3MJH: Human Rab5A

Crystal Structure of Human Rab5A in complex with the C2H2 Zinc Finger of EEA1. Determined by X-ray diffraction at 2.03 Å resolution. Released 5 May 2010.

Method: X-ray diffraction
Resolution: 2.03 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,518
Mol. weight: 46.18 kDa
Ligands: ZN, MG, GTP
Released: 5 May 2010

Explore 3MJH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3MJH contains 18 α-helices and 20 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: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	17-26	10	1
α-helix	33-42	10
α-helix	49-52	4
β-strand	55-64	10	1
β-strand	67-76	10	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	145-153	9
β-strand	158-161	4	1
α-helix	170-180	11

Chains B and D: 1 helix, 3 β-strands

Element	Residues	Length	Sheet
β-strand	39-40	2	1
β-strand	41-42	2	2
β-strand	49-50	2	2
α-helix	53-63	11

Chain C: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	18-26	9	3
α-helix	33-42	10
α-helix	50-52	3
β-strand	55-63	9	3
β-strand	68-76	9	3
α-helix	80-85	6
α-helix	86-90	5
β-strand	95-101	7	3
α-helix	105-120	16
β-strand	127-133	7	3
α-helix	138-140	3
α-helix	145-154	10
β-strand	158-161	4	3
β-strand	163	1	4
β-strand	168	1	4
α-helix	170-180	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rab-5A	A, C	protein	168	Homo sapiens	P20339 (AlphaFold model)
Early endosome antigen 1	B, D	protein	34	Homo sapiens	Q15075 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3MJH_1 Ras-related protein Rab-5A (chains A, C)
NKICQFKLVLLGESAVGKSSLVLRFVKGQFHEFQESTIGAAFLTQTVCLDDTTVKFEIWD
TAGLERYHSLAPMYYRGAQAAIVVYDITNEESFARAKNWVKELQRQASPNIVIALSGNKA
DLANKRAVDFQEAQSYADDNSLLFMETSAKTSMNVNEIFMAIAKKLPK

Sequence of entity 2 (B, D), FASTA

>3MJH_2 Early endosome antigen 1 (chains B, D)
SSSEGFICPQCMKSLGSADELFKHYEAVHDAGND

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
MG	Magnesium ion	Mg	2
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	2

Primary citation

Structural basis for Rab GTPase recognition and endosome tethering by the C2H2 zinc finger of Early Endosomal Autoantigen 1 (EEA1). Mishra, A., Eathiraj, S., Corvera, S. et al. Proc Natl Acad Sci U S A (2010) 107:10866-10871. DOI 10.1073/pnas.1000843107 · 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
1TU4 2.2 Å, Crystal Structure of Rab5-GDP Complex
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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