6X1H: ULP_PROTEASE domain-containing protein

Crystal structure of a guanine nucleotide exchange factor (GEF) domain from the Orientia tsutsugamushi protein OtDUB. Determined by X-ray diffraction at 2.91 Å resolution. Released 25 Nov 2020.

Method: X-ray diffraction
Resolution: 2.91 Å
Organism: Orientia tsutsugamushi
Chains: 6
Atoms: 10,290
Mol. weight: 151.2 kDa
Ligands: NI
Released: 25 Nov 2020

Explore 6X1H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6X1H contains 66 α-helices and 12 β-strands across 6 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.

Chains A and B: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	550-579	30
α-helix	589-600	12
α-helix	609-625	17
α-helix	630-650	21
α-helix	654-672	19
β-strand	675	1	6
α-helix	680-687	8
α-helix	688-690	3
α-helix	697-700	4
α-helix	710-722	13
β-strand	731	1	6
α-helix	733-738	6
α-helix	741-758	18

Chain C: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	550-579	30
α-helix	589-600	12
α-helix	609-625	17
α-helix	630-650	21
α-helix	654-672	19
β-strand	675	1	5
α-helix	680-687	8
α-helix	688-690	3
α-helix	697-700	4
α-helix	710-722	13
β-strand	731	1	5
α-helix	733-738	6
α-helix	741-759	19

Chain D: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	550-579	30
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	709-722	14
β-strand	731	1	2
α-helix	733-738	6
α-helix	741-763	23

Chain E: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	550-579	30
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	741-762	22

Chain F: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	550-579	30
α-helix	589-600	12
α-helix	609-625	17
α-helix	630-650	21
α-helix	654-672	19
β-strand	675	1	4
α-helix	680-687	8
α-helix	688-690	3
α-helix	697-700	4
α-helix	710-722	13
β-strand	731	1	4
α-helix	733-738	6
α-helix	741-760	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ULP_PROTEASE domain-containing protein	A, B, C, D, E, F	protein	219	Orientia tsutsugamushi	B3CVM3

Sequence of entity 1 (A, B, C, D, E, F), FASTA

>6X1H_1 ULP_PROTEASE domain-containing protein (chains A, B, C, D, E, F)
MERLVKKVTSNLETELKFFKGRLVQELMQIVKNENGRIDHTSKNWQESASVLLNSQEKGA
VSLAEVERAVSKMTQKLRDQKVSEEEVVNIESKLKFERASLEAKLFDDNEIKELINKRIK
EDALRAIPFLGSDSESFMEKISPFVKLPDDSYSLLKANDKHHPFQNILYSNALKFFADSS
DIGYLNDDSLKNLTPENLNAFEQAVAADIDKLMHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NI	Nickel (II) ion	Ni	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:

6X1G 1.6 Å, Crystal structure of a GEF domain from the Orientia tsutsugamushi protein OtDUB in…
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…

Browse structure collections

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