4RH7: Human cytoplasmic dynein 2 motor domain

Crystal structure of human cytoplasmic dynein 2 motor domain in complex with ADP.Vi. Determined by X-ray diffraction at 3.41 Å resolution. Released 10 Dec 2014.

Method
X-ray diffraction
Resolution
3.41 Å
Organisms
synthetic construct, Homo sapiens
Chains
1
Atoms
22,816
Mol. weight
394.92 kDa
Ligands
ADP, ATP, MG, AOV
Released
10 Dec 2014

Explore 4RH7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4RH7 contains 137 α-helices and 75 β-strands across 1 chain. 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: 137 helices, 75 β-strands

ElementResiduesLengthSheet
α-helix1257-127317
β-strand127511
β-strand1278-128142
β-strand1289-129242
α-helix1295-131420
α-helix1316-13216
α-helix1322-135837
α-helix1362-138423
β-strand138711
α-helix1389-13924
α-helix1397-142529
α-helix1427-14315
α-helix1434-14429
α-helix1447-14548
β-strand1463-146423
β-strand1475-147733
β-strand1483-148533
α-helix1496-152328
α-helix1536-155722
α-helix1561-158020
α-helix1593-161624
α-helix1624-16285
β-strand1631-163444
β-strand1640-164454
β-strand1647-165044
α-helix1660-16645
α-helix1666-168116
β-strand1684-168855
α-helix1695-170511
β-strand1710-171455
α-helix1721-173414
β-strand1737-174155
α-helix1748-176720
β-strand1771-177446
β-strand1777-178046
β-strand1786-179165
α-helix1802-18054
α-helix1806-18094
β-strand1812-181655
α-helix1823-183311
α-helix1838-185518
α-helix1866-188621
α-helix1891-190616
α-helix1912-192514
α-helix1938-195013
α-helix1952-19543
α-helix1956-197116
β-strand1974-197857
α-helix1985-199915
β-strand2004-200857
α-helix2015-20195
β-strand2021-202338
β-strand2028-203038
α-helix2033-204311
β-strand2050-205567
α-helix2060-20634
α-helix2064-20663
α-helix2067-20704
β-strand207719
β-strand208319
β-strand2090-209677
α-helix2104-21096
β-strand2111-211447
α-helix2122-213211
α-helix2138-215922
α-helix2168-217710
α-helix2185-219713
α-helix2202-221514
α-helix2226-22283
β-strand2244110
β-strand2264110
α-helix2266-227914
α-helix2281-22833
β-strand2287-2290411
α-helix2297-230711
β-strand2312-2316511
α-helix2324-23329
β-strand2335112
β-strand2338113
β-strand2345-2346213
β-strand2348112
β-strand2354-2358511
β-strand2366114
β-strand2372114
α-helix2373-238412
β-strand2386-2388313
β-strand2394-2397413
β-strand2401-2406611
α-helix2419-24224
β-strand2426-2429411
α-helix2432-24343
α-helix2435-245218
α-helix2463-248321
α-helix2496-25049
α-helix2505-25084
β-strand2509115
α-helix2516-25172
α-helix2520-253415
α-helix2542-255918
β-strand2571-2574416
α-helix2579-25813
α-helix2592-25932
β-strand2599115
β-strand2600-2603416
α-helix2604-262118
α-helix2631-264515
β-strand2651-2654417
α-helix2661-267212
β-strand2675-2677317
α-helix2687-269913
α-helix2700-27045
β-strand2708-2713617
α-helix2714-27163
α-helix2721-273212
α-helix2741-275818
α-helix2764-277512
β-strand2776-2782717
α-helix2789-27957
α-helix2797-28026
β-strand2804-2807417
α-helix2813-282513
α-helix2849-286214
α-helix2869-2994126
α-helix2998-30047
α-helix3011-302313
α-helix3031-30388
α-helix3043-30464
α-helix3057-307014
α-helix3076-30805
α-helix3088-3197110
α-helix3200-321415
α-helix3219-323315
α-helix3240-32445
α-helix3247-32559
α-helix3262-32709
β-strand3277-3281518
α-helix3286-329510
β-strand3301-3303319
α-helix3310-332011
β-strand3324-3326319
α-helix3334-33363
α-helix3337-33404
β-strand3344-3347420
β-strand3350-3355620
β-strand3358-3362520
β-strand3368119
β-strand3370-3372318
α-helix3381-33844
β-strand3387-3391518
α-helix3396-341116
α-helix3413-344634
α-helix3455-349036
α-helix3493-351220
α-helix3520-353213
α-helix3540-356223
α-helix3565-357915
α-helix3588-35936
α-helix3620-363213
α-helix3634-36407
α-helix3647-36537
α-helix3658-36603
α-helix3663-36686
α-helix3673-36819
α-helix3683-369816
α-helix3710-37145
β-strand3723-3726421
α-helix3734-374411
β-strand3751-3754421
α-helix3759-377315
β-strand3776-3780521
α-helix3782-37843
α-helix3789-379810
α-helix3799-38013
β-strand3806-3811621
α-helix3819-38235
β-strand3826-3829421
α-helix3836-384611
α-helix3849-38524
α-helix3861-387717
α-helix3893-390816
α-helix3916-39216
α-helix3922-39265
α-helix3934-394815
α-helix3977-398610
α-helix3993-39964
α-helix4001-402020
α-helix4031-40366
α-helix4041-405111
α-helix4055-40595
α-helix4061-40622
α-helix4066-40683
α-helix4071-410232
α-helix4109-412012
α-helix4125-41306
α-helix4137-415923
β-strand4167122
α-helix4170-41723
α-helix4176-419116
α-helix4195-41973
β-strand4198-4202522
β-strand4214-4217422
β-strand4221-4223323
β-strand4226-4228324
β-strand4231-4233324
α-helix4234-42363
β-strand4242-4244323
α-helix4246-42472
β-strand4248-4254722
β-strand4266-4272723
β-strand4280-4287823
α-helix4292-42987
β-strand4301-4303323

