6X1G: ULP_PROTEASE domain-containing protein

Crystal structure of a GEF domain from the Orientia tsutsugamushi protein OtDUB in complex with Rac1. Determined by X-ray diffraction at 1.6 Å resolution. Released 25 Nov 2020.

Method: X-ray diffraction
Resolution: 1.6 Å
Organisms: Orientia tsutsugamushi, Homo sapiens
Chains: 4
Atoms: 6,578
Mol. weight: 91.48 kDa
Ligands: MG
Released: 25 Nov 2020

Explore 6X1G in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6X1G contains 47 α-helices and 16 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: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	548-579	32
α-helix	589-600	12
α-helix	609-625	17
α-helix	630-650	21
α-helix	654-672	19
β-strand	675	1	1
α-helix	680-687	8
α-helix	688-690	3
α-helix	697-700	4
α-helix	710-722	13
β-strand	731	1	1
α-helix	733-738	6
α-helix	741-759	19

Chain B: 13 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	3
α-helix	12-14	3
α-helix	16-25	10
α-helix	27-28	2
β-strand	42-46	5	3
β-strand	49-57	9	3
α-helix	62-64	3
α-helix	68-71	4
β-strand	77-83	7	3
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	3
α-helix	117-119	3
α-helix	123-130	8
α-helix	136-138	3
α-helix	139-149	11
β-strand	153-156	4	3
α-helix	165-177	13

Chain C: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	549-579	31
α-helix	589-600	12
α-helix	609-625	17
α-helix	630-650	21
α-helix	654-672	19
β-strand	675	1	2
α-helix	680-687	8
α-helix	688-690	3
α-helix	697-700	4
α-helix	710-722	13
β-strand	731	1	2
α-helix	733-738	6
α-helix	741-759	19

Chain D: 12 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	4
α-helix	16-25	10
α-helix	27-28	2
β-strand	42-46	5	4
β-strand	49-57	9	4
α-helix	62-64	3
α-helix	68-71	4
β-strand	77-83	7	4
α-helix	87-92	6
α-helix	93-97	5
α-helix	98-104	7
β-strand	110-115	6	4
α-helix	117-119	3
α-helix	123-130	8
α-helix	136-138	3
α-helix	139-149	11
β-strand	153-156	4	4
α-helix	165-177	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ULP_PROTEASE domain-containing protein	A, C	protein	219	Orientia tsutsugamushi	B3CVM3
Ras-related C3 botulinum toxin substrate 1	B, D	protein	183	Homo sapiens	P63000 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6X1G_1 ULP_PROTEASE domain-containing protein (chains A, C)
MERLVKKVTSNLETELKFFKGRLVQELMQIVKNENGRIDHTSKNWQESASVLLNSQEKGA
VSLAEVERAVSKMTQKLRDQKVSEEEVVNIESKLKFERASLEAKLFDDNEIKELINKRIK
EDALRAIPFLGSDSESFMEKISPFVKLPDDSYSLLKANDKHHPFQNILYSNALKFFADSS
DIGYLNDDSLKNLTPENLNAFEQAVAADIDKLMHHHHHH

Sequence of entity 2 (B, D), FASTA

>6X1G_2 Ras-related C3 botulinum toxin substrate 1 (chains B, D)
MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAG
QEDYDRLRPLSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLR
DDKDTIEKLKEKKLTPITYPQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVLHHH
HHH

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Primary citation

Crystal structure of a guanine nucleotide exchange factor encoded by the scrub typhus pathogen Orientia tsutsugamushi . Lim, C., Berk, J.M., Blaise, A. et al. Proc Natl Acad Sci U S A (2020) 117:30380-30390. DOI 10.1073/pnas.2018163117 · PubMed

Other PDB entries of the same protein (UniProt B3CVM3), best resolution first:

6UPS 2.0 Å, Crystal structure of the deubiquitylase domain from the Orientia tsutsugamushi protein…
6UPU 2.2 Å, Crystal structure of the Orientia tsutsugamushi OtDUB in complex with three molecules of…
6X1H 2.91 Å, Crystal structure of a guanine nucleotide exchange factor (GEF) domain from the Orientia…

Browse structure collections

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