6V6U: RhoA-GDP with novel Switch I conformation

Crystal structure of RhoA-GDP with novel Switch I conformation. Determined by X-ray diffraction at 1.16 Å resolution. Released 23 Dec 2020.

Method: X-ray diffraction
Resolution: 1.16 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,704
Mol. weight: 21.22 kDa
Ligands: DIO, MG, GDP
Released: 23 Dec 2020

Explore 6V6U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6V6U contains 11 α-helices and 6 β-strands across 1 chain. 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: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	1
α-helix	18-23	6
β-strand	42-48	7	1
β-strand	51-58	8	1
α-helix	64-66	3
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	167-180	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transforming protein RhoA	A	protein	183	Homo sapiens	P61586 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6V6U_1 Transforming protein RhoA (chains A)
GSMAAIRKKLVIVGDGACGKTCLLIVNSKDQFPEVYVPTVFENYVADIEVDGKQVELALW
DTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNK
KDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAA
LQA

Ligands and cofactors

ID	Name	Formula	Copies
DIO	1,4-diethylene dioxide	C4 H8 O2	2
MG	Magnesium ion	Mg	1
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1

Primary citation

Structure of an inactive conformation of GTP-bound RhoA GTPase. Lin, Y., Lu, S., Zhang, J. et al. Structure (2021) 29:553-563.e5. DOI 10.1016/j.str.2020.12.015 · PubMed

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

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
7G8B 1.42 Å, ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z100643660

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