6J7F: PDB entry 6J7F

Complex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), and GGPP. Determined by X-ray diffraction at 2.88 Å resolution. Released 22 Jan 2020.

Method
X-ray diffraction
Resolution
2.88 Å
Organism
Homo sapiens
Chains
3
Atoms
6,533
Mol. weight
98.31 kDa
Ligands
DPO, GER, FAR, TLA
Released
22 Jan 2020

Explore 6J7F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6J7F contains 45 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

ElementResiduesLengthSheet
α-helix8-2518
β-strand31-3551
α-helix40-412
β-strand47-5041
β-strand53-5751
α-helix58-7619
α-helix84-9512
α-helix102-11413
α-helix119-13214
α-helix137-14913
α-helix168-1703
α-helix171-19020
α-helix195-20713
α-helix213-22816
α-helix234-25017
α-helix284-30320
α-helix310-32415
Chain B: 24 helices, 16 β-strands
ElementResiduesLengthSheet
α-helix20-289
α-helix36-427
α-helix43-453
α-helix46-5914
α-helix63-653
α-helix68-7710
β-strand7912
β-strand8512
β-strand8613
α-helix921
β-strand9313
α-helix95-10713
α-helix111-1133
α-helix116-1249
β-strand12714
β-strand13314
β-strand13415
β-strand14115
α-helix143-15614
α-helix159-1613
α-helix164-1729
β-strand17516
β-strand18116
α-helix187-1893
α-helix191-20313
α-helix207-2093
α-helix212-2209
β-strand22317
β-strand22917
α-helix241-25212
α-helix255-2573
α-helix260-26910
β-strand27118
β-strand27818
α-helix285-2862
α-helix288-30114
α-helix307-3082
β-strand309-31029
β-strand315-31629
α-helix317-3226
Chain C: 7 helices, 6 β-strands
ElementResiduesLengthSheet
β-strand3-11910
β-strand16-23810
α-helix30-323
α-helix33-4816
β-strand55-61710
β-strand64-70710
β-strand75-81710
α-helix87-10418
α-helix123-1297
α-helix140-1445
β-strand152-154310
α-helix168-1714
α-helix179-1868

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Protein prenyltransferase alpha subunit repeat-containing protein 1Aprotein327Homo sapiensQ7Z6K3 (AlphaFold model)
Geranylgeranyl transferase type-2 subunit betaBprotein336Homo sapiensP53611 (AlphaFold model)
Synaptobrevin homolog YKT6Cprotein195Homo sapiensO15498 (AlphaFold model)
Sequence of entity 1 (A), FASTA
>6J7F_1 Protein prenyltransferase alpha subunit repeat-containing protein 1 (chains A)
MAETSEEVAVLVQRVVKDITNAFRRNPHIDEIGLIPCPEARYNRSPIVLVENKLGVESWC
VKFLLPYVHNKLLLYRTRKQWLNRDELIDVTCTLLLLNPDFTTAWNVRKELILSGTLNPI
KDLHLGKLALTKFPKSPETWIHRRWVLQQLIQETSLPSFVTKGNLGTIPTERAQRLIQEE
MEVCGEAAGRYPSNYNAWSHRIWVLQHLAKLDVKILLDELSSTKHWASMHVSDHSGFHYR
QFLLKSLISQTVIDSSVMEQNPLRSEPALVPPKDEEAAVSTEEPRINLPHLLEEEVEFST
DLIDSYPGHETLWCHRRHIFYLQHHLN
Sequence of entity 2 (B), FASTA
>6J7F_2 Geranylgeranyl transferase type-2 subunit beta (chains B)
GPLGSMGTPQKDVIIKSDAPDTLLLEKHADYIASYGSKKDDYEYCMSEYLRMSGIYWGLT
VMDLMGQLHRMNREEILAFIKSCQHECGGISASIGHDPHLLYTLSAVQILTLYDSINVID
VNKVVEYVKGLQKEDGSFAGDIWGEIDTRFSFCAVATLALLGKLDAINVEKAIEFVLSCM
NFDGGFGCRPGSESHAGQIYCCTGFLAITSQLHQVNSDLLGWWLCERQLPSGGLNGRPEK
LPDVCYSWWVLASLKIIGRLHWIDREKLRNFILACQDEETGGFADRPGDMVDPFHTLFGI
AGLSLLGEEQIKPVNPVFCMPEEVLQRVNVQPELVS
Sequence of entity 3 (C), FASTA
>6J7F_3 Synaptobrevin homolog YKT6 (chains C)
MKLYSLSVLYKGEAKVVLLKAAYDVSSFSFFQRSSVQEFMTFTSQLIVERSSKGTRASVK
EQDYLCHVYVRNDSLAGVVIADNEYPSRVAFTLLEKVLDEFSKQVDRIDWPVGSPATIHY
PALDGHLSRYQNPREADPMTKVQAELDETKIILHNTMESLLERGEKLDDLVSKSEVLGTQ
SKAFYKTARKQNSCC

Ligands and cofactors

IDNameFormulaCopies
DPODiphosphateO7 P21
GERGeran-8-yl geranC20 H341
FARFarnesylC15 H261
TLAL(+)-tartaric acidC4 H6 O61

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:

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