6J6X: Apo GGTaseIII

Crystal structure of apo GGTaseIII. Determined by X-ray diffraction at 2.96 Å resolution. Released 22 Jan 2020.

Method: X-ray diffraction
Resolution: 2.96 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,681
Mol. weight: 79.86 kDa
Ligands: MG
Released: 22 Jan 2020

Explore 6J6X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6J6X contains 32 α-helices and 17 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: 13 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
β-strand	31-33	3	1
β-strand	47-49	3	1
β-strand	53-56	4	1
α-helix	58-76	19
α-helix	84-95	12
α-helix	102-112	11
α-helix	119-130	12
α-helix	137-150	14
α-helix	171-186	16
α-helix	195-207	13
α-helix	213-222	10
α-helix	224-229	6
α-helix	234-249	16
α-helix	288-305	18
α-helix	310-325	16

Chain B: 19 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	21-28	8
α-helix	38-41	4
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
α-helix	92-93	2
β-strand	94	1	2
α-helix	96-107	12
α-helix	111-113	3
α-helix	116-124	9
β-strand	127	1	3
β-strand	133	1	3
β-strand	134	1	4
β-strand	141	1	4
α-helix	143-156	14
α-helix	159-161	3
α-helix	164-172	9
β-strand	175	1	5
β-strand	181	1	5
α-helix	187-189	3
α-helix	191-203	13
α-helix	207-209	3
α-helix	212-221	10
α-helix	238-252	15
α-helix	260-269	10
β-strand	271	1	6
β-strand	278	1	6
β-strand	287	1	6
α-helix	288-301	14
β-strand	309	1	7
β-strand	316	1	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein prenyltransferase alpha subunit repeat-containing protein 1	A	protein	366	Homo sapiens	Q7Z6K3 (AlphaFold model)
Geranylgeranyl transferase type-2 subunit beta	B	protein	336	Homo sapiens	P53611 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6J6X_1 Protein prenyltransferase alpha subunit repeat-containing protein 1 (chains A)
MAETSEEVAVLVQRVVKDITNAFRRNPHIDEIGLIPCPEARYNRSPIVLVENKLGVESWC
VKFLLPYVHNKLLLYRTRKQWLNRDELIDVTCTLLLLNPDFTTAWNVRKELILSGTLNPI
KDLHLGKLALTKFPKSPETWIHRRWVLQQLIQETSLPSFVTKGNLGTIPTERAQRLIQEE
MEVCGEAAGRYPSNYNAWSHRIWVLQHLAKLDVKILLDELSSTKHWASMHVSDHSGFHYR
QFLLKSLISQTVIDSSVMEQNPLRSEPALVPPKDEEAAVSTEEPRINLPHLLEEEVEFST
DLIDSYPGHETLWCHRRHIFYLQHHLNGRFPHSMTQLSPADSPGGTLSDLHLIPAGSQLS
QAMEVD

Sequence of entity 2 (B), FASTA

>6J6X_2 Geranylgeranyl transferase type-2 subunit beta (chains B)
GPLGSMGTPQKDVIIKSDAPDTLLLEKHADYIASYGSKKDDYEYCMSEYLRMSGIYWGLT
VMDLMGQLHRMNREEILAFIKSCQHECGGISASIGHDPHLLYTLSAVQILTLYDSINVID
VNKVVEYVKGLQKEDGSFAGDIWGEIDTRFSFCAVATLALLGKLDAINVEKAIEFVLSCM
NFDGGFGCRPGSESHAGQIYCCTGFLAITSQLHQVNSDLLGWWLCERQLPSGGLNGRPEK
LPDVCYSWWVLASLKIIGRLHWIDREKLRNFILACQDEETGGFADRPGDMVDPFHTLFGI
AGLSLLGEEQIKPVNPVFCMPEEVLQRVNVQPELVS

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Water and common crystallization additives (MPD) are not listed.

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
6J74 3.21 Å, Complex of GGTaseIII and full-length Ykt6

Browse structure collections

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