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Green fluorescent protein/Cytoplasmic dynein 2 heavy chain 1Aprotein3450synthetic construct, Homo sapiensQ8NCM8 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>4RH7_1 Green fluorescent protein/Cytoplasmic dynein 2 heavy chain 1 (chains A)
MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTL
VTTFGYGVQCFARYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLV
NRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLAD
HYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITGSDDLEVTRK
KLVDDCHHFRLEEPNFSLASSISKDIESCAQIWAFYEEFQQGFQEMANEDWITFRTKTYL
FEEFLMNWHDRLRKVEEHSVMTVKLQSEVDKYKIVIPILKYVRGEHLSPDHWLDLFRLLG
LPRGTSLEKLLFGDLLRVADTIVAKAADLKDLNSRAQGEVTIREALRELDLWGVGAVFTL
IDYEDSQSRTMKLIKDWKDIVNQVGDNRCLLQSLKDSPYYKGFEDKVSIWERKLAELDEY
LQNLNHIQRKWVYLEPIFGRGALPKEQTRFNRVDEDFRSIMTDIKKDNRVTTLTTHAGIR
NSLLTILDQLQRCQRSLNEFLEEKRSAFPRFYFIGDDDLLEILGQSTNPSVIQSHLKKLF
AGINSVCFDEKSKHITAMKSLEGEVVPFKNKVPLSNNVETWLNDLALEMKKTLEQLLKEC
VTTGRSSQGAVDPSLFPSQILCLAEQIKFTEDVENAIKDHSLHQIETQLVNKLEQYTNID
TSSEDPGNTESGILELKLKALILDIIHNIDVVKQLNQIQVHTTEDWAWKKQLRFYMKSDH
TCCVQMVDSEFQYTYEYQGNASKLVYTPLTDKCYLTLTQAMKMGLGGNPYGPAGTGKTES
VKALGGLLGRQVLVFNCDEGIDVKSMGRIFVGLVKCGAWGCFDEFNRLEESVLSAVSMQI
QTIQDALKNHRTVCELLGKEVEVNSNSGIFITMNPAGKGYGGRQKLPDNLKQLFRPVAMS
HPDNELIAEVILYSEGFKDAKVLSRKLVAIFNLSRELLTPQQHYDWGLRALKTVLRGSGN
LLRQLNKSGTTQNANESHIVVQALRLNTMSKFTFTDCTRFDALIKDVFPGIELKEVEYDE
LSAALKQVFEEANYEIIPNQIKKALELYEQLCQRMGVVIVGPSGAGKSTLWRMLRAALCK
TGKVVKQYTMNPKAMPRYQLLGHIDMDTREWSDGVLTNSARQVVREPQDVSSWIICDGDI
DPEWIESLNSVLDDNRLLTMPSGERIQFGPNVNFVFETHDLSCASPATISRMGMIFLSDE
ETDLNSLIKSWLRNQPAEYRNNLENWIGDYFEKALQWVLKQNDYVVETSLVGTVMNGLSH
LHGCRDHDEFIINLIRGLGGNLNMKSRLEFTKEVFHWARESPPDFHKPMDTYYDSTRGRL
ATYVLKKPEDLTADDFSNGLTLPVIQTPDMQRGLDYFKPWLSSDTKQPFILVGPEGCGKG
MLLRYAFSQLRSTQIATVHCSAQTTSRHLLQKLSQTCMVISTNTGRVYRPKDCERLVLYL
KDINLPKLDKWGTSTLVAFLQQVLTYQGFYDENLEWVGLENIQIVASMSAGGRLGRHKLT
TRFTSIVRLCSIDYPEREQLQTIYGAYLEPVLHKNLKNHSIWGSSSKIYLLAGSMVQVYE
QVRAKFTVDDYSHYFFTPCILTQWVLGLFRYDLEGGSSNHPLDYVLEIVAYEARRLFRDK
IVGAKELHLFDIILTSVFQGDWGSDILDNMSDSFYVTWGARHNSGARAAPGQPLPPHGKP
LGKLNSTDLKDVIKKGLIHYGRDNQNLDILLFHEVLEYMSRIDRVLSFPGGSLLLAGRSG
VGRRTITSLVSHMHGAVLFSPKISRGYELKQFKNDLKHVLQLAGIEAQQVVLLLEDYQFV
