4D0N: AKAP13 (AKAP-Lbc) RhoGEF domain

AKAP13 (AKAP-Lbc) RhoGEF domain in complex with RhoA. Determined by X-ray diffraction at 2.1 Å resolution. Released 21 May 2014.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 4,613
Mol. weight: 65.35 kDa
Ligands: GDP
Released: 21 May 2014

Explore 4D0N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4D0N contains 31 α-helices and 19 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	5-12	8	1
α-helix	18-26	9
β-strand	42-48	7	1
β-strand	51-59	9	1
α-helix	70-73	4
β-strand	79-85	7	1
α-helix	89-94	6
α-helix	95-99	5
α-helix	100-106	7
β-strand	112-117	6	1
α-helix	119-121	3
α-helix	125-132	8
α-helix	138-140	3
α-helix	141-151	11
β-strand	155-158	4	1
α-helix	167-179	13

Chain B: 21 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	1971-1974	4
α-helix	1980-1983	4
α-helix	1986-1990	5
α-helix	1994-2019	26
α-helix	2020-2025	6
α-helix	2026-2031	6
α-helix	2036-2042	7
α-helix	2046-2065	20
β-strand	2068	1	2
β-strand	2076	1	2
α-helix	2082-2088	7
α-helix	2091-2121	31
α-helix	2123-2131	9
α-helix	2132-2136	5
α-helix	2139-2141	3
α-helix	2143-2153	11
α-helix	2154-2156	3
α-helix	2157-2167	11
α-helix	2172-2211	40
β-strand	2212	1	3
β-strand	2217-2219	3	4
β-strand	2225-2227	3	4
α-helix	2228-2230	3
β-strand	2236-2245	10	3
β-strand	2251-2259	9	3
β-strand	2262-2269	8	3
β-strand	2272-2275	4	3
α-helix	2276-2277	2
β-strand	2284-2286	3	3
β-strand	2290-2294	5	3
α-helix	2295	1
β-strand	2301-2306	6	3
β-strand	2314-2318	5	3
α-helix	2322-2339	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transforming protein rhoa	A	protein	185	HOMO SAPIENS	P61586 (AlphaFold model)
A-kinase anchor protein 13	B	protein	373	HOMO SAPIENS	Q12802 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4D0N_1 TRANSFORMING PROTEIN RHOA (chains A)
SMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWD
TAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKK
DLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAAL
QARRG

Sequence of entity 2 (B), FASTA

>4D0N_2 A-KINASE ANCHOR PROTEIN 13 (chains B)
SMSKQLEAESWSRIIDSKFLKQQKKDVVKRQEVIYELMQTEFHHVRTLKIMSGVYSQGMM
ADLLFEQQMVEKLFPCLDELISIHSQFFQRILERKKESLVDKSEKNFLIKRIGDVLVNQF
SGENAERLKKTYGKFCGQHNQSVNYFKDLYAKDKRFQAFVKKKMSSSVVRRLGIPECILL
VTQRITKYPVLFQRILQCTKDNEVEQEDLAQSLSLVKDVIGAVDSKVASYEKKVRLNEIY
TKTDSKSIMRMKSGQMFAKEDLKRKKLVRDGSVFLKNAAGRLKEVQAVLLTDILVFLQEK
DQKYIFASLDQKSTVISLKKLIVREVAHEEKGLFLISMGMTDPEMVEVHASSKEERNSWI
QIIQDTINTLNRD

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1

Water and common crystallization additives (SO4, EDO) are not listed.

Primary citation

The Crystal Structure of the Rhoa : Akap-Lbc Dh-Ph Domain Complex. Abdul Azeez, K.R., Knapp, S., Fernandes, J.M.P. et al. Biochem J (2014) 464:231. DOI 10.1042/BJ20140606 · 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

Browse structure collections

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