4LWZ: Myo5b globular tail domain

Crystal structure of Myo5b globular tail domain in complex with inactive Rab11a. Determined by X-ray diffraction at 2.55 Å resolution. Released 20 Nov 2013.

Method: X-ray diffraction
Resolution: 2.55 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,137
Mol. weight: 139.36 kDa
Ligands: MG, GDP
Released: 20 Nov 2013

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

Secondary structure: helices and β-sheets

4LWZ contains 63 α-helices and 16 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	10-17	8	1
α-helix	24-33	10
α-helix	41-43	3
β-strand	46-55	10	1
β-strand	58-67	10	1
α-helix	75-81	7
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	161-172	12

Chain B: 25 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	1470-1471	2	2
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	1588-1618	31
α-helix	1619-1623	5
α-helix	1654-1670	17
α-helix	1675-1697	23
α-helix	1706-1725	20
α-helix	1734-1737	4
α-helix	1738-1746	9
α-helix	1754-1763	10
α-helix	1769-1777	9
α-helix	1787-1790	4
α-helix	1791-1800	10
α-helix	1801-1803	3
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	2

Chain C: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	12-17	6	3
α-helix	24-33	10
α-helix	40-42	3
β-strand	46-54	9	3
β-strand	59-67	9	3
α-helix	78-81	4
β-strand	86-92	7	3
α-helix	96-100	5
α-helix	102-112	11
β-strand	118-124	7	3
α-helix	129-131	3
α-helix	136-146	11
β-strand	149-152	4	3
α-helix	161-171	11

Chain D: 22 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	1470-1471	2	4
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	1567-1570	4
α-helix	1577-1580	4
α-helix	1588-1613	26
α-helix	1654-1670	17
α-helix	1675-1694	20
α-helix	1706-1725	20
α-helix	1733-1736	4
α-helix	1738-1746	9
α-helix	1754-1763	10
α-helix	1769-1777	9
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	4

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

>4LWZ_1 Ras-related protein Rab-11A (chains A, C)
MGTRDDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGKTI
KAQIWDTAGQERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIM
LVGNKSDLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIYRIVS

Sequence of entity 2 (B, D), FASTA

>4LWZ_2 Unconventional myosin-Vb (chains B, D)
MRSETMSYYHHHHHHDYDIPTTENLYFQGAMGSMQVTVQRKEKDFQGMLEYHKEDEALLI
RNLVTDLKPQMLSGTVPCLPAYILYMCIRHADYTNDDLKVHSLLTSTINGIKKVLKKHND
DFEMTSFWLSNTCRLLHCLKQYSGDEGFMTQNTAKQNEHCLKNFDLTEYRQVLSDLSIQI
YQQLIKIAEGVLQPMIVSAMLENESIQGLSGVKPTGYRKRSSSMADGDNSYCLEAIIRQM
NAFHTVMCDQGLDPEIILQVFKQLFYMINAVTLNNLLLRKDVCSWSTGMQLRYNISQLEE
WLRGRNLHQSGAVQTMEPLIQAAQLLQLKKKTQEDAEAICSLCTSLSTQQIVKILNLYTP
LNEFEERVTVAFIRTIQAQLQERNDPQQLLLDAKHMFPVLFPFNPSSLTMDSIHIPACLN
LEFLNEV

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 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
4LX0 2.19 Å, Crystal structure of Myo5b globular tail domain in complex with active Rab11a
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

Browse structure collections

About this viewer

MolViewer shows 4LWZ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.