7RPK: Murine Dispatched

Cryo-EM structure of murine Dispatched in complex with Sonic hedgehog. Determined by electron microscopy at 2.7 Å resolution. Released 27 Oct 2021.

Method
Electron microscopy
Resolution
2.7 Å
Organism
Mus musculus
Chains
2
Atoms
10,018
Mol. weight
187.27 kDa
Ligands
Y01, AV0, 6OE, NAG
Released
27 Oct 2021

Explore 7RPK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7RPK contains 68 α-helices and 34 β-strands across 2 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: 60 helices, 25 β-strands

ElementResiduesLengthSheet
α-helix180-1867
α-helix188-20821
α-helix211-2133
β-strand22411
α-helix228-24114
β-strand24312
β-strand24912
β-strand25013
α-helix254-26411
α-helix265-2695
α-helix270-2723
α-helix281-2833
β-strand299-30684
α-helix315-32511
α-helix326-3305
α-helix335-3384
β-strand34315
α-helix347-3504
β-strand35114
α-helix353-3608
α-helix366-3683
α-helix371-38919
α-helix398-4036
α-helix415-4184
α-helix422-4254
α-helix426-4305
β-strand43114
β-strand450-45894
α-helix461-4633
α-helix464-4707
β-strand47714
β-strand481-48774
α-helix491-50111
α-helix504-52118
α-helix524-54320
α-helix544-5485
α-helix556-5583
α-helix561-5699
α-helix573-58614
α-helix592-61928
α-helix620-6234
β-strand62611
α-helix627-64822
α-helix650-6578
α-helix658-6625
α-helix682-6843
α-helix686-6905
α-helix691-70212
α-helix703-7075
α-helix708-7147
α-helix716-73520
α-helix740-7434
α-helix747-7493
β-strand75316
α-helix758-7614
α-helix762-7665
α-helix771-7777
α-helix7811
β-strand782-78983
β-strand79117
β-strand81017
α-helix819-83214
β-strand83818
α-helix850-85910
α-helix866-8716
α-helix881-89818
β-strand909-91243
β-strand918-92693
β-strand92718
β-strand928-93033
α-helix9311
α-helix935-95319
α-helix958-9603
β-strand964-96633
α-helix970-100031
β-strand100319
α-helix1004-102724
α-helix1034-106027
α-helix1066-109328
β-strand110016
α-helix1101-111919
α-helix1120-11256
α-helix1126-11327
β-strand114019
α-helix1141-11422
Chain H: 8 helices, 9 β-strands
ElementResiduesLengthSheet
α-helix42-443
β-strand48110
β-strand5115
α-helix72-765
β-strand78-79211
β-strand85-87310
α-helix95-973
β-strand98-99211
α-helix101-11717
α-helix121-1222
β-strand123-127510
α-helix140-1434
β-strand146-151610
α-helix156-1583
α-helix159-16911
β-strand173-178610
β-strand181-185510

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Protein dispatched homolog 1Aprotein1352Mus musculusQ3TDN0 (AlphaFold model)
Sonic hedgehog proteinHprotein164Mus musculusQ62226 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>7RPK_1 Protein dispatched homolog 1 (chains A)
MARPFKFPRSYAALLADWPVVVLGMCTLLIVVCALVGVLVPELPDFSDPLLGFEPRGTTI
GQRLVTWNNMMRNTGYKATLANYPYKYAEEQARSHRDDRWSDDHHERERREVDWNFQKDS
FFCDVPSDGYSRVVFASAGGETLWNLPAIKSMCDVDNSRIRSHPQFSDLCQRTTAVSCCP
SWTLGNYIAILNNRSSCQKIVERDVSHTLKLLRTCAKHYQNGTLGPDCWDKAARRKDQLK
CTNVPRKCTKYNAVYQILHYLVDKDFMTPKTADYAVPALKYSMLFSPTEKGESMMNIYLD
NFENWNSSDGITTVTGIEFGIKHSLFQDYLLMDTVYPAIAIAIVLLIMCVYTKSMFITLM
TMFAIISSLIVSYFLYRVVFNFEFFPFMNLTALIILVGIGADDAFVLCDVWNYTKFDKPR
AETSEAVSVTLQHAALSMFVTSFTTAAAFYANYVSNITAIRCFGVYAGTAILVNYVLMVT
WLPAVIVLHERYLLNIFTCFRKPQPQAYDKSCWAVLCQKCRRVLFAVSEASRIFFEKVLP
CIVIKFRYLWLIWFLALTVGGAYIVCVNPKMKLPSLELSEFQVFRSSHPFERYDAEFKKL
FMFERVHHGEELHMPITVIWGVSPEDSGDPLNPKSKGELTLDSTFNIASPASQAWILHFC
QKLRNQTFFHQTEQQDFTSCFIETFKQWMENQDCDEPALYPCCSHCSFPYKQEVFELCIK
KAIMELDRSTGYHLNNKTPGPRFDINDTIRAVVLEFQSTFLFTLAYEKMQQFYKEVDSWI
SHELSSAPEGLSRGWFVSNLEFYDLQDSLSDGTLIAMGLSVAVAFSVMLLTTWNIIISLY
AIVSIAGTIFVTVGSLVLLGWELNVLESVTISVAVGLSVDFAVHYGVAYRLAPDPDREGK
VIFSLSRMGSAIAMAALTTFVAGAMMMPSTVLAYTQLGTFMMLVMCVSWAFATFFFQCLC
RCLGPQGTCGQIPFPTKLQCSPFSHTLSARPGDRGPSKTHAASAYSVDARGQKSQLEHEF
YELQPLASHSCTSSEKTTYEEPHTCSEFFNGQAKNLRMPVPAAYSSELTKSPSSEPGSAL
LQSCLEQDTVCHFSLNPRCNCRDAYTHLQYGLPEIHCQQMGDSLCHKCASTAGGFVQIQS
SVAPLKASHQAAEGLLHPAQHMLPPGMQNSRPRNFFLHSVQHFQAQENLGRTSTHSTDER
LPRTAELSPPPSDSRSTESFQRACCHPENNQRRLCKSRDPGDTEGSGGTKSKVSGLPNQT
DKEEKQVEPSLLQTDETVNSEHLNHNESNFTFSHLPGEAGCRSCPNSPQSCRSIMRSKCG
TEDCQTPNLEANVPAVPTHSDLSGESLLIKTL
Sequence of entity 2 (H), FASTA
>7RPK_2 Sonic hedgehog protein (chains H)
GPGRGFGKRRHPKKLTPLAYKQFIPNVAEKTLGASGRYEGKITRNSERFKELTPNYNPDI
IFKDEENTGADRLMTQRCKDKLNALAISVMNQWPGVKLRVTEGWDEDGHHSEESLHYEGR
AVDITTSDRDRSKYGMLARLAVEAGFDWVYYESKAHIHCSVKAE

Ligands and cofactors

IDNameFormulaCopies
Y01Cholesterol hemisuccinateC31 H50 O426
AV0Lauryl Maltose Neopentyl GlycolC47 H88 O222
6OE(2S)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(hexanoyloxy)propyl…C17 H34 N O8 P1
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O65
CACalcium ionCa2
ZNZinc ionZn1

Water and common crystallization additives (NA, SO4) are not listed.

Primary citation

Dispatched uses Na + flux to power release of lipid-modified Hedgehog. Wang, Q., Asarnow, D.E., Ding, K. et al. Nature (2021) 599:320-324. DOI 10.1038/s41586-021-03996-0 · PubMed

Other PDB entries of the same protein (UniProt Q3TDN0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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