6S6D: Ras-related GTP-binding protein A

Crystal structure of RagA-Q66L-GTP/RagC-S75N-GDP GTPase heterodimer complex. Determined by X-ray diffraction at 2.5 Å resolution. Released 16 Oct 2019.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,584
Mol. weight: 163.99 kDa
Ligands: GTP, MG, GDP, 9JE
Released: 16 Oct 2019

Explore 6S6D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6S6D contains 45 α-helices and 42 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: 11 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	6-13	8	1
α-helix	20-28	9
α-helix	33-38	6
β-strand	45-53	9	1
β-strand	56-63	8	1
α-helix	67-73	7
α-helix	78-82	5
β-strand	85-93	9	1
α-helix	99-116	18
β-strand	121-127	7	1
α-helix	129-131	3
α-helix	134-151	18
β-strand	158-161	4	1
α-helix	168-178	11
α-helix	184-198	15
β-strand	202-207	6	2
β-strand	213-218	6	2
α-helix	227-245	19
β-strand	249-256	8	2
β-strand	259-265	7	2
β-strand	270-276	7	2
α-helix	283-298	16

Chain B: 12 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	6-14	9	4
α-helix	20-28	9
α-helix	34-36	3
β-strand	45-46	2	4
β-strand	49-52	4	4
β-strand	56-63	8	4
α-helix	67-74	8
α-helix	78-82	5
β-strand	85-93	9	4
α-helix	99-116	18
β-strand	121-127	7	4
α-helix	129-131	3
α-helix	134-136	3
α-helix	137-151	15
β-strand	158-162	5	4
α-helix	168-178	11
α-helix	184-197	14
β-strand	202-207	6	5
β-strand	213-218	6	5
α-helix	227-244	18
β-strand	249-255	7	5
β-strand	260-265	6	5
β-strand	270-276	7	5
α-helix	283-299	17

Chain C: 10 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	63-67	5	3
α-helix	74-82	9
α-helix	88-91	4
β-strand	111-114	4	3
β-strand	139-145	7	3
α-helix	151-167	17
β-strand	172-178	7	3
α-helix	180-182	3
α-helix	185-205	21
β-strand	213-217	5	3
α-helix	224-235	12
α-helix	240-252	13
β-strand	258-263	6	2
β-strand	268-272	5	2
α-helix	279-298	20
β-strand	315-320	6	2
β-strand	324-330	7	2
β-strand	335-342	8	2
α-helix	343-346	4
α-helix	349-366	18

Chain D: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	61-63	3
β-strand	65-68	4	6
α-helix	74-81	8
α-helix	134-136	3
β-strand	139-145	7	6
α-helix	155-161	7
α-helix	163-167	5
β-strand	172-178	7	6
α-helix	186-201	16
α-helix	212	1
β-strand	213-217	5	6
α-helix	224-234	11
α-helix	240-254	15
β-strand	259-263	5	5
β-strand	269-271	3	5
α-helix	279-298	20
β-strand	315-320	6	5
β-strand	324-330	7	5
β-strand	335-342	8	5
α-helix	343-347	5
α-helix	349-366	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related GTP-binding protein A	A, B	protein	313	Homo sapiens	Q7L523 (AlphaFold model)
Ras-related GTP-binding protein C	C, D	protein	399	Homo sapiens	Q9HB90 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6S6D_1 Ras-related GTP-binding protein A (chains A, B)
MPNTAMKKKVLLMGKSGSGKTSMRSIIFANYIARDTRRLGATIDVEHSHVRFLGNLVLNL
WDCGGLDTFMENYFTSQRDNIFRNVEVLIYVFDVESRELEKDMHYYQSCLEAILQNSPDA
KIFCLVHKMDLVQEDQRDLIFKEREEDLRRLSRPLECACFRTSIWDETLYKAWSSIVYQL
IPNVQQLEMNLRNFAQIIEADEVLLFERATFLVISHYQCKEQRDVHRFEKISNIIKQFKL
SCSKLAASFQSMEVRNSNFAAFIDIFTSNTYVMVVMSDPSIPSAATLINIRNARKHFEKL
ERVDGPKHSLLMR

Sequence of entity 2 (C, D), FASTA

>6S6D_2 Ras-related GTP-binding protein C (chains C, D)
MSLQYGAEETPLAGSYGAADSFPKDFGYGVEEEEEEAAAAGGGVGAGAGGGCGPGGADSS
KPRILLMGLRRSGKNSIQKVVFHKMSPNETLFLESTNKIYKDDISNSSFVNFQIWDFPGQ
MDFFDPTFDYEMIFRGTGALIYVIDAQDDYMEALTRLHITVSKAYKVNPDMNFEVFIHKV
DGLSDDHKIETQRDIHQRANDDLADAGLEKLHLSFYLTSIYDHSIFEAFSKVVQKLIPQL
PTLENLLNIFISNSGIEKAFLFDVVSKIYIATDSSPVDMQSYELCCDMIDVVIDVSCIYG
LKEDGSGSAYDKESMAIIKLNNTTVLYLKEVTKFLALVCILREESFERKGLIDYNFHCFR
KAIHEVFEVGVTSHRSCGHQTSASSLKALTHNGTPRNAI

Ligands and cofactors

ID	Name	Formula	Copies
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2
MG	Magnesium ion	Mg	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
9JE	pentane-1,5-diol	C5 H12 O2	2

Primary citation

Architecture of human Rag GTPase heterodimers and their complex with mTORC1. Anandapadamanaban, M., Masson, G.R., Perisic, O. et al. Science (2019) 366:203-210. DOI 10.1126/science.aax3939 · PubMed

Other PDB entries of the same protein (UniProt Q7L523 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5X6V 2.02 Å, Crystal structure of human heteroheptameric complex
6S6A 2.63 Å, Crystal structure of RagA-Q66L/RagC-T90N GTPase heterodimer complex
6EHR 2.9 Å, The crystal structure of the human LAMTOR-RagA CTD-RagC CTD complex
7UX2 2.9 Å, cryo-EM structure of the Raptor-TFEB-Rag-Ragulator complex
6U62 3.18 Å, Raptor-Rag-Ragulator complex
6WJ2 3.2 Å, CryoEM structure of the SLC38A9-RagA-RagC-Ragulator complex in the pre-GAP state
7UXC 3.2 Å, cryo-EM structure of the mTORC1-TFEB-Rag-Ragulator complex with symmetry expansion
7UXH 3.2 Å, cryo-EM structure of the mTORC1-TFEB-Rag-Ragulator complex
9ED4 3.23 Å, A composite map of mTORC1-Rag-Ragultor-4EBP1 on membrane
6ULG 3.31 Å, Cryo-EM structure of the FLCN-FNIP2-Rag-Ragulator complex
8DHB 3.53 Å, Active FLCN GAP complex
6NZD 3.6 Å, Cryo-EM Structure of the Lysosomal Folliculin Complex (FLCN-FNIP2-RagA-RagC-Ragulator)

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