7RHQ: Xenopus Patched-1

Cryo-EM structure of Xenopus Patched-1 in complex with GAS1 and Sonic Hedgehog. Determined by electron microscopy at 3.53 Å resolution. Released 2 Mar 2022.

Method
Electron microscopy
Resolution
3.53 Å
Organisms
Xenopus laevis, Homo sapiens
Chains
3
Atoms
10,499
Mol. weight
188.93 kDa
Ligands
CLR, Y01, NAG, ZN
Released
2 Mar 2022

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

Secondary structure: helices and β-sheets

7RHQ contains 74 α-helices and 40 β-strands across 3 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: 56 helices, 30 β-strands

ElementResiduesLengthSheet
α-helix70-8617
α-helix88-10417
α-helix105-1073
β-strand11111
α-helix115-1173
α-helix125-1306
α-helix139-1413
β-strand143-14642
β-strand147-15263
α-helix164-17512
β-strand180-18234
β-strand185-18734
α-helix189-1913
β-strand19312
α-helix207-2104
α-helix215-2162
β-strand218-21922
α-helix221-2244
α-helix226-2316
β-strand23615
α-helix242-2432
β-strand24415
α-helix251-2588
α-helix266-27510
α-helix306-3072
α-helix309-3124
β-strand317-31826
β-strand326-32726
β-strand333-33423
β-strand337-33827
β-strand344-34637
β-strand349-35133
β-strand353-35752
α-helix3581
α-helix359-3657
α-helix379-39921
β-strand407-41263
α-helix414-4229
α-helix429-44517
α-helix457-48024
β-strand48511
α-helix493-51523
α-helix527-54923
α-helix558-58023
α-helix582-59110
α-helix727-7304
α-helix731-7333
α-helix737-75721
β-strand76318
α-helix767-7693
α-helix777-7848
β-strand79119
β-strand794-797410
α-helix807-8148
α-helix815-8173
β-strand82219
α-helix830-8323
α-helix834-85421
α-helix868-87811
β-strand879111
β-strand886111
β-strand898112
α-helix9031
β-strand904112
α-helix9051
α-helix909-91911
α-helix921-9266
α-helix934-9374
α-helix952-9587
β-strand961-964410
β-strand96719
α-helix973-99018
β-strand997-1000410
α-helix1002-10043
α-helix1014-103623
α-helix1039-106325
β-strand106718
α-helix1069-109527
α-helix1100-111112
α-helix1113-112513
α-helix1127-11293
α-helix1135-11373
α-helix1138-11425
α-helix1143-115311
α-helix1154-11596
α-helix1160-11667
Chain C: 5 helices, 8 β-strands
ElementResiduesLengthSheet
α-helix39-424
β-strand47-48213
β-strand77-78214
β-strand84-86313
β-strand97-98214
α-helix100-11617
β-strand122-126513
α-helix139-1424
β-strand145-150613
α-helix155-1573
α-helix158-16710
β-strand172-174313
β-strand181-184413
Chain G: 13 helices, 2 β-strands
ElementResiduesLengthSheet
β-strand47115
α-helix48-558
α-helix61-7111
α-helix73-797
α-helix109-11810
α-helix123-1253
β-strand129115
α-helix137-1437
α-helix167-1759
α-helix177-18913
α-helix191-1944
α-helix201-21010
α-helix214-2207
α-helix222-2243
α-helix229-24214

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Patched-1Aprotein1205Xenopus laevisQ98SW6
Sonic hedgehog protein N-productCprotein192Homo sapiensQ15465 (AlphaFold model)
Growth arrest-specific protein 1Gprotein282Homo sapiensP54826 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>7RHQ_1 Patched-1 (chains A)
MASAACAAELGASGEAAAQPRVVRRRGRSRRVAPPDHDYLQRPSYCDANFALQQISEGKA
IGRKAPLWLRAFFQRQLFKLGCYIQKNCGKFLVVGLLIFGAFAVGLRAANLETNVEELWV
EVGGRVSRELDYTRQKIGEEAMFNPQLMIQTPLEDGANVLTTEALLQHLHSALEATKVQV
YMYNKPWKLEELCFKSGELITEAVYVSQIIDSMYPCLIITPLDCFWEGAKLQSGMAYLPG
KDILQWTNFDPLELLEELKKGKLHIDIWEEMINKAEVGHGYMDRPCLNPSDKNCPYTAPN
KNSTKPVDVSLILSGGCYGLSKKYMHWQEELIIGGTVKNASGQIVSALALQTMFQLMTPK
QMYEHFKGHEVVSHMNWNEDKAAAILEAWQRTYVQVVHQSVPQNSSQKVLPFTTTTLDDI
LKSFSDVSVIRVASGYLLMLAYACLTMLRWDCAKSQGAVGLAGVLLVALSVAAGLGLCSL
IGISFNAATTQVLPFLALGVGVDDVFLLAHAFSETGQNKRIPFEDRTGECLKRTGASVAL
TSISNVTAFFMAALIPIPALRAFSLQAAVVVVFNFAMVLLIFPAILSMDLYRREVRRLDI
FCCFSSPCVSRVIQIEPQAYTDNNDNTRYSLPPTYSSHSFAHETQITMQSTVQLRTEYDP
RTQLYYTTAQPRSEISVQPAASTPQDVSGQTPESTSSTRDLISQFSVHGGSMQCTPDSKW
TLSSFAEKHYAPFLLKPKTKVAVILGFLALLSVSLYGTTRVRDGLDLTDIVPRETREYDF
IATQFKYFSFYHMYVVTQKADYPRAQRLLYELHKSFVGVRYVLLEGNKQLPKMWLHYFRD
WLQGLQDTFDHEWEAGKITRNDYRNASDDAVLAYKLLIQTGNSDKPINLNQLTKQRLVDA
DGIIQPNAFYIYLTAWVSNDPVAYAASQANIRPHPPEWLHDKADDRPETRTIRAAEPIEY
VQFPFYLNGLRETSDFVEAIEKVRAICNNYTSLGVSSYPNGYPFLFWEQYISLRHWLLLS
ISVVLACTFLVCALFLLNPWTAGIIVMVLALMTVELFGMMGLIGIKLSAVPVVILIASVG
IGVEFTVHVALAFLTAVGDKNRRAVLALEHMFAPVLDGAVSTLLGVLMLAGSEFDFIVRY
FFAVLAILTLLGVLNGLVLLPVLLSFFGPYPEVSPTNGSSSPAAAHHHHHHHHEDQVDPR
LIDGK
Sequence of entity 2 (C), FASTA
>7RHQ_2 Sonic hedgehog protein N-product (chains C)
CGPGRGFGKRRHPKKLTPLAYKQFIPNVAEKTLGASGRYEGKISRNSERFKELTPNYNPD
IIFKDEENTGADRLMTQRCKDKLNALAISVMNQWPGVKLRVTEGWDEGGTEDQVDPRLID
GKSGGDGHHSEESLHYEGRAVDITTSDRDRSKYGMLARLAVEAGFDWVYYESKAHIHCSV
KAENSVAAKSGG
Sequence of entity 3 (G), FASTA
>7RHQ_3 Growth arrest-specific protein 1 (chains G)
GPGSLAHGRRLICWQALLQCQGEPECSYAYNQYAEACAPVLAQHGGGDAPGAAAAAFPAS
AASFSSRWRCPSHCISALIQLNHTRRGPALEDCDCAQDENCKSTKRAIEPCLPRTSGGGA
GGPGAGGVMGCTEARRRCDRDSRCNLALSRYLTYCGKVFNGLRCTDECRTVIEDMLAMPK
AALLNDCVCDGLERPICESVKENMARLCFGAELGNGPGSSGSDGGLDDYYDEDYDDEQRT
GGAGGEQPLDDDDGVPHPPRPGSGAAASGGRGDLPYGPGRRS

Ligands and cofactors

IDNameFormulaCopies
CLRCholesterolC27 H46 O2
Y01Cholesterol hemisuccinateC31 H50 O41
NAG2-acetamido-2-deoxy-beta-D-glucopyranoseC8 H15 N O62
ZNZinc ionZn1
CACalcium ionCa2
PLMPalmitic acidC16 H32 O21

Primary citation

Structural basis for catalyzed assembly of the Sonic hedgehog-Patched1 signaling complex. Huang, P., Wierbowski, B.M., Lian, T. et al. Dev Cell (2022) 57:670-685.e8. DOI 10.1016/j.devcel.2022.02.008 · PubMed

Other PDB entries of the same protein (UniProt Q98SW6), best resolution first:

Browse structure collections

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