6GGR: Salmonella zinc metalloprotease effector GtgA

Crystal structure of Salmonella zinc metalloprotease effector GtgA in complex with p65. Determined by X-ray diffraction at 2.1 Å resolution. Released 29 Aug 2018.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Mus musculus, Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
Chains: 2
Atoms: 3,028
Mol. weight: 43.49 kDa
Released: 29 Aug 2018

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

Secondary structure: helices and β-sheets

6GGR contains 24 α-helices and 24 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: 11 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	20-25	6	1
α-helix	26	1
β-strand	27	1	2
α-helix	28	1
β-strand	35	1	3
β-strand	39	1	4
α-helix	46-47	2
β-strand	48	1	2
β-strand	60-64	5	1
β-strand	71-77	7	5
α-helix	84	1
β-strand	85	1	5
α-helix	86	1
β-strand	89-91	3	3
β-strand	95-96	2	5
β-strand	99-103	5	5
α-helix	104-105	2
β-strand	110-112	3	1
β-strand	117-119	3	3
α-helix	120-122	3
α-helix	123-125	3
α-helix	126-135	10
α-helix	145-147	3
β-strand	156-166	11	5
β-strand	172-174	3	5
α-helix	175-177	3
β-strand	178-184	7	5

Chain B: 13 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	32-35	4
α-helix	40-46	7
α-helix	58-60	3
α-helix	61-65	5
β-strand	66-69	4	4
α-helix	80-100	21
α-helix	102-111	10
α-helix	112-116	5
β-strand	123-127	5	4
α-helix	130	1
β-strand	132-133	2	4
β-strand	148-151	4	4
α-helix	154-156	3
α-helix	161-162	2
β-strand	164-165	2	6
β-strand	166	1	7
β-strand	172-173	2	6
α-helix	176-189	14
α-helix	202-213	12
α-helix	219-220	2
β-strand	223	1	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription factor p65	A	protein	170	Mus musculus	Q04207 (AlphaFold model)
Bacteriophage virulence determinant	B	protein	212	Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S	A0A0F6AZI6 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6GGR_1 Transcription factor p65 (chains A)
AYVEIIEQPKQRGMRFRYKCEGRSAGSIPGERSTDTTKTHPTIKINGYTGPGTVRISLVT
KDPPHRPHPHELVGKDCRDGYYEADLCPDRSIHSFQNLGIQCVKKRDLEQAISQRIQTNN
NPFHVPIEEQRGDYDLNAVRLCFQVTVRDPAGRPLLLTPVLSHPIFDNRA

Sequence of entity 2 (B), FASTA

>6GGR_2 Bacteriophage virulence determinant (chains B)
GAMSHPHDSKVFPDLPEHQDNPSQLRLQHDGLATDDKARLEPMCLAEYLISGPGGMDPDI
EIDDDTYDECREVLSRILEDAYTQSGTFRRLMNYAYDQELHDVEQRWLLGAGENFGTTVT
DEDLESSEGRKVIALNLDDTDDDSIPEYYESNDGPQQFDTTRSFIHQVVHALTHLQDKED
SNPRGPVVEYTNIILKEMGHTSPPRIAYEFSN

Primary citation

Structure-function analyses of the bacterial zinc metalloprotease effector protein GtgA uncover key residues required for deactivating NF-kappa B. Jennings, E., Esposito, D., Rittinger, K. et al. J Biol Chem (2018) 293:15316-15329. DOI 10.1074/jbc.RA118.004255 · PubMed

Other PDB entries of the same protein (UniProt Q04207 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1MY7 1.49 Å, NF-kappaB p65 subunit dimerization domain homodimer N202R mutation
1MY5 1.8 Å, NF-kappaB p65 subunit dimerization domain homodimer
9BDW 1.87 Å, NF-kappaB RelA homo-dimer bound to GC-centric kappaB DNA
9BDV 1.9 Å, NF-kappaB RelA homo-dimer bound to TA-centric kappaB DNA
1BFT 2.0 Å, Structure of nf-kb P65 homodimer bound to a kb site
9BDU 2.03 Å, NF-kappaB RelA homo-dimer bound to AT-centric kappaB DNA
9E6W 2.04 Å, NF-kappaB RelA homo-dimer bound to a kappaB site of Cxcl2 gene
1OY3 2.05 Å, Crystal structure of an ikbbeta/nf-kb P65 homodimer complex
1IKN 2.3 Å, Ikappabalpha/nf-kappab complex
2RAM 2.4 Å, A novel DNA recognition mode by nf-kb P65 homodimer
1K3Z 2.5 Å, X-ray crystal structure of the IkBb/NF-kB p65 homodimer complex
5U01 2.5 Å, Cooperative DNA binding by two RelA dimers

Browse structure collections

About this viewer

MolViewer shows 6GGR directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.