPSQYDIPRLAAFLRRVEAMVI
RELNKNWQSHAFDGFEVNWTEQQQMVSCLYTLGYPPAQAQGLHVTSISWNSTGSVVACAY
GRLDHGDWSTLKSFVCAWNLDRRDLRPQQPSAVVEVPSAVLCLAFHPTQPSHVAGGLYSG
EVLVWDLSRLEDPLLWRTGLTDDTHTDPVSQVVWLPEPGHSHRFQVLSVATDGKVLLWQG
IGVGQLQLTEGFALVMQQLPRSTKLKKHPRGETEVGATAVAFSSFDPRLFILGTEGGFPL
KCSLAAGEAALTRMPSSVPLRAPAQFTFSPHGGPIYSVSCSPFHRNLFLSAGTDGHVHLY
SMLQAPPLTSLQLSLKYLFAVRWSPVRPLVFAAASGKGDVQLFDLQKSSQKPTVLIKQTQ
DESPVYCLEFNSQQTQLLAAGDAQGTVKVWQLSTEFTEQGPREAEDLDCLAAEVAAWSHP
QFEKGSAGSAAGSGAGWSHPQFEK
Sequence of entity 4 (G, H), FASTA
>8RGG_4 Dynein light chain roadblock-type 1 (chains G, H)
MAEVEETLKRLQSQKGVQGIIVVNTEGIPIKSTMDNPTTTQYASLMHSFILKARSTVRDI
DPQNDLTFLRIRSKKNEIMVAPDKDYFLIVIQNPTE
Sequence of entity 5 (I, J), FASTA
>8RGG_5 Dynein light chain 1, cytoplasmic (chains I, J)
MCDRKAVIKNADMSEEMQQDSVECATQALEKYNIEKDIAAHIKKEFDKKYNPTWHCIVGR
NFGSYVTHETKHFIYFYLGQVAILLFKSG
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…
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