3BH6: RP2-Arl3 complex

Crystal structure of the RP2-Arl3 complex bound to GppNHp. Determined by X-ray diffraction at 2.6 Å resolution. Released 25 Mar 2008.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Mus musculus, Homo sapiens
Chains: 2
Atoms: 3,825
Mol. weight: 58.74 kDa
Ligands: GNP, MG
Released: 25 Mar 2008

Explore 3BH6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3BH6 contains 24 α-helices and 28 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: 10 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	18-23	6	1
α-helix	30-37	8
α-helix	45-48	4
β-strand	51-58	8	1
β-strand	61-68	8	1
α-helix	72-81	10
β-strand	87-93	7	1
α-helix	97-99	3
α-helix	100-112	13
α-helix	114-116	3
β-strand	121-126	6	1
α-helix	133-135	3
α-helix	136-142	7
α-helix	145-147	3
β-strand	153-157	5	1
α-helix	166-175	10

Chain B: 14 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	41-43	3	2
β-strand	46	1	2
β-strand	49-52	4	2
β-strand	62-65	4	2
β-strand	68	1	2
β-strand	71-74	4	2
β-strand	78	1	2
β-strand	81-84	4	2
β-strand	87	1	2
β-strand	90-103	14	2
β-strand	106-120	15	2
β-strand	123-131	9	2
β-strand	136-138	3	2
β-strand	141-147	7	2
β-strand	151	1	3
α-helix	155-161	7
β-strand	175-176	2	2
β-strand	186-188	3	2
α-helix	189-190	2
α-helix	195-198	4
α-helix	200-202	3
α-helix	205-208	4
β-strand	213	1	3
α-helix	216-218	3
α-helix	222-223	2
β-strand	235-240	6	4
α-helix	246-259	14
β-strand	263-270	8	4
α-helix	271-273	3
α-helix	274-281	8
α-helix	282-284	3
α-helix	289-291	3
β-strand	297-303	7	4
α-helix	307-318	12
β-strand	324-326	3	4
α-helix	330-348	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ADP-ribosylation factor-like protein 3	A	protein	164	Mus musculus	Q9WUL7 (AlphaFold model)
Protein XRP2	B	protein	352	Homo sapiens	O75695 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3BH6_1 ADP-ribosylation factor-like protein 3 (chains A)
GGSEVRILLLGLDNAGKTTLLKQLASEDISHITPTQGFNIKSVQSQGFKLNVWDIGGLRK
IRPYWRSYFENTDILIYVIDSADRKRFEETGQELTELLEEEKLSCVPVLIFANKQDLLTA
APASEIAEGLNLHTIRDRVWQIQSCSALTGEGVQDGMNWVCKNV

Sequence of entity 2 (B), FASTA

>3BH6_2 Protein XRP2 (chains B)
GSMGCFFSKRRKADKESRPENEEERPKQYSWDQREKVDPKDYMFSGLKDETVGRLPGTVA
GQQFLIQDCENCNIYIFDHSATVTIDDCTNCIIFLGPVKGSVFFRNCRDCKCTLACQQFR
VRDCRKLEVFLCCATQPIIESSSNIKFGCFQWYYPELAFQFKDAGLSIFNNTWSNIHDFT
PVSGELNWSLLPEDAVVQDYVPIPTTEELKAVRVSTEANRSIVPISRGQRQKSSDESCLV
VLFAGDYTIANARKLIDEMVGKGFFLVQTKEVSMKAEDAQRVFREKAPDFLPLLNKGPVI
ALEFNGDGAVEVCQLIVNEIFNGTKMFVSESKETASGDVDSFYNFADIQMGI

Ligands and cofactors

ID	Name	Formula	Copies
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	1
MG	Magnesium ion	Mg	1

Primary citation

The retinitis pigmentosa 2 gene product is a GTPase-activating protein for Arf-like 3. Veltel, S., Gasper, R., Eisenacher, E. et al. Nat Struct Mol Biol (2008) 15:373-380. DOI 10.1038/nsmb.1396 · PubMed

Other PDB entries of the same protein (UniProt Q9WUL7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1FZQ 1.7 Å, Crystal structure of murine ARL3-GDP
3BH7 1.9 Å, Crystal structure of the RP2-Arl3 complex bound to GDP-AlF4
4ZI3 2.0 Å, BART-like domain of BARTL1/CCDC104 aa1-133 in complex with Arl3FL bound to GppNHp in P1…
4GOJ 2.1 Å, The Crystal Structure of full length Arl3GppNHp in complex with UNC119a
4ZI2 2.2 Å, BART-like domain of BARTL1/CCDC104 in complex with Arl3FL bound to GppNHp in P21 21 21
7OK7 3.15 Å, Crystal structure of the UNC119B ARL3 complex

Browse structure collections

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