4LX0: Myo5b globular tail domain

Crystal structure of Myo5b globular tail domain in complex with active Rab11a. Determined by X-ray diffraction at 2.19 Å resolution. Released 20 Nov 2013.

Method: X-ray diffraction
Resolution: 2.19 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,344
Mol. weight: 139.58 kDa
Ligands: GDP, BEF, MG
Released: 20 Nov 2013

Explore 4LX0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4LX0 contains 65 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: 9 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	1
α-helix	24-33	10
α-helix	40-43	4
β-strand	46-55	10	1
β-strand	58-67	10	1
α-helix	71-73	3
β-strand	75	1	2
α-helix	78-81	4
β-strand	86-92	7	1
α-helix	96-100	5
α-helix	102-112	11
β-strand	118-124	7	1
α-helix	129-131	3
α-helix	136-145	10
β-strand	149-152	4	1
α-helix	161-176	16

Chain B: 24 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	1460-1462	3
β-strand	1470-1471	2	3
α-helix	1474-1476	3
α-helix	1477-1481	5
α-helix	1482-1486	5
α-helix	1490-1493	4
α-helix	1500-1514	15
α-helix	1518-1538	21
α-helix	1543-1562	20
α-helix	1567-1569	3
α-helix	1575-1578	4
α-helix	1588-1622	35
α-helix	1654-1670	17
α-helix	1675-1697	23
α-helix	1701-1703	3
α-helix	1706-1725	20
α-helix	1735-1737	3
α-helix	1738-1748	11
β-strand	1749	1	2
α-helix	1754-1763	10
α-helix	1769-1778	10
α-helix	1788-1790	3
α-helix	1791-1800	10
α-helix	1818-1820	3
α-helix	1831-1833	3
α-helix	1838-1840	3
β-strand	1846-1847	2	3

Chain C: 9 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	4
α-helix	24-33	10
α-helix	41-43	3
β-strand	46-55	10	4
β-strand	58-67	10	4
α-helix	71-73	3
α-helix	78-81	4
β-strand	86-92	7	4
α-helix	96-100	5
α-helix	102-112	11
β-strand	118-124	7	4
α-helix	129-131	3
α-helix	136-145	10
β-strand	149-152	4	4
α-helix	161-176	16

Chain D: 23 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	1446-1447	2	5
β-strand	1455-1456	2	5
β-strand	1470-1471	2	6
α-helix	1474-1476	3
α-helix	1477-1481	5
α-helix	1482-1486	5
α-helix	1490-1493	4
α-helix	1500-1514	15
α-helix	1518-1538	21
α-helix	1543-1562	20
α-helix	1567-1569	3
α-helix	1575-1578	4
α-helix	1588-1621	34
α-helix	1654-1670	17
α-helix	1675-1698	24
α-helix	1706-1725	20
α-helix	1735-1737	3
α-helix	1738-1748	11
α-helix	1754-1763	10
α-helix	1769-1778	10
α-helix	1788-1790	3
α-helix	1791-1800	10
α-helix	1818-1820	3
α-helix	1822-1824	3
α-helix	1831-1833	3
α-helix	1838-1840	3
β-strand	1846-1847	2	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rab-11A	A, C	protein	177	Homo sapiens	P62491 (AlphaFold model)
Unconventional myosin-Vb	B, D	protein	427	Homo sapiens	Q9ULV0 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4LX0_1 Ras-related protein Rab-11A (chains A, C)
MGTRDDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGKTI
KAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIM
LVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIYRIVS

Sequence of entity 2 (B, D), FASTA

>4LX0_2 Unconventional myosin-Vb (chains B, D)
MRSETMSYYHHHHHHDYDIPTTENLYFQGAMGSMQVTVQRKEKDFQGMLEYHKEDEALLI
RNLVTDLKPQMLSGTVPCLPAYILYMCIRHADYTNDDLKVHSLLTSTINGIKKVLKKHND
DFEMTSFWLSNTCRLLHCLKQYSGDEGFMTQNTAKQNEHCLKNFDLTEYRQVLSDLSIQI
YQQLIKIAEGVLQPMIVSAMLENESIQGLSGVKPTGYRKRSSSMADGDNSYCLEAIIRQM
NAFHTVMCDQGLDPEIILQVFKQLFYMINAVTLNNLLLRKDVCSWSTGMQLRYNISQLEE
WLRGRNLHQSGAVQTMEPLIQAAQLLQLKKKTQEDAEAICSLCTSLSTQQIVKILNLYTP
LNEFEERVTVAFIRTIQAQLQERNDPQQLLLDAKHMFPVLFPFNPSSLTMDSIHIPACLN
LEFLNEV

Ligands and cofactors

ID	Name	Formula	Copies
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2
BEF	Beryllium trifluoride ion	Be F3	2
MG	Magnesium ion	Mg	2

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

Primary citation

Structural basis of myosin V Rab GTPase-dependent cargo recognition. Pylypenko, O., Attanda, W., Gauquelin, C. et al. Proc Natl Acad Sci U S A (2013) 110:20443-20448. DOI 10.1073/pnas.1314329110 · PubMed

Other PDB entries of the same protein (UniProt P62491 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1OIX 1.7 Å, X-ray structure of the small G protein Rab11a in complex with GDP and Pi
2D7C 1.75 Å, Crystal structure of human Rab11 in complex with FIP3 Rab-binding domain
2HV8 1.86 Å, Crystal structure of GTP-bound Rab11 in complex with FIP3
1OIV 1.98 Å, X-ray structure of the small G protein Rab11a in complex with GDP
1YZK 2.0 Å, GppNHp bound Rab11 GTPase
4C4P 2.0 Å, Crystal Structure of Wild-Type Rab11 Complexed to FIP2
1OIW 2.05 Å, X-ray structure of the small G protein Rab11a in complex with GTPgammaS
5JCZ 2.06 Å, Rab11 bound to MyoVa-GTD
6IY1 2.11 Å, Structure of human Ras-related protein Rab11
5EZ5 2.4 Å, Crystal structure of active Rab11A (S20V) in complex with GTP
2GZD 2.44 Å, Crystal Structure of Rab11 in Complex with Rab11-FIP2
2GZH 2.47 Å, Crystal Structure of Rab11 in Complex with Rab11-Family Interacting Protein 2

Browse structure collections

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