3O47: ARFGAP1-ARF1 fusion protein

Crystal structure of ARFGAP1-ARF1 fusion protein. Determined by X-ray diffraction at 2.8 Å resolution. Released 11 Aug 2010.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,504
Mol. weight: 76.91 kDa
Ligands: ZN, GDP
Released: 11 Aug 2010

Explore 3O47 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3O47 contains 29 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: 14 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	6-15	10
β-strand	21	1	1
β-strand	28	1	1
β-strand	32-34	3	2
α-helix	35-37	3
β-strand	39-41	3	2
α-helix	43-52	10
β-strand	59-61	3	2
α-helix	69-77	9
α-helix	80-88	9
α-helix	99-104	6
α-helix	106-119	14
β-strand	148-154	7	3
α-helix	160-166	7
β-strand	173-178	6	3
β-strand	181-188	8	3
β-strand	191-197	7	3
α-helix	208-212	5
β-strand	215-223	9	3
α-helix	230-241	12
α-helix	244-246	3
β-strand	250-256	7	3
α-helix	263-265	3
α-helix	266-273	8
β-strand	283-287	5	3
β-strand	289	1	4
β-strand	294	1	4
α-helix	296-307	12

Chain B: 15 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	4-15	12
β-strand	21	1	5
β-strand	28	1	5
β-strand	32-34	3	6
α-helix	35-37	3
β-strand	39-41	3	6
α-helix	43-50	8
β-strand	59-61	3	6
α-helix	69-77	9
α-helix	80-88	9
α-helix	99-104	6
α-helix	106-119	14
β-strand	148-154	7	7
α-helix	160-167	8
β-strand	173-178	6	7
β-strand	181-188	8	7
β-strand	191-197	7	7
α-helix	208-212	5
β-strand	217-223	7	7
α-helix	230-241	12
α-helix	244-246	3
α-helix	249	1
β-strand	250-256	7	7
α-helix	263-265	3
α-helix	266-273	8
β-strand	283-287	5	7
β-strand	289	1	8
β-strand	294	1	8
α-helix	296-307	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ADP-ribosylation factor GTPase-activating protein 1, ADP-ribosylation factor 1	A, B	protein	329	Homo sapiens	P84077 (AlphaFold model), Q8N6T3 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3O47_1 ADP-ribosylation factor GTPase-activating protein 1, ADP-ribosylation factor 1 (chains A, B)
MHHHHHHSSGRENLYFQGMASPRTRKVLKEVRVQDENNVCFECGAFNPQWVSVTYGIWIC
LECSGRHRGLGVHLSFVRSVTMDKWKDIELEKMKAGGNAKFREFLESQEDYDPCWSLQEK
YNSRAAALFRDKVVALAEGREWSLESSPAQNWTPPQPRGLFGKKEMRILMVGLDAAGKTT
ILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVV
DSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAAEITDKLGLHSLRHRN
WYIQATCATSGDGLYEGLDWLSNQLRNQK

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2

Primary citation

Crystal structure of ARFGAP1-ARF1 fusion protein. Wang, H., Tong, Y., Nedyalkova, L. et al. To be published.

Other PDB entries of the same protein (UniProt P84077 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8SDW 1.75 Å, Crystal structure of the non-myristoylated mutant [L8K]Arf1 in complex with a GDP analogue
1HUR 2.0 Å, Human ADP-ribosylation factor 1 complexed with GDP, full length non-myristoylated
7R4H 2.34 Å, phospho-STING binding to adaptor protein complex-1
6FAE 2.35 Å, The Sec7 domain of IQSEC2 (Brag1) in complex with the small GTPase Arf1
1RE0 2.4 Å, Structure of ARF1-GDP bound to Sec7 domain complexed with Brefeldin A
9QLO 2.47 Å, NMT1-NAC bound human RNC with full length ARF1 - State 1
9QLQ 2.57 Å, NMT1-NAC bound human RNC with full length ARF1 - alternative State
7DN8 2.61 Å, Crystal structure of Salmonella effector SopF in complex with ARF1
9QLP 2.75 Å, NMT1-NAC bound human RNC with full length ARF1 - State 2
7DN9 3.29 Å, Crystal structure of Salmonella effector in complex with NAD and host co-factor ARF1
6CM9 3.73 Å, Structure of the cargo bound AP-1:Arf1:tetherin-Nef closed trimer monomeric subunit
6DFF 3.9 Å, Structure of the cargo bound AP-1:Arf1:tetherin-Nef monomer

Browse structure collections

About this viewer

MolViewer shows 3O47 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.