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- PDB-4uj3: Crystal structure of human Rab11-Rabin8-FIP3 -

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Basic information

Entry
Database: PDB / ID: 4uj3
TitleCrystal structure of human Rab11-Rabin8-FIP3
Components
  • RAB-3A-INTERACTING PROTEIN
  • RAB11 FAMILY-INTERACTING PROTEIN 3
  • RAS-RELATED PROTEIN RAB-11A
KeywordsTRANSPORT PROTEIN / CILIARY TARGETING COMPLEX / CILIUM / VESICULAR TRANSPORT / MEMBRANE TRAFFICKING
Function / homology
Function and homology information


ciliary basal body-plasma membrane docking / regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / protein localization to cleavage furrow / synaptic vesicle endosomal processing / early endosome to recycling endosome transport / postsynaptic recycling endosome membrane / regulation of endocytic recycling / negative regulation of filopodium assembly / establishment of protein localization to organelle ...ciliary basal body-plasma membrane docking / regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / protein localization to cleavage furrow / synaptic vesicle endosomal processing / early endosome to recycling endosome transport / postsynaptic recycling endosome membrane / regulation of endocytic recycling / negative regulation of filopodium assembly / establishment of protein localization to organelle / negative regulation of adiponectin secretion / postsynaptic recycling endosome / positive regulation of mitotic cytokinetic process / plasma membrane to endosome transport / establishment of vesicle localization / protein localization to organelle / exosomal secretion / amyloid-beta clearance by transcytosis / regulation of cilium assembly / regulation of protein transport / presynaptic endosome / astral microtubule organization / neurotransmitter receptor transport, endosome to postsynaptic membrane / VxPx cargo-targeting to cilium / vesicle-mediated transport in synapse / protein transmembrane transport / regulation of vesicle-mediated transport / BBSome-mediated cargo-targeting to cilium / myosin V binding / positive regulation of cilium assembly / RAB geranylgeranylation / Golgi to plasma membrane transport / proximal dendrite / melanosome transport / multivesicular body assembly / protein localization to cilium / RAB GEFs exchange GTP for GDP on RABs / endocytic recycling / Golgi to plasma membrane protein transport / establishment of protein localization to membrane / TBC/RABGAPs / protein localization to cell surface / syntaxin binding / protein targeting to membrane / dynein light intermediate chain binding / mitotic metaphase chromosome alignment / exocytosis / cleavage furrow / positive regulation of epithelial cell migration / endocytic vesicle / cilium assembly / mitotic spindle assembly / positive regulation of G2/M transition of mitotic cell cycle / transport vesicle / intercellular bridge / vesicle-mediated transport / phagocytic vesicle / multivesicular body / centriole / Anchoring of the basal body to the plasma membrane / cytoplasmic vesicle membrane / guanyl-nucleotide exchange factor activity / trans-Golgi network membrane / small monomeric GTPase / regulation of cytokinesis / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / trans-Golgi network / regulation of long-term neuronal synaptic plasticity / recycling endosome / small GTPase binding / centriolar satellite / Schaffer collateral - CA1 synapse / recycling endosome membrane / neuron projection development / spindle pole / Vasopressin regulates renal water homeostasis via Aquaporins / endocytic vesicle membrane / synaptic vesicle membrane / protein transport / lamellipodium / G protein activity / GTPase binding / cytoplasmic vesicle / midbody / protein-macromolecule adaptor activity / microtubule binding