6BBO: Human APOBEC3H/RNA complex

Crystal structure of human APOBEC3H/RNA complex. Determined by X-ray diffraction at 3.43 Å resolution. Released 10 Jan 2018.

Method: X-ray diffraction
Resolution: 3.43 Å
Organisms: Homo sapiens, Escherichia coli, Discosoma sp.
Chains: 8
Atoms: 6,934
Mol. weight: 102.86 kDa
Ligands: ZN
Released: 10 Jan 2018

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

Secondary structure: helices and β-sheets

6BBO contains 26 α-helices and 46 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: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
α-helix	6-12	7
β-strand	29-34	6	2
β-strand	36	1	2
β-strand	43-48	6	2
β-strand	50	1	3
β-strand	53	1	3
α-helix	55-66	12
β-strand	74-82	9	2
α-helix	86-97	12
β-strand	102-110	9	2
α-helix	118-121	4
α-helix	126-129	4
β-strand	133-135	3	2
α-helix	139-147	9
β-strand	149	1	1
α-helix	161-169	9
α-helix	170-174	5
α-helix	175-181	7

Chains D and H: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	12-22	11	4
β-strand	25-36	12	4
β-strand	41-50	10	4
α-helix	58-60	3
α-helix	62-64	3
β-strand	74	1	4
α-helix	82-85	4
β-strand	91-99	9	4
β-strand	104-111	8	4
β-strand	119-127	9	4
β-strand	140-143	4	4
α-helix	144-145	2
β-strand	146-150	5	4
β-strand	157-167	11	4
β-strand	172-183	12	4
β-strand	193-204	12	4
β-strand	210-221	12	4

Chain E: 9 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	5
α-helix	6-12	7
β-strand	29-34	6	6
β-strand	36	1	6
β-strand	43-48	6	6
β-strand	50	1	7
β-strand	53	1	7
α-helix	55-66	12
β-strand	74-82	9	6
α-helix	86-97	12
β-strand	102-110	9	6
α-helix	118-121	4
α-helix	126-129	4
β-strand	133-135	3	6
α-helix	138-147	10
β-strand	149	1	5
α-helix	161-169	9
α-helix	170-174	5
α-helix	175-181	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
APOBEC3H	A, E	protein	180	Homo sapiens	Q6NTF7 (AlphaFold model)
RNA (5'-r(upapapapapapapa)-3')	B, F	RNA	8	Escherichia coli
RNA (5'-r(upupupupupupupu)-3')	C, G	RNA	8	Escherichia coli
MCherry fluorescent protein	D, H	protein	219	Discosoma sp.	D1MPT3 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>6BBO_1 APOBEC3H (chains A, E)
LLTAETFRLQFNNKRRLRRPYYPRKALLCYQLTPQNGSTPTRGYFENKKECHAAICFINE
IKSMGLDETQCYQVTCYLTWSPCSSCAWELVDFIKAHDHLNLRIFASRLYYHWCKPQQDG
LRLLCGSQVPVEVMGFPEFADCWENFVDHEKPLSFNPYKMLEELDKNSRAIKRRLDRIKQ

Sequence of entity 2 (B, F), FASTA

>6BBO_2 RNA (5'-R(*UP*AP*AP*AP*AP*AP*AP*A)-3') (chains B, F)
UAAAAAAA

Sequence of entity 3 (C, G), FASTA

>6BBO_3 RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*U)-3') (chains C, G)
UUUUUUUU

Sequence of entity 4 (D, H), FASTA

>6BBO_4 MCherry fluorescent protein (chains D, H)
NMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGTQTAKLKVTKGGPLPFAWDILSP
QFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGEFIYKVK
LRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALKGEIKQRLKLKDGGHYDAEVKTTYKA
KKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERAEGRHS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2

Water and common crystallization additives (GOL) are not listed.

Primary citation

The Antiviral and Cancer Genomic DNA Deaminase APOBEC3H Is Regulated by an RNA-Mediated Dimerization Mechanism. Shaban, N.M., Shi, K., Lauer, K.V. et al. Mol Cell (2018) 69:75-86.e9. DOI 10.1016/j.molcel.2017.12.010 · PubMed

Other PDB entries of the same protein (UniProt Q6NTF7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5W45 2.49 Å, Crystal structure of APOBEC3H
8FVI 3.24 Å, Human APOBEC3H bound to HIV-1 Vif in complex with CBF-beta, ELOB, ELOC, and CUL5
6B0B 3.28 Å, Crystal structure of human APOBEC3H

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