5X6U: Human heteropentameric complex

Crystal structure of human heteropentameric complex. Determined by X-ray diffraction at 2.4 Å resolution. Released 6 Dec 2017.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Homo sapiens
Chains: 5
Atoms: 3,929
Mol. weight: 61.17 kDa
Released: 6 Dec 2017

Explore 5X6U in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5X6U contains 21 α-helices and 20 β-strands across 5 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: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	1-12	12
α-helix	13-15	3
β-strand	19-25	7	1
β-strand	31-36	6	1
α-helix	42-45	4
α-helix	47-50	4
α-helix	52-60	9
β-strand	68-75	8	1
β-strand	78-85	8	1
β-strand	88-95	8	1
α-helix	100-117	18
α-helix	118-120	3

Chain B: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	7-12	6
β-strand	19-26	8	1
β-strand	31-36	6	1
α-helix	42-59	18
β-strand	69-76	8	1
β-strand	79-86	8	1
β-strand	89-95	7	1
α-helix	101-124	24

Chain C: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-12	10
β-strand	18-24	7	2
β-strand	30-35	6	2
α-helix	39-41	3
α-helix	42-53	12
β-strand	64-68	5	2
β-strand	72-79	8	2
β-strand	82-89	8	2

Chain D: 2 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	3-10	8
β-strand	15-21	7	2
β-strand	26-31	6	2
α-helix	37-52	16
β-strand	65-69	5	2
β-strand	73-80	8	2
β-strand	83-90	8	2

Chain E: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	80-93	14
α-helix	100-104	5
α-helix	115-120	6
α-helix	123-125	3
α-helix	126-142	17
α-helix	143-145	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ragulator complex protein LAMTOR3	A	protein	127	Homo sapiens	Q9UHA4 (AlphaFold model)
Ragulator complex protein LAMTOR2	B	protein	125	Homo sapiens	Q9Y2Q5 (AlphaFold model)
Ragulator complex protein LAMTOR5	C	protein	91	Homo sapiens	O43504 (AlphaFold model)
Ragulator complex protein LAMTOR4	D	protein	99	Homo sapiens	Q0VGL1 (AlphaFold model)
Ragulator complex protein LAMTOR1	E	protein	123	Homo sapiens	Q6IAA8

Sequence of entity 1 (A), FASTA

>5X6U_1 Ragulator complex protein LAMTOR3 (chains A)
MGSSADDLKRFLYKKLPSVEGLHAIVVSDRDGVPVIKVANDNAPEHALRPGFLSTFALAT
DQGSKLGLSKNKSIICYYNTYQVVQFNRLPLVVSFIASSSANTGLIVSLEKELAPLFEEL
RQVVEVS

Sequence of entity 2 (B), FASTA

>5X6U_2 Ragulator complex protein LAMTOR2 (chains B)
MLRPKALTQVLSQANTGGVQSTLLLNNEGSLLAYSGYGDTDARVTAAIASNIWAAYDRNG
NQAFNEDNLKFILMDCMEGRVAITRVANLLLCMYAKETVGFGMLKAKAQALVQYLEEPLT
QVAAS

Sequence of entity 3 (C), FASTA

>5X6U_3 Ragulator complex protein LAMTOR5 (chains C)
MEATLEQHLEDTMKNPSIVGVLCTDSQGLNLGCRGTLSDEHAGVISVLAQQAAKLTSDPT
DIPVVCLESDNGNIMIQKHDGITVAVHKMAS

Sequence of entity 4 (D), FASTA

>5X6U_4 Ragulator complex protein LAMTOR4 (chains D)
MTSALTQGLERIPDQLGYLVLSEGAVLASSGDLENDEQAASAISELVSTACGFRLHRGMN
VPFKRLSVVFGEHTLLVTVSGQRVFVVKRQNRGREPIDV

Sequence of entity 5 (E), FASTA

>5X6U_5 Ragulator complex protein LAMTOR1 (chains E)
GAASLPSARTDEQALLSSILAKTASNIIDVSAADSQGMEQHEYMDRARQYSTRLAVLSSD
LTHWKKLPPLPSLTSQPHQVLASEPIPFSDLQQVSRIAAYAYSALSQIRVDAKEELVVQF
GIP

Primary citation

Structural basis for the assembly of the Ragulator-Rag GTPase complex. Yonehara, R., Nada, S., Nakai, T. et al. Nat Commun (2017) 8:1625-1625. DOI 10.1038/s41467-017-01762-3 · PubMed

Other PDB entries of the same protein (UniProt Q9UHA4 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6B9X 1.42 Å, Crystal structure of Ragulator
3CPT 1.9 Å, MP1-p14 Scaffolding complex
1SKO 2.0 Å, MP1-p14 Complex
2ZL1 2.0 Å, MP1-p14 Scaffolding complex
5X6V 2.02 Å, Crystal structure of human heteroheptameric complex
6EHP 2.3 Å, The crystal structure of the human LAMTOR complex
5Y39 2.65 Å, Crystal structure of Ragulator complex (p18 76-145)
6EHR 2.9 Å, The crystal structure of the human LAMTOR-RagA CTD-RagC CTD complex
5Y3A 2.9 Å, Crystal structure of Ragulator complex (p18 49-161)
7UX2 2.9 Å, cryo-EM structure of the Raptor-TFEB-Rag-Ragulator complex
5YK3 3.01 Å, human Ragulator complex
6U62 3.18 Å, Raptor-Rag-Ragulator complex

Browse structure collections

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