9MEY: RIT1(GDP)

Crystal structure of RIT1(GDP) bound to LZTR1(Kelch domain). Determined by X-ray diffraction at 2.95 Å resolution. Released 10 Sept 2025.

Method: X-ray diffraction
Resolution: 2.95 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,997
Mol. weight: 119.05 kDa
Ligands: MG, GDP
Released: 10 Sept 2025

Explore 9MEY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MEY contains 32 α-helices and 97 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: 6 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	21-28	8	1
α-helix	34-43	10
β-strand	56-64	9	1
β-strand	67-75	9	1
α-helix	82-83	2
α-helix	84-92	9
β-strand	95-101	7	1
α-helix	105-122	18
β-strand	129-134	6	1
α-helix	146-156	11
β-strand	160-162	3	1
β-strand	164	1	2
β-strand	169	1	2
α-helix	171-192	22

Chain B: 9 helices, 40 β-strands

Element	Residues	Length	Sheet
β-strand	54-57	4	3
α-helix	58-61	4
β-strand	69	1	4
β-strand	72-76	5	4
β-strand	79-86	8	4
β-strand	91-99	9	4
β-strand	104-107	4	4
α-helix	108-109	2
β-strand	111	1	5
α-helix	114-116	3
β-strand	118-119	2	6
β-strand	122-125	4	5
β-strand	129-133	5	5
β-strand	136-139	4	6
β-strand	144-148	5	6
β-strand	149	1	7
β-strand	152-156	5	5
β-strand	161-164	4	5
α-helix	172-174	3
β-strand	175	1	7
β-strand	176	1	8
β-strand	179-183	5	8
β-strand	186-193	8	8
β-strand	198-206	9	8
β-strand	215-217	3	8
β-strand	221-222	2	9
α-helix	224-226	3
β-strand	229	1	10
β-strand	233-236	4	9
β-strand	239-243	5	9
β-strand	246	1	10
α-helix	248-250	3
β-strand	255-259	5	9
β-strand	264-268	5	9
α-helix	277-283	7
β-strand	285	1	11
β-strand	288-292	5	12
β-strand	295-299	5	12
β-strand	302	1	11
β-strand	312-315	4	12
β-strand	320-323	4	12
α-helix	324-327	4
α-helix	384-387	4
β-strand	389	1	13
β-strand	392-395	4	3
β-strand	399-403	5	3
β-strand	406-408	3	13
β-strand	411-412	2	13
β-strand	416-420	5	3

Chain C: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	21-28	8	14
α-helix	34-43	10
β-strand	56-64	9	14
β-strand	67-75	9	14
α-helix	82-83	2
α-helix	84-92	9
β-strand	95-101	7	14
α-helix	105-122	18
β-strand	129-134	6	14
α-helix	139-141	3
α-helix	146-156	11
β-strand	160-162	3	14
β-strand	164	1	15
β-strand	169	1	15
α-helix	171-192	22

Chain D: 10 helices, 41 β-strands

Element	Residues	Length	Sheet
β-strand	54-57	4	16
α-helix	58-61	4
β-strand	69	1	17
β-strand	72-76	5	17
β-strand	79-86	8	17
β-strand	91-99	9	17
β-strand	104-107	4	17
α-helix	108-109	2
β-strand	111	1	18
α-helix	114-116	3
β-strand	119	1	19
β-strand	122-125	4	18
β-strand	129-133	5	18
β-strand	136-139	4	19
β-strand	144-148	5	19
β-strand	149	1	20
β-strand	152-156	5	18
β-strand	161-164	4	18
α-helix	172-174	3
β-strand	175	1	20
β-strand	176	1	21
β-strand	179-183	5	21
β-strand	186-193	8	21
β-strand	198-206	9	21
β-strand	215-217	3	21
β-strand	221-222	2	22
α-helix	224-226	3
β-strand	228	1	21
β-strand	229	1	23
β-strand	233-236	4	22
β-strand	239-243	5	22
β-strand	246	1	23
α-helix	248-250	3
β-strand	255-259	5	22
β-strand	264-268	5	22
α-helix	277-283	7
β-strand	285	1	24
β-strand	288-292	5	25
β-strand	295-299	5	25
β-strand	302	1	24
α-helix	310	1
β-strand	311-315	5	25
β-strand	320-324	5	25
α-helix	325-327	3
α-helix	384-387	4
β-strand	389	1	26
β-strand	392-395	4	16
β-strand	399-403	5	16
β-strand	406	1	26
β-strand	412	1	26
β-strand	416-420	5	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GTP-binding protein Rit1	A, C	protein	197	Homo sapiens	Q92963 (AlphaFold model)
Leucine-zipper-like transcriptional regulator 1	B, D	protein	322	Homo sapiens	Q8N653 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>9MEY_1 GTP-binding protein Rit1 (chains A, C)
GDSGTRPVGSCCSSPAGLSREYKLVMLGAGGVGKSAMTMQFISHRFPEDHDPTIEDAYKI
RIRIDDEPANLDILDTAGQAEFTAMRDQYMRAGEGFIICYSITDRRSFHEVREFKQLIYR
VRRTDDTPVVLVGNKSDLKQLRQVTKEEGLALAREFSCPFFETSAAYRYYIDDVFHALVR
EIRRKEKEAVLAMEKKS

Sequence of entity 2 (B, D), FASTA

>9MEY_2 Leucine-zipper-like transcriptional regulator 1 (chains B, D)
GTVHRWRRLPPCDEFVGARRSKHTVVAYKDAIYVFGGDNGKTMLNDLLRFDVKDCSWCRA
FTTGTPPAPRYHHSAVVYGSSMFVFGGYTGDIYSNSNLKNKNDLFEYKFATGQWTEWKIE
GRLPVARSAHGATVYSDKLWIFAGYDGNARLNDMWTIGLQDRELTCWEEVAQSGEIPPSC
CNFPVAVCRDKMFVFSGQSGAKITNNLFQFEFKDKTWTRIPTEHLLRGSPPPPQRRYGHT
MVAFDRHLYVFGGAADNTLPNELHCYDVDFQTWEVVQPSSDSELPSGRLFHAAAVISDAM
YIFGGTVDNNIRSGEMYRFQFS

Ligands and cofactors

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

Primary citation

Structural basis for LZTR1 recognition of RAS GTPases for degradation. Dharmaiah, S., Bonsor, D.A., Mo, S.P. et al. Science (2025) 389:1112-1117. DOI 10.1126/science.adv7088 · PubMed

Other PDB entries of the same protein (UniProt Q92963 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9MF1 2.2 Å, Crystal structure of RIT1 in the GDP state
4KLZ 2.3 Å, Inhibition of Small GTPases by Stabilization of the GDP Complex, a Novel Approach…

Browse structure collections

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