6O60: GGTase3-FBXL2-SKP1 complex

Crystal structure of GGTase3-FBXL2-SKP1 complex. Determined by X-ray diffraction at 2.5 Å resolution. Released 26 Jun 2019.

Method
X-ray diffraction
Resolution
2.5 Å
Organism
Homo sapiens
Chains
4
Atoms
9,299
Mol. weight
149.9 kDa
Ligands
ZN
Released
26 Jun 2019

Explore 6O60 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6O60 contains 68 α-helices and 35 β-strands across 4 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: 15 helices, 3 β-strands

ElementResiduesLengthSheet
α-helix7-2519
β-strand31-3551
β-strand47-5041
β-strand53-5751
α-helix58-603
α-helix61-7616
α-helix84-9714
α-helix102-11413
α-helix119-13214
α-helix137-14913
α-helix172-19019
α-helix195-20713
α-helix213-22917
α-helix234-24815
α-helix290-30516
α-helix310-32314
α-helix368-37912
α-helix384-39714
Chain B: 24 helices, 15 β-strands
ElementResiduesLengthSheet
α-helix20-2910
α-helix37-426
α-helix43-453
α-helix46-5914
α-helix63-653
α-helix68-769
β-strand7912
β-strand8512
α-helix92-932
α-helix95-10713
α-helix111-1133
α-helix116-12510
β-strand12713
β-strand13313
β-strand13414
β-strand14114
α-helix143-15614
α-helix159-1613
α-helix164-1729
β-strand17515
β-strand18115
α-helix187-1893
α-helix191-20313
α-helix207-2093
α-helix212-2209
β-strand22316
β-strand22916
α-helix235-2373
α-helix239-25113
α-helix255-2573
α-helix260-26910
β-strand27117
β-strand278-27927
β-strand286-28727
α-helix288-30114
α-helix307-3082
β-strand30918
β-strand31618
α-helix317-3248
Chain C: 19 helices, 14 β-strands
ElementResiduesLengthSheet
α-helix10-145
α-helix17-248
α-helix29-357
α-helix40-467
α-helix49-513
β-strand54-5639
α-helix67-759
β-strand82-8439
α-helix93-10210
β-strand108-11039
α-helix119-12810
β-strand134-13639
α-helix145-15410
β-strand160-16239
α-helix171-18010
β-strand186-18839
α-helix197-20610
β-strand212-21439
α-helix223-23210
β-strand238-24039
α-helix249-25810
β-strand264-26639
α-helix275-28410
β-strand290-29239
α-helix301-31010
β-strand316-31839
α-helix327-3348
α-helix337-3415
β-strand345-34739
α-helix356-3616
β-strand370-37239
α-helix381-39010
β-strand395-39739
Chain D: 10 helices, 3 β-strands
ElementResiduesLengthSheet
β-strand3-7510
β-strand13-17510
α-helix18-214
α-helix25-339
α-helix43-442
β-strand45-46210
α-helix52-6312
α-helix87-926
α-helix97-11014
α-helix113-12715
α-helix132-1387
α-helix147-1537
α-helix156-1583

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Protein prenyltransferase alpha subunit repeat-containing protein 1Aprotein407Homo sapiensQ7Z6K3 (AlphaFold model)
Geranylgeranyl transferase type-2 subunit betaBprotein332Homo sapiensP53611 (AlphaFold model)
F-box/LRR-repeat protein 2Cprotein424Homo sapiensQ9UKC9 (AlphaFold model)
S-phase kinase-associated protein 1Dprotein164Homo sapiensP63208 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>6O60_1 Protein prenyltransferase alpha subunit repeat-containing protein 1 (chains A)
SGSGGMAETSEEVAVLVQRVVKDITNAFRRNPHIDEIGLIPCPEARYNRSPIVLVENKLG
VESWCVKFLLPYVHNKLLLYRTRKQWLNRDELIDVTCTLLLLNPDFTTAWNVRKELILSG
TLNPIKDLHLGKLALTKFPKSPETWIHRRWVLQQLIQETSLPSFVTKGNLGTIPTERAQR
LIQEEMEVCGEAAGRYPSNYNAWSHRIWVLQHLAKLDVKILLDELSSTKHWASMHVSDHS
GFHYRQFLLKSLISQTVIDSSVMEQNPLRSEPALVPPKDEEAAVSTEEPRINLPHLLEEE
VEFSTDLIDSYPGHETLWCHRRHIFYLQHHLNAGSQLSQAMEVDGLNDSSKQGYSQETKR
LKRTPVPDSLGLEMEHRFIDQVLSTCRNVEQARFASAYRKWLVTLSQ
Sequence of entity 2 (B), FASTA
>6O60_2 Geranylgeranyl transferase type-2 subunit beta (chains B)
SMGTPQKDVIIKSDAPDTLLLEKHADYIASYGSKKDDYEYCMSEYLRMSGIYWGLTVMDL
MGQLHRMNREEILAFIKSCQHECGGISASIGHDPHLLYTLSAVQILTLYDSINVIDVNKV
VEYVKGLQKEDGSFAGDIWGEIDTRFSFCAVATLALLGKLDAINVEKAIEFVLSCMNFDG
GFGCRPGSESHAGQIYCCTGFLAITSQLHQVNSDLLGWWLCERQLPSGGLNGRPEKLPDV
CYSWWVLASLKIIGRLHWIDREKLRNFILACQDEETGGFADRPGDMVDPFHTLFGIAGLS
LLGEEQIKPVNPVFCMPEEVLQRVNVQPELVS
Sequence of entity 3 (C), FASTA
>6O60_3 F-box/LRR-repeat protein 2 (chains C)
SMVFSNNDEGLINKKLPKELLLRIFSFLDIVTLCRCAQISKAWNILALDGSNWQRIDLFN
FQTDVEGRVVENISKRCGGFLRKLSLRGCIGVGDSSLKTFAQNCRNIEHLNLNGCTKITD
STCYSLSRFCSKLKHLDLTSCVSITNSSLKGISEGCRNLEYLNLSWCDQITKDGIEALVR
GCRGLKALLLRGCTQLEDEALKHIQNYCHELVSLNLQSCSRITDEGVVQICRGCHRLQAL
CLSGCSNLTDASLTALGLNCPRLQILEAARCSHLTDAGFTLLARNCHELEKMDLEECILI
TDSTLIQLSIHCPKLQALSLSHCELITDDGILHLSNSTCGHERLRVLELDNCLLITDVAL
EHLENCRGLERLELYDCQQVTRAGIKRMRAQLPHVKVHAYFAPVTPPTAVAGSGQRLCRC
CVIL
Sequence of entity 4 (D), FASTA
>6O60_4 S-phase kinase-associated protein 1 (chains D)
SMPSIKLQSSDGEIFEVDVEIAKQSVTIKTMLEDLGMDDEGDDDPVPLPNVNAAILKKVI
QWCTHHKDDPPPPEDDENKEKRTDDIPVWDQEFLKVDQGTLFELILAANYLDIKGLLDVT
CKTVANMIKGKTPEEIRKTFNIKNDFTEEEEAQVRKENQWCEEK

Ligands and cofactors

IDNameFormulaCopies
ZNZinc ionZn1

Primary citation

GGTase3 is a newly identified geranylgeranyltransferase targeting a ubiquitin ligase. Kuchay, S., Wang, H., Marzio, A. et al. Nat Struct Mol Biol (2019) 26:628-636. DOI 10.1038/s41594-019-0249-3 · PubMed

Other PDB entries of the same protein (UniProt Q7Z6K3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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