5M6X: Human RhoGAP mutated in its arginine finger

Crystal Structure of human RhoGAP mutated in its arginine finger (R85A) in complex with RhoA.GDP.MgF3- human. Determined by X-ray diffraction at 2.4 Å resolution. Released 17 May 2017.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 6,107
Mol. weight: 98.74 kDa
Ligands: GDP, MGF, MG
Released: 17 May 2017

Explore 5M6X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5M6X contains 54 α-helices and 14 β-strands across 4 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: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	49-55	7
α-helix	64-76	13
α-helix	90-102	13
α-helix	104-106	3
α-helix	108-110	3
α-helix	115-126	12
α-helix	135-137	3
α-helix	138-142	5
α-helix	144-146	3
α-helix	152-161	10
α-helix	165-183	19
α-helix	185-188	4
α-helix	192-203	12
α-helix	209-214	6
α-helix	216-228	13
α-helix	230-233	4

Chain B: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	4-12	9	1
α-helix	18-27	10
β-strand	39-48	10	1
β-strand	51-60	10	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	119-122	4
α-helix	125-133	9
α-helix	138-140	3
α-helix	141-151	11
β-strand	155-158	4	1
α-helix	167-179	13

Chain H: 16 helices, 0 β-strands

Element	Residues	Length
α-helix	49-54	6
α-helix	64-76	13
α-helix	87-89	3
α-helix	90-101	12
α-helix	108-110	3
α-helix	115-126	12
α-helix	135-137	3
α-helix	138-142	5
α-helix	144-146	3
α-helix	152-160	9
α-helix	165-182	18
α-helix	185-188	4
α-helix	192-203	12
α-helix	209-214	6
α-helix	216-228	13
α-helix	230-233	4

Chain I: 11 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	5-12	8	1
α-helix	18-27	10
β-strand	39-47	9	1
β-strand	52-60	9	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
β-strand	160	1	2
β-strand	165	1	2
α-helix	167-178	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Rho GTPase-activating protein 1	A, H	protein	240	Homo sapiens	Q07960 (AlphaFold model)
Transforming protein RhoA	B, I	protein	192	Homo sapiens	P61586 (AlphaFold model)

Sequence of entity 1 (A, H), FASTA

>5M6X_1 Rho GTPase-activating protein 1 (chains A, H)
HVKLEQLGIPRQVLKYDDFLKSTQKSPATAPKPMPPRPPLPNQQFGVSLQHLQEKNPEQE
PIPIVLRETVAYLQAHALTTEGIFARSANTQVVREVQQKYNMGLPVDFDQYNELHLPAVI
LKTFLRELPEPLLTFDLYPHVVGFLNIDESQRVPATLQVLQTLPEENYQVLRFLTAFLVQ
ISAHSDQNKMTNTNLAVVFGPNLLWAKDAAITLKAINPINTFTKFLLDHQGELFPSPDPS

Sequence of entity 2 (B, I), FASTA

>5M6X_2 Transforming protein RhoA (chains B, I)
AAIRKKLVIVGDGACGKTCLLIVNSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTA
GQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDL
RNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQA
RRGKKKSGCLVL

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
MGF	Trifluoromagnesate	F3 Mg	2
MG	Magnesium ion	Mg	2

Primary citation

Assessing the Influence of Mutation on GTPase Transition States by Using X-ray Crystallography, (19) F NMR, and DFT Approaches. Jin, Y., Molt, R.W., Pellegrini, E. et al. Angew Chem Int Ed Engl (2017) 56:9732-9735. DOI 10.1002/anie.201703074 · PubMed

Other PDB entries of the same protein (UniProt Q07960 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1TX4 1.65 Å, RHO/RHOGAP/GDP(DOT)ALF4 complex
6R3V 1.75 Å, Crystal Structure of RhoA-GDP-Pi in Complex with RhoGAP
1OW3 1.8 Å, Crystal Structure of RhoA.GDP.MgF3-in Complex with RhoGAP
2NGR 1.9 Å, Transition state complex for GTP hydrolysis by CDC42: comparisons of the high resolution…
7QSC 1.91 Å, Gtpase in complex with GDP.MGF3-
1RGP 2.0 Å, Gtpase-activation domain from rhogap
1GRN 2.1 Å, Crystal structure of the CDC42/CDC42GAP/ALF3 complex.
5M70 2.2 Å, Crystal Structure of human RhoGAP mutated in its arginin finger (R85A) in complex with…
7QTM 2.25 Å, Transition state analogue of small G protein in complex with relevant GAP
1AM4 2.7 Å, Complex between CDC42HS.GMPPNP and P50 rhogap (H. Sapiens)

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