5JCP: RhoGAP domain of ARAP3

RhoGAP domain of ARAP3 in complex with RhoA in the transition state. Determined by X-ray diffraction at 2.1 Å resolution. Released 22 Jun 2016.

Method: X-ray diffraction
Resolution: 2.1 Å
Organisms: Homo sapiens, synthetic construct
Chains: 2
Atoms: 5,841
Mol. weight: 95.41 kDa
Ligands: GDP, ALF, MG
Released: 22 Jun 2016

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

Secondary structure: helices and β-sheets

5JCP contains 50 α-helices and 16 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: 25 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	909-911	3
β-strand	914	1	3
β-strand	920	1	3
α-helix	921-933	13
α-helix	947-960	14
α-helix	961-963	3
α-helix	973-986	14
α-helix	994-996	3
α-helix	997-1004	8
α-helix	1009-1021	13
α-helix	1025-1043	19
α-helix	1045-1048	4
α-helix	1052-1064	13
α-helix	1071-1082	12
α-helix	1084-1087	4
α-helix	1092-1100	9
β-strand	4-12	9	4
α-helix	18-25	8
β-strand	42-48	7	4
β-strand	51-58	8	4
α-helix	64-66	3
α-helix	70-73	4
β-strand	79-85	7	4
α-helix	89-94	6
α-helix	95-99	5
α-helix	100-106	7
β-strand	112-117	6	4
α-helix	119-121	3
α-helix	125-133	9
α-helix	138-140	3
α-helix	141-151	11
β-strand	155-158	4	4
α-helix	167-179	13

Chain B: 25 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	909-911	3
β-strand	914	1	1
β-strand	920	1	1
α-helix	921-933	13
α-helix	947-960	14
α-helix	961-963	3
α-helix	973-986	14
α-helix	994-996	3
α-helix	997-1004	8
α-helix	1009-1022	14
α-helix	1025-1043	19
α-helix	1045-1048	4
α-helix	1052-1064	13
α-helix	1071-1082	12
α-helix	1084-1087	4
α-helix	1092-1099	8
β-strand	4-12	9	2
α-helix	18-25	8
β-strand	42-48	7	2
β-strand	51-58	8	2
α-helix	64-66	3
α-helix	70-73	4
β-strand	79-85	7	2
α-helix	89-94	6
α-helix	95-99	5
α-helix	100-106	7
β-strand	112-117	6	2
α-helix	119-121	3
α-helix	125-133	9
α-helix	138-140	3
α-helix	141-151	11
β-strand	155-158	4	2
α-helix	167-179	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3,Linker,Transforming…	A, B	protein	419	Homo sapiens, synthetic construct	P61586 (AlphaFold model), Q8WWN8 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5JCP_1 Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3,Linker,Transforming protein RhoA (chains A, B)
MGHHHHHHMGTGLQEQQMSRGDIPIIVDACISFVTQHGLRLEGVYRKGGARARSLRLLAE
FRRDARSVKLRPGEHFVEDVTDTLKRFFRELDDPVTSARLLPRWREAAELPQKNQRLEKY
KDVIGCLPRVNRRTLATLIGHLYRVQKCAALNQMCTRNLALLFAPSVFQTDGRGEHEVRV
LQELIDGYISVFDIDSDQVAQIDLEVSLITTNLSSDSSLSSPSALNSTASNSPGIEGLSA
AIRKKLVIVGDGACGKTCLLIVNSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAG
QEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLR
NDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQA

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
ALF	Tetrafluoroaluminate ion	Al F4	2
MG	Magnesium ion	Mg	2

Primary citation

Structural Basis for the Specific Recognition of RhoA by the Dual GTPase-activating Protein ARAP3. Bao, H., Li, F., Wang, C. et al. J Biol Chem (2016) 291:16709-16719. DOI 10.1074/jbc.M116.736140 · PubMed

Other PDB entries of the same protein (UniProt P61586 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6V6U 1.16 Å, Crystal structure of RhoA-GDP with novel Switch I conformation
5C4M 1.3 Å, RhoA GDP with novel switch II conformation
7G83 1.31 Å, ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z108545814
7G8T 1.39 Å, ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1273312142
6V6M 1.39 Å, Crystal structure of an inactive state of GMPPNP-bound RhoA
6V6V 1.4 Å, Crystal structure of oncogenic RhoA mutant G14V complexed with GDP
8BNT 1.4 Å, The DH domain of ARHGEF2 bound to RhoA
8FPW 1.4 Å, Crystal structure of tumor related RhoA mutant A161V in complex with GDP
8GI6 1.4 Å, Crystal structure of RhoA mutant L69R complexed with GDP
6BCB 1.4 Å, A Complex between PH Domain of p114RhoGEF and Activated RhoA Bound to a GTP Analog
7G82 1.41 Å, ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1079512010
5C2K 1.42 Å, Crystal structure of the fusion protein linked by RhoA and the GAP domain of MgcRacGAP

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