1TU3: Rab5 complex with Rabaptin5 C-terminal Domain

Crystal Structure of Rab5 complex with Rabaptin5 C-terminal Domain. Determined by X-ray diffraction at 2.31 Å resolution. Released 5 Oct 2004.

Method: X-ray diffraction
Resolution: 2.31 Å
Organism: Homo sapiens
Chains: 10
Atoms: 8,735
Mol. weight: 143.71 kDa
Ligands: GNP, MG
Released: 5 Oct 2004

Explore 1TU3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1TU3 contains 46 α-helices and 35 β-strands across 10 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: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	19-26	8	1
α-helix	33-42	10
α-helix	49-52	4
β-strand	55-63	9	1
β-strand	68-76	9	1
α-helix	80-85	6
α-helix	86-90	5
β-strand	95-101	7	1
α-helix	105-121	17
β-strand	127-133	7	1
α-helix	135-140	6
α-helix	145-154	10
β-strand	158-161	4	1
α-helix	170-180	11

Chain B: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	18-26	9	2
α-helix	33-42	10
α-helix	49-52	4
β-strand	55-63	9	2
β-strand	68-76	9	2
α-helix	80-85	6
α-helix	87-90	4
β-strand	95-101	7	2
α-helix	106-121	16
α-helix	126	1
β-strand	127-133	7	2
α-helix	135-140	6
α-helix	145-154	10
β-strand	158-162	5	2
α-helix	170-180	11

Chain C: 6 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	21-26	6	3
α-helix	33-41	9
β-strand	55-58	4	3
β-strand	61-63	3	4
β-strand	68-70	3	4
β-strand	71-76	6	3
α-helix	80-85	6
α-helix	87-90	4
β-strand	95-101	7	3
α-helix	105-121	17
β-strand	127-133	7	3
α-helix	145-154	10
β-strand	160-161	2	3
β-strand	163	1	5
β-strand	168	1	5
α-helix	170-180	11

Chain D: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	23-26	4	6
α-helix	33-41	9
α-helix	50-52	3
β-strand	55-58	4	6
β-strand	73-76	4	6
α-helix	80-88	9
β-strand	95-101	7	6
β-strand	104	1	6
α-helix	105-117	13
β-strand	127-133	7	6
α-helix	145-155	11
β-strand	161	1	6
α-helix	170-178	9

Chain E: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	18-26	9	7
α-helix	33-42	10
β-strand	55-63	9	7
β-strand	68-76	9	7
α-helix	80-85	6
α-helix	87-90	4
β-strand	95-101	7	7
α-helix	105-121	17
β-strand	127-133	7	7
α-helix	135-137	3
α-helix	145-154	10
β-strand	158-161	4	7
α-helix	170-180	11

Chain F: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	805-836	32
α-helix	841-847	7

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	803-837	35
α-helix	841-847	7

Chain H: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	807-836	30
α-helix	843-846	4

2 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-related protein Rab-5A	A, B, C, D, E	protein	171	Homo sapiens	P20339 (AlphaFold model)
Rab GTPase binding effector protein 1	F, G, H, I, J	protein	79	Homo sapiens	Q15276 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E), FASTA

>1TU3_1 Ras-related protein Rab-5A (chains A, B, C, D, E)
MGNKICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEI
WDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGN
KADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPKN

Sequence of entity 2 (F, G, H, I, J), FASTA

>1TU3_2 Rab GTPase binding effector protein 1 (chains F, G, H, I, J)
GPLGSAKATVEQLMFEEKNKAQRLQTELDVSEQVQRDFVKLSQTLQVQLERIRQADSLER
IRAILNDTKLTDINQLPET

Ligands and cofactors

ID	Name	Formula	Copies
GNP	Phosphoaminophosphonic acid-guanylate ester	C10 H17 N6 O13 P3	5
MG	Magnesium ion	Mg	5

Primary citation

Structural basis of Rab5-Rabaptin5 interaction in endocytosis. Zhu, G., Zhai, P., Liu, J. et al. Nat Struct Mol Biol (2004) 11:975-983. DOI 10.1038/nsmb832 · PubMed

Other PDB entries of the same protein (UniProt P20339 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1R2Q 1.05 Å, Crystal Structure of Human Rab5a GTPase Domain at 1.05 A resolution
1N6H 1.51 Å, Crystal Structure of Human Rab5a
1N6P 1.54 Å, Crystal Structure of Human Rab5a A30E mutant complex with GppNHp
1N6K 1.55 Å, Crystal Structure of Human Rab5a A30P mutant complex with GDP and aluminum fluoride
1N6R 1.55 Å, Crystal Structure of Human Rab5a A30L mutant complex with GppNHp
1N6I 1.6 Å, Crystal Structure of Human Rab5a A30P mutant Complex with GDP
1N6L 1.6 Å, Crystal Structure of Human Rab5a A30P mutant complex with GTP
1N6N 1.6 Å, Crystal Structure of Human Rab5a A30R mutant complex with GppNHp
1N6O 1.8 Å, Crystal Structure of Human Rab5a A30K mutant complex with GppNHp
3MJH 2.03 Å, Crystal Structure of Human Rab5A in complex with the C2H2 Zinc Finger of EEA1
1TU4 2.2 Å, Crystal Structure of Rab5-GDP Complex
9RX5 3.15 Å, VPS34-CII (VPS34 199-REIE-202 to 199-AAAA-202 mutant) bound to RAB5A (Q79L)

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