1RE0: ARF1-GDP

Structure of ARF1-GDP bound to Sec7 domain complexed with Brefeldin A. Determined by X-ray diffraction at 2.4 Å resolution. Released 16 Dec 2003.

Method: X-ray diffraction
Resolution: 2.4 Å
Organisms: Homo sapiens, Saccharomyces cerevisiae
Chains: 2
Atoms: 3,062
Mol. weight: 45.18 kDa
Ligands: CIT, AFB, GDP, MG
Released: 16 Dec 2003

Explore 1RE0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1RE0 contains 25 α-helices and 10 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, 8 β-strands

Element	Residues	Length	Sheet
β-strand	19-24	6	1
α-helix	30-38	9
α-helix	46-48	3
β-strand	55-58	4	1
β-strand	61-65	5	1
α-helix	72-78	7
α-helix	79-82	4
β-strand	85-93	9	1
α-helix	100-111	12
α-helix	114-116	3
β-strand	120-126	7	1
α-helix	133-135	3
α-helix	136-142	7
α-helix	145-147	3
β-strand	153-157	5	1
β-strand	159	1	2
β-strand	164	1	2
α-helix	166-178	13

Chain B: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	98-115	18
α-helix	117-126	10
α-helix	135-145	11
α-helix	146-148	3
α-helix	151-158	8
α-helix	161-163	3
α-helix	164-171	8
α-helix	181-188	8
α-helix	198-214	17
α-helix	248-266	19
α-helix	273-275	3
α-helix	276-282	7
β-strand	287	1	3
β-strand	290	1	3
α-helix	291-293	3
α-helix	294-306	13
α-helix	312-314	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
ADP-ribosylation factor 1	A	protein	164	Homo sapiens	P84077 (AlphaFold model)
ARF guanine-nucleotide exchange factor 1	B	protein	221	Saccharomyces cerevisiae	P47102 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1RE0_1 ADP-ribosylation factor 1 (chains A)
MRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPL
WRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVLLVFANKQDLPNAMNAA
EITDKLGLHSLRHRNWYIQATCATSGDGLYEGLDWLSNQLRNQK

Sequence of entity 2 (B), FASTA

>1RE0_2 ARF guanine-nucleotide exchange factor 1 (chains B)
GSHMASDRKTEFILCVETFNEKAKKGIQMLIEKGFIDSDSNRDIASFLFLNNGRLNKKTI
GLLLCDPKKTSLLKEFIDLFDFKGLRVDEAIRILLTKFRLPGESQQIERIVEAFSSKYSA
DQSNDKVELEDKKAGKNGSESMTEDDIIHVQPDADSVFVLSYSIIMLNTDSHNPQVKDHM
TFDDYSNNLRGCYNGKDFPRWYLHKIYTSIKVKEIVMPEEH

Ligands and cofactors

ID	Name	Formula	Copies
CIT	Citric acid	C6 H8 O7	1
AFB	1,6,7,8,9,11A,12,13,14,14A-decahydro-1,13-dihydroxy-6-methyl-4H-cyclopent[f]oxa…	C16 H24 O4	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1
MG	Magnesium ion	Mg	1

Primary citation

Crystal structure of ARF1*Sec7 complexed with Brefeldin A and its implications for the guanine nucleotide exchange mechanism. Mossessova, E., Corpina, R.A., Goldberg, J. Mol Cell (2003) 12:1403-1411. DOI 10.1016/S1097-2765(03)00475-1 · PubMed

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
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
3O47 2.8 Å, Crystal structure of ARFGAP1-ARF1 fusion protein
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

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