5Z98: Primate APOBEC3H Dimer mediated by RNA Duplex

Crystal Structure of the Primate APOBEC3H Dimer mediated by RNA Duplex. Determined by X-ray diffraction at 2.2 Å resolution. Released 15 Aug 2018.

Method: X-ray diffraction
Resolution: 2.2 Å
Organisms: Pan troglodytes, unidentified
Chains: 4
Atoms: 3,477
Mol. weight: 50.31 kDa
Ligands: ZN
Released: 15 Aug 2018

Explore 5Z98 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5Z98 contains 20 α-helices and 14 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: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
α-helix	6-12	7
α-helix	23	1
β-strand	29-36	8	2
β-strand	43-48	6	2
α-helix	55-62	8
β-strand	74-82	9	2
α-helix	83-84	2
α-helix	86-98	13
β-strand	102-110	9	2
α-helix	117-127	11
β-strand	133-135	3	2
α-helix	138-148	11
β-strand	149	1	1
α-helix	154-155	2
α-helix	159-182	24

Chain B: 11 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	3	1
β-strand	4	1	3
α-helix	5	1
α-helix	6-12	7
α-helix	19-20	2
α-helix	23	1
β-strand	29-36	8	4
β-strand	43-48	6	4
α-helix	55-66	12
β-strand	74-82	9	4
α-helix	86-98	13
β-strand	102-110	9	4
α-helix	117-128	12
β-strand	133-135	3	4
α-helix	138-148	11
β-strand	149	1	3
α-helix	154-155	2
α-helix	159-181	23

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like protein 3H	A, B	protein	185	Pan troglodytes	B7T0U6 (AlphaFold model)
RNA (5'-r(pcpupgpcpcpgpgpgpupa)-3')	C	RNA	10	unidentified
RNA (5'-r(apupapcpcpcpgpgpcpa)-3')	D	RNA	10	unidentified

Sequence of entity 1 (A, B), FASTA

>5Z98_1 Apolipoprotein B mRNA editing enzyme catalytic polypeptide-like protein 3H (chains A, B)
GSMALLTAETFRLQFNNRRRLRRPYYPRKALLCYQLTPQNGSTPTRGYFENKKKCHAEIC
FINEIKSMGLDETQCYQVTCYLTWSPCSSCAWKLVDFIQAHDHLNLRIFASRLYYHWCKP
QQEGLRLLCGSQVPVEVMGLPEFNDCWENFVDHEKPLSFDPCKMLEELDKNSRAIKRRLE
RIKQS

Sequence of entity 2 (C), FASTA

>5Z98_2 RNA (5'-R(P*CP*UP*GP*CP*CP*GP*GP*GP*UP*A)-3') (chains C)
CUGCCGGGUA

Sequence of entity 3 (D), FASTA

>5Z98_3 RNA (5'-R(*AP*UP*AP*CP*CP*CP*GP*GP*CP*A)-3') (chains D)
AUACCCGGCA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Primary citation

Structural basis of chimpanzee APOBEC3H dimerization stabilized by double-stranded RNA. Matsuoka, T., Nagae, T., Ode, H. et al. Nucleic Acids Res (2018) 46:10368-10379. DOI 10.1093/nar/gky676 · PubMed

Other PDB entries of the same protein (UniProt B7T0U6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9E93 3.58 Å, Structural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H
9E9V 4.0 Å, Structural Insights into HIV-1 Vif-Mediated Ubiquitination and Degradation of APOBEC3H

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