HPTFLEMINSLLSSGEVPGLYTLEELEPLLLPLKDQASQDGFFGPVFNYFTYRIQQNLHI
VLIMDSANSNFMINCESNPALHKKCQVLWMEGWSNSSMKKIPEMLFSETGGGEKYNDKKR
KEEKKKNSVDPDFLKSFLLIHESCKAYGATPSQYMTFLHVYSAISSSKKKELLKRQSHLQ
AGVSKLNEAKALVDELNRKAGEQSVLLKTKQDEADAALQMITVSMQDASEQKTELERLKH
RIAEEVVKIEERKNKIDDELKEVQPLVNEAKLAVGNIKPESLSEIRSLRMPPDVIRDILE
GVLRLMGIFDTSWVSMKSFLAKRGVREDIATFDARNISKEIRESVEELLFKNKGSFDPKN
AKRASTAAAPLAAWVKANIQYSHVLERIHPLETEQAGLESNLKKTEDRKRKLEELLNSVG
QKVSELKEKFQSRTSEAAKLEAEVSKAQETIKAAEVLINQLDREHKRWNAQVVEITEELA
TLPKRAQLAAAFITYLSAAPESLRKTCLEEWTKSAGLEKFDLRRFLCTESEQLIWKSEGL
PSDDLSIENALVILQSRVCPFLIDPSSQATEWLKTHLKDSRLEVINQQDSNFITALELAV
RFGKTLIIQEMDGVEPVLYPLLRRDLVAQGPRYVVQIGDKIIDYNEEFRLFLSTRNPNPF
IPPDAASIVTEVNFTTTRSGLRGQLLALTIQHEKPDLEEQKTKLLQQEEDKKIQLAKLEE
SLLETLATSQGNILENKDLIESLNQTKASSALIQESLKESYKLQISLDQERDAYLPLAES
ASKMYFIISDLSKINNMYRFSLAAFLRLFQRALQNKQDSENTEQRIQSLISSLQHMVYEY
ICRCLFKADQLMFALHFVRGMHPELFQENEWDTFTGVVVGDMLRKADSQQKIRDQLPSWI
DQERSWAVATLKIALPSLYQTLCFEDAALWRTYYNNSMCEQEFPSILAKKVSLFQQILVV
QVLRPDRLQSAMALFACKTLGLKEVSPLPLNLKRLYKETLEIEPILIIISPGADPSQELQ
ELANAERSGECYHQVAMGQGQADLAIQMLKECARNGDWLCLKNLHLVVSWLPVLEKELNT
LQPKDTFRLWLTAEVHPNFTPILLQSSLKITYESPPGLKKNLMRTYESWTPEQISKKDNT
HRAHALFSLAWFHAACQERRNYIPQGWTKFYEFSLSDLRAGYNIIDRLFDGAKDVQWEFV
HGLLENAIYGGRIDNYFDLRVLQSYLKQFFNSSVIDVFNQRNKKSIFPYSVSLPQSCSIL
DYRAVIEKIPEDDKPSFFGLPANIARSSQRMISSQVISQLRILGRSITAGSKFDREIWSN
ELSPVLNLWKKLNQNSNLIHQKVPPPNDRQGSPILSFIILEQFNAIRLVQSVHQSLAALS
KVIRGTTLLSSEVQKLASALLNQKCPLAWQSKWEGPEDPLQYLRGLVARALAIQNWVDKA
EKQALLSETLDLSELFHPDTFLNALRQETARAVGRSVDSLKFVASWKGRLQEAKLQIKIS
GLLLEGCSFDGNQLSENQLDSPSVSSVLPCFMGWIPQDACGPYSPDECISLPVYTSAERD
RVVTNIDVPCGGNQDQWIQCGAALFLKNQV

Ligands and cofactors

IDNameFormulaCopies
ADPAdenosine-5'-diphosphateC10 H15 N5 O10 P22
ATPAdenosine-5'-triphosphateC10 H16 N5 O13 P31
MGMagnesium ionMg2
AOVADP orthovanadateC10 H17 N5 O14 P2 V1

Primary citation

Structure of human cytoplasmic dynein-2 primed for its power stroke. Schmidt, H., Zalyte, R., Urnavicius, L. et al. Nature (2015) 518:435-438. DOI 10.1038/nature14023 · PubMed

Other PDB entries of the same protein (UniProt Q8NCM8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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