5M70: Human RhoGAP mutated in its arginin finger

Crystal Structure of human RhoGAP mutated in its arginin finger (R85A) in complex with RhoA.GDP.AlF4- human. Determined by X-ray diffraction at 2.2 Å resolution. Released 17 May 2017.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,933
Mol. weight: 98.79 kDa
Ligands: ALF, GDP, MG
Released: 17 May 2017

Explore 5M70 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5M70 contains 55 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: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	49-55	7
α-helix	64-76	13
α-helix	90-101	12
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	149-151	3
α-helix	152-160	9
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, 8 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	1
α-helix	18-26	9
β-strand	39-46	8	1
β-strand	53-60	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
β-strand	160	1	2
β-strand	165	1	2
α-helix	167-178	12

Chain F: 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 G: 11 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	6-12	7	1
α-helix	18-27	10
β-strand	39-46	8	1
β-strand	53-60	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	119-122	4
α-helix	125-132	8
α-helix	138-140	3
α-helix	141-151	11
β-strand	155-158	4	1
α-helix	167-178	12

Molecules and chains

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

Sequence of entity 1 (A, F), FASTA

>5M70_1 Rho GTPase-activating protein 1 (chains A, F)
HVKLEQLGIPRQVLKYDDFLKSTQKSPATAPKPMPPRPPLPNQQFGVSLQHLQEKNPEQE
PIPIVLRETVAYLQAHALTTEGIFARSANTQVVREVQQKYNMGLPVDFDQYNELHLPAVI
LKTFLRELPEPLLTFDLYPHVVGFLNIDESQRVPATLQVLQTLPEENYQVLRFLTAFLVQ
ISAHSDQNKMTNTNLAVVFGPNLLWAKDAAITLKAINPINTFTKFLLDHQGELFPSPDPS

Sequence of entity 2 (B, G), FASTA

>5M70_2 Transforming protein RhoA (chains B, G)
AAIRKKLVIVGDGACGKTCLLIVNSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTA
GQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDL
RNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQA
RRGKKKSGCLVL

Ligands and cofactors

ID	Name	Formula	Copies
ALF	Tetrafluoroaluminate ion	Al F4	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	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.
7QTM 2.25 Å, Transition state analogue of small G protein in complex with relevant GAP
5M6X 2.4 Å, Crystal Structure of human RhoGAP mutated in its arginine finger (R85A) in complex with…
1AM4 2.7 Å, Complex between CDC42HS.GMPPNP and P50 rhogap (H. Sapiens)

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