2D7C: Human Rab11

Crystal structure of human Rab11 in complex with FIP3 Rab-binding domain. Determined by X-ray diffraction at 1.75 Å resolution. Released 26 Sept 2006.

Method: X-ray diffraction
Resolution: 1.75 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,844
Mol. weight: 49.21 kDa
Ligands: GTP, MG
Released: 26 Sept 2006

Explore 2D7C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2D7C contains 20 α-helices and 14 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	10-18	9	1
α-helix	24-33	10
α-helix	40-44	5
β-strand	46-55	10	1
β-strand	58-67	10	1
α-helix	77-81	5
β-strand	86-92	7	1
α-helix	96-100	5
α-helix	102-110	9
β-strand	118-124	7	1
α-helix	126-131	6
α-helix	136-145	10
β-strand	149-152	4	1
α-helix	161-172	12

Chain B: 8 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	10-17	8	2
α-helix	24-33	10
α-helix	40-44	5
β-strand	46-55	10	2
β-strand	58-67	10	2
α-helix	77-81	5
β-strand	86-92	7	2
α-helix	96-100	5
α-helix	102-112	11
β-strand	118-124	7	2
α-helix	129-131	3
α-helix	136-145	10
β-strand	149-152	4	2
α-helix	161-172	12

Chains C and D: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	717-746	30
α-helix	750-753	4
β-strand	754	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Ras-related protein Rab-11A	A, B	protein	167	Homo sapiens	P62491 (AlphaFold model)
Rab11 family-interacting protein 3	C, D	protein	42	Homo sapiens	O75154 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2D7C_1 Ras-related protein Rab-11A (chains A, B)
EYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGKTIKAQIWD
TAGLERYRAITSAYYRGAVGALLVYDIAKHLTYENVERWLKELRDHADSNIVIMLVGNKS
DLRHLRAVPTDEARAFAEKNGLSFIETSALDSTNVEAAFQTILTEIY

Sequence of entity 2 (C, D), FASTA

>2D7C_2 Rab11 family-interacting protein 3 (chains C, D)
VSRDELMEAIQKQEEINFRLQDYIDRIIVAIMETNPSILEVK

Ligands and cofactors

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

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

Primary citation

Structural basis for Rab11-dependent membrane recruitment of a family of Rab11-interacting protein 3 (FIP3)/Arfophilin-1. Shiba, T., Koga, H., Shin, H.W. et al. Proc Natl Acad Sci U S A (2006) 103:15416-15421. DOI 10.1073/pnas.0605357103 · 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
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
2GZH 2.47 Å, Crystal Structure of Rab11 in Complex with Rab11-Family Interacting Protein 2

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