6J74: Complex of GGTaseIII and full-length Ykt6

Complex of GGTaseIII and full-length Ykt6. Determined by X-ray diffraction at 3.21 Å resolution. Released 22 Jan 2020.

Method: X-ray diffraction
Resolution: 3.21 Å
Organism: Homo sapiens
Chains: 3
Atoms: 6,417
Mol. weight: 98.06 kDa
Ligands: ZN, PO4
Released: 22 Jan 2020

Explore 6J74 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6J74 contains 43 α-helices and 25 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: 14 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	8-25	18
β-strand	32-35	4	1
α-helix	40-41	2
β-strand	47-50	4	1
β-strand	53-57	5	1
α-helix	58-76	19
α-helix	84-95	12
α-helix	102-113	12
α-helix	119-129	11
α-helix	137-149	13
α-helix	171-190	20
α-helix	195-207	13
α-helix	213-222	10
α-helix	224-229	6
α-helix	234-250	17
α-helix	288-305	18
α-helix	310-324	15

Chain B: 22 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	20-29	10
α-helix	36-41	6
α-helix	43-45	3
α-helix	46-59	14
α-helix	63-65	3
α-helix	68-76	9
β-strand	79	1	2
β-strand	85	1	2
β-strand	86	1	3
α-helix	92	1
β-strand	93	1	3
α-helix	95-107	13
α-helix	111-113	3
α-helix	116-124	9
β-strand	127	1	4
β-strand	133	1	4
β-strand	134	1	5
β-strand	141	1	5
α-helix	143-154	12
α-helix	159-161	3
α-helix	164-171	8
α-helix	172-174	3
β-strand	175	1	6
β-strand	181	1	6
α-helix	187-189	3
α-helix	191-203	13
α-helix	207-209	3
α-helix	212-220	9
β-strand	223	1	7
β-strand	229	1	7
α-helix	239-252	14
α-helix	260-269	10
β-strand	271	1	8
β-strand	278	1	8
α-helix	288-300	13
β-strand	309	1	9
β-strand	316	1	9
α-helix	317-322	6

Chain C: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-11	9	10
β-strand	16-23	8	10
α-helix	30-32	3
α-helix	33-50	18
β-strand	55-61	7	10
β-strand	64-70	7	10
β-strand	75-81	7	10
α-helix	87-101	15
α-helix	123-129	7
α-helix	140-147	8
β-strand	152-154	3	10
α-helix	167-172	6
α-helix	179-191	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein prenyltransferase alpha subunit repeat-containing protein 1	A	protein	327	Homo sapiens	Q7Z6K3 (AlphaFold model)
Geranylgeranyl transferase type-2 subunit beta	B	protein	336	Homo sapiens	P53611 (AlphaFold model)
Synaptobrevin homolog YKT6	C	protein	198	Homo sapiens	O15498 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6J74_1 Protein prenyltransferase alpha subunit repeat-containing protein 1 (chains A)
MAETSEEVAVLVQRVVKDITNAFRRNPHIDEIGLIPCPEARYNRSPIVLVENKLGVESWC
VKFLLPYVHNKLLLYRTRKQWLNRDELIDVTCTLLLLNPDFTTAWNVRKELILSGTLNPI
KDLHLGKLALTKFPKSPETWIHRRWVLQQLIQETSLPSFVTKGNLGTIPTERAQRLIQEE
MEVCGEAAGRYPSNYNAWSHRIWVLQHLAKLDVKILLDELSSTKHWASMHVSDHSGFHYR
QFLLKSLISQTVIDSSVMEQNPLRSEPALVPPKDEEAAVSTEEPRINLPHLLEEEVEFST
DLIDSYPGHETLWCHRRHIFYLQHHLN

Sequence of entity 2 (B), FASTA

>6J74_2 Geranylgeranyl transferase type-2 subunit beta (chains B)
GPLGSMGTPQKDVIIKSDAPDTLLLEKHADYIASYGSKKDDYEYCMSEYLRMSGIYWGLT
VMDLMGQLHRMNREEILAFIKSCQHECGGISASIGHDPHLLYTLSAVQILTLYDSINVID
VNKVVEYVKGLQKEDGSFAGDIWGEIDTRFSFCAVATLALLGKLDAINVEKAIEFVLSCM
NFDGGFGCRPGSESHAGQIYCCTGFLAITSQLHQVNSDLLGWWLCERQLPSGGLNGRPEK
LPDVCYSWWVLASLKIIGRLHWIDREKLRNFILACQDEETGGFADRPGDMVDPFHTLFGI
AGLSLLGEEQIKPVNPVFCMPEEVLQRVNVQPELVS

Sequence of entity 3 (C), FASTA

>6J74_3 Synaptobrevin homolog YKT6 (chains C)
MKLYSLSVLYKGEAKVVLLKAAYDVSSFSFFQRSSVQEFMTFTSQLIVERSSKGTRASVK
EQDYLCHVYVRNDSLAGVVIADNEYPSRVAFTLLEKVLDEFSKQVDRIDWPVGSPATIHY
PALDGHLSRYQNPREADPMTKVQAELDETKIILHNTMESLLERGEKLDDLVSKSEVLGTQ
SKAFYKTARKQNSCCAIM

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
PO4	Phosphate ion	O4 P	2

Primary citation

A SNARE geranylgeranyltransferase essential for the organization of the Golgi apparatus. Shirakawa, R., Goto-Ito, S., Goto, K. et al. EMBO J (2020) 39:e104120-e104120. DOI 10.15252/embj.2019104120 · PubMed

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

6O60 2.5 Å, Crystal structure of GGTase3-FBXL2-SKP1 complex
6J7X 2.75 Å, Complex of GGTaseIII, farnesyl-Ykt6, and GGPP
6J7F 2.88 Å, Complex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), and GGPP
6J6X 2.96 Å, Crystal structure of apo GGTaseIII

Browse structure collections

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