1TU4: Rab5-GDP Complex

Crystal Structure of Rab5-GDP Complex. Determined by X-ray diffraction at 2.2 Å resolution. Released 5 Oct 2004.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,659
Mol. weight: 79.93 kDa
Ligands: GDP, CO
Released: 5 Oct 2004

Explore 1TU4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1TU4 contains 34 α-helices and 31 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, 8 β-strands

Element	Residues	Length	Sheet
α-helix	17-18	2
β-strand	19-26	8	1
α-helix	33-42	10
β-strand	46	1	1
α-helix	47-49	3
β-strand	50-51	2	1
α-helix	53-55	3
β-strand	57-63	7	1
α-helix	64	1
β-strand	69-76	8	1
α-helix	79-81	3
α-helix	87-90	4
β-strand	93-101	9	1
α-helix	105-121	17
β-strand	127-133	7	1
α-helix	138-140	3
α-helix	145-154	10
β-strand	158-161	4	1
α-helix	170-180	11

Chain B: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	19-26	8	2
α-helix	33-40	8
β-strand	55-64	10	2
β-strand	67-76	10	2
α-helix	80-85	6
α-helix	87-90	4
β-strand	95-101	7	2
α-helix	105-121	17
β-strand	127-133	7	2
α-helix	135-140	6
α-helix	145-154	10
β-strand	158-161	4	2
α-helix	170-180	11

Chain C: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	17-18	2
β-strand	19-26	8	3
α-helix	33-42	10
β-strand	45-46	2	3
β-strand	50-51	2	3
α-helix	53-55	3
β-strand	57-63	7	3
β-strand	69-76	8	3
α-helix	79-81	3
α-helix	87-90	4
β-strand	95-101	7	3
α-helix	105-121	17
β-strand	127-133	7	3
α-helix	135-140	6
α-helix	145-153	9
β-strand	158-161	4	3
α-helix	170-180	11

Chain D: 7 helices, 9 β-strands

Element	Residues	Length	Sheet
β-strand	18-27	10	4
α-helix	33-40	8
β-strand	52	1	4
β-strand	55-64	10	4
β-strand	67-76	10	4
α-helix	80-85	6
α-helix	87-90	4
β-strand	95-101	7	4
α-helix	105-121	17
β-strand	127-133	7	4
α-helix	135-140	6
α-helix	145-155	11
β-strand	158-161	4	4
β-strand	163	1	5
β-strand	168	1	5
α-helix	170-180	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rab-5A	A, B, C, D	protein	171	Homo sapiens	P20339 (AlphaFold model)

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

>1TU4_1 Ras-related protein Rab-5A (chains A, B, C, D)
MGNKICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEI
WDTAGQERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGN
KADLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPKN

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	4
CO	Cobalt (II) ion	Co	6

Water and common crystallization additives (SO4) are not listed.

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
1TU3 2.31 Å, Crystal Structure of Rab5 complex with Rabaptin5 C-terminal Domain
9RX5 3.15 Å, VPS34-CII (VPS34 199-REIE-202 to 199-AAAA-202 mutant) bound to RAB5A (Q79L)

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