4DVZ: Helicobacter pylori CagA oncoprotein

Name: PDB 4DVZ: Crystal structure of the Helicobacter pylori CagA oncoprotein
Published: 2012-07-25
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: oncoprotein

Crystal structure of the Helicobacter pylori CagA oncoprotein. Determined by X-ray diffraction at 3.19 Å resolution. Released 25 Jul 2012.

Method: X-ray diffraction
Resolution: 3.19 Å
Organism: Helicobacter pylori
Chains: 1
Atoms: 3,635
Mol. weight: 63.63 kDa
Released: 25 Jul 2012

Explore 4DVZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4DVZ contains 16 α-helices and 14 β-strands across 1 chain. 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: 16 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	310-313	4	1
β-strand	320-324	5	1
β-strand	336-343	8	1
β-strand	350-358	9	1
β-strand	363-367	5	1
β-strand	373	1	1
α-helix	376-379	4
β-strand	381-383	3	2
β-strand	390-392	3	2
α-helix	393-394	2
α-helix	395-410	16
α-helix	420-425	6
α-helix	427-435	9
α-helix	437-446	10
β-strand	448-452	5	1
α-helix	453-456	4
β-strand	460-466	7	1
β-strand	471-477	7	1
β-strand	492-497	6	1
α-helix	498-501	4
β-strand	503-508	6	1
β-strand	538-543	6	1
α-helix	556-567	12
α-helix	572-606	35
α-helix	610-638	29
α-helix	651-710	60
α-helix	720-734	15
α-helix	738-755	18
α-helix	763-802	40
α-helix	806-826	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cytotoxicity-associated immunodominant antigen	A	protein	569	Helicobacter pylori	P55980 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4DVZ_1 Cytotoxicity-associated immunodominant antigen (chains A)
DLLDERGNFSKFTLGDMEMLDVEGVADIDPNYKFNQLLIHNNALSSVLMGSHNGIEPEKV
SLLYAGNGGFGDKHDWNATVGYKDQQGNNVATLINVHMKNGSGLVIAGGEKGINNPSFYL
YKEDQLTGSQRALSQEEIRNKVDFMEFLAQNNTKLDNLSEKEKEKFQNEIEDFQKDSKAY
LDALGNDRIAFVSKKDTKHSALITEFNNGDLSYTLKDYGKKADKALDREKNVTLQGSLKH
DGVMFVDYSNFKYTNASKNPNKGVGATNGVSHLEAGFNKVAVFNLPDLNNLAITSFVRRN
LENKLTAKGLSLQEANKLIKDFLSSNKELAGKALNFNKAVAEAKSTGNYDEVKKAQKDLE
KSLRKREHLEKEVEKKLESKSGNKNKMEAKAQANSQKDEIFALINKEANRDARAIAYTQN
LKGIKRELSDKLEKISKDLKDFSKSFDEFKNGKNKDFSKAEETLKALKGSVKDLGINPEW
ISKVENLNAALNEFKNGKNKDFSKVTQAKSDLENSVKDVIINQKVTDKVDNLNQAVSVAK
AMGDFSRVEQVLADLKNFSKEQLAQQAQK

Primary citation

Tertiary structure-function analysis reveals the pathogenic signaling potentiation mechanism of Helicobacter pylori oncogenic effector CagA. Hayashi, T., Senda, M., Morohashi, H. et al. Cell Host Microbe (2012) 12:20-33. DOI 10.1016/j.chom.2012.05.010 · PubMed

Other PDB entries of the same protein (UniProt P55980 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4IRV 2.04 Å, Structure of the Helicobacter pylori CagA Oncogene Bound to the Human Tumor Suppressor…
3IEC 2.2 Å, Helicobacter pylori CagA Inhibits PAR1/MARK Family Kinases by Mimicking Host Substrates
5X7B 2.45 Å, Crystal structure of SHP2_SH2-CagA EPIYA_C peptide complex
5X94 2.6 Å, Crystal structure of SHP2_SH2-CagA EPIYA_D peptide complex
4DVY 3.3 Å, Crystal structure of the Helicobacter pylori CagA oncoprotein
4G0H 3.6 Å, Crystal structure of the N-terminal domain of Helicobacter pylori CagA protein

Browse structure collections

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