6AXF: RasGRP2

Structure of RasGRP2 in complex with Rap1B. Determined by X-ray diffraction at 3.1 Å resolution. Released 11 Oct 2017.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 16
Atoms: 34,903
Mol. weight: 520.24 kDa
Released: 11 Oct 2017

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

Secondary structure: helices and β-sheets

6AXF contains 252 α-helices and 128 β-strands across 16 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, 9 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	1
α-helix	13-22	10
β-strand	24	1	2
β-strand	30	1	2
α-helix	33-42	10
α-helix	43-45	3
α-helix	49-65	17
α-helix	69-85	17
α-helix	87-92	6
α-helix	94-106	13
α-helix	107-111	5
α-helix	116-118	3
α-helix	129-132	4
β-strand	137-138	2	3
α-helix	145-150	6
α-helix	155-170	16
α-helix	175-184	10
α-helix	191-212	22
α-helix	217-236	20
β-strand	239	1	4
α-helix	240-250	11
α-helix	253-256	4
α-helix	259-263	5
α-helix	267-279	13
α-helix	287-294	8
β-strand	301	1	4
α-helix	306-317	12
β-strand	321	1	5
β-strand	328	1	1
β-strand	329	1	5
α-helix	331-346	16
α-helix	347-349	3
α-helix	358-369	12
α-helix	374-384	11

Chain B: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	6
α-helix	12-14	3
α-helix	16-24	9
α-helix	37-39	3
β-strand	41-46	6	6
β-strand	49-57	9	6
α-helix	65-74	10
β-strand	77-83	7	6
α-helix	87-91	5
α-helix	93-103	11
β-strand	111-116	6	6
α-helix	121-123	3
α-helix	128-137	10
β-strand	142-145	4	6
β-strand	147	1	7
β-strand	152	1	7
α-helix	154-166	13

Chain C: 25 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	11-12	2	8
α-helix	13-22	10
β-strand	24	1	9
β-strand	30	1	9
α-helix	33-42	10
α-helix	43-45	3
α-helix	49-64	16
α-helix	65-67	3
α-helix	69-85	17
α-helix	87-92	6
α-helix	94-109	16
α-helix	116-118	3
α-helix	128-130	3
β-strand	135-136	2	3
α-helix	142-150	9
α-helix	155-170	16
α-helix	175-184	10
α-helix	191-212	22
α-helix	217-236	20
β-strand	239	1	10
α-helix	240-250	11
α-helix	253-256	4
α-helix	259-263	5
α-helix	267-279	13
α-helix	287-295	9
β-strand	301	1	10
α-helix	306-317	12
β-strand	321	1	8
β-strand	328-329	2	8
α-helix	331-346	16
α-helix	347-349	3
α-helix	358-369	12
α-helix	374-384	11

Chain D: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	11
α-helix	16-24	9
α-helix	37-40	4
β-strand	41-46	6	11
β-strand	49-57	9	11
α-helix	65-74	10
β-strand	77-83	7	11
α-helix	88-91	4
α-helix	93-103	11
β-strand	111-116	6	11
α-helix	121-123	3
α-helix	128-137	10
β-strand	142-145	4	11
β-strand	147	1	12
β-strand	152	1	12
α-helix	154-166	13

Chain E: 24 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	13
α-helix	13-22	10
β-strand	24	1	14
β-strand	30	1	14
α-helix	33-42	10
α-helix	43-45	3
α-helix	49-66	18
α-helix	69-85	17
α-helix	87-92	6
α-helix	94-109	16
α-helix	113-116	4
α-helix	127-129	3
α-helix	133-135	3
α-helix	145-152	8
α-helix	155-170	16
α-helix	175-184	10
α-helix	191-213	23
α-helix	217-236	20
β-strand	239	1	15
α-helix	240-250	11
α-helix	253-256	4
α-helix	259-264	6
α-helix	267-279	13
α-helix	283-295	13
β-strand	301	1	15
α-helix	306-317	12
β-strand	321	1	16
β-strand	328	1	13
β-strand	329	1	16
α-helix	331-346	16
α-helix	358-368	11
α-helix	374-384	11

Chain F: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	17
α-helix	16-24	9
α-helix	37-39	3
β-strand	41-46	6	17
β-strand	49-57	9	17
α-helix	65-74	10
β-strand	77-83	7	17
α-helix	88-91	4
α-helix	93-103	11
β-strand	111-116	6	17
α-helix	128-137	10
β-strand	142-145	4	17
β-strand	147	1	18
β-strand	152	1	18
α-helix	154-165	12

Chain G: 23 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	12	1	19
α-helix	13-22	10
β-strand	24	1	20
β-strand	30	1	20
α-helix	33-42	10
α-helix	43-45	3
α-helix	49-65	17
α-helix	69-85	17
α-helix	87-92	6
α-helix	94-109	16
α-helix	129-132	4
α-helix	145-152	8
α-helix	155-170	16
α-helix	175-184	10
α-helix	191-212	22
α-helix	217-236	20
β-strand	239	1	21
α-helix	240-250	11
α-helix	253-256	4
α-helix	259-262	4
α-helix	267-279	13
α-helix	287-294	8
β-strand	301	1	21
α-helix	306-317	12
β-strand	321	1	22
β-strand	328	1	19
β-strand	329	1	22
α-helix	331-346	16
α-helix	347-349	3
α-helix	358-369	12
α-helix	374-384	11

Chain H: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	2-10	9	23
α-helix	16-24	9
α-helix	37-40	4
β-strand	41-46	6	23
β-strand	49-57	9	23
α-helix	65-74	10
β-strand	77-83	7	23
α-helix	87-91	5
α-helix	93-103	11
β-strand	111-116	6	23
α-helix	121-123	3
α-helix	128-137	10
β-strand	142-145	4	23
β-strand	147	1	24
β-strand	152	1	24
α-helix	154-166	13

8 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RAS guanyl-releasing protein 2	A, C, E, G, I, K, M, O	protein	397	Homo sapiens	Q7LDG7 (AlphaFold model)
Ras-related protein Rap-1b	B, D, F, H, J, L, N, P	protein	169	Homo sapiens	P61224 (AlphaFold model)

Sequence of entity 1 (A, C, E, G, I, K, M, O), FASTA

>6AXF_1 RAS guanyl-releasing protein 2 (chains A, C, E, G, I, K, M, O)
SNAMAGTLDLDKGCTVEELLRGCIEAFDDSGKVRDPQLVRMFLMMHPWYIPSSQLAAKLL
HIYQQSRKDNSNSLQVKTCHLVRYWISAFPAEFDLNPELAEQIKELKALLDQEGNRRHSS
LIDIDSVPTYKWKRQVTQRNPVGQKKRKMSLLFDHLEPMELAEHLTYLEYRSFCKILFQD
YHSFVTHGCTVDNPVLERFISLFNSVSQWVQLMILSKPTAPQRALVITHFVHVAEKLLQL
QNFNTLMAVVGGLSHSSISRLKETHSHVSPETIKLWEGLTELVTATGNYGNYRRRLAACV
GFRFPILGVHLKDLVALQLALPDWLDPARTRLNGAKMKQLFSILEELAMVTSLRPPVQAN
PDLLSLLTVSLDQYQTEDELYQLSLQREPRSKSSPTS

Sequence of entity 2 (B, D, F, H, J, L, N, P), FASTA

>6AXF_2 Ras-related protein Rap-1b (chains B, D, F, H, J, L, N, P)
GAMREYKLVVLGSGGVGKSALTVQFVQGIFVEKYDPTIEDSYRKQVEVDAQQCMLEILDT
AGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLREQILRVKDTDDVPMILVGNKC
DLEDERVVGKEQGQNLARQWNNCAFLESSAKSKINVNEIFYDLVRQINR

Primary citation

A histidine pH sensor regulates activation of the Ras-specific guanine nucleotide exchange factor RasGRP1. Vercoulen, Y., Kondo, Y., Iwig, J.S. et al. Elife (2017) 6. DOI 10.7554/eLife.29002 · PubMed

Other PDB entries of the same protein (UniProt Q7LDG7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2MA2 Solution structure of RasGRP2 EF hands bound to calcium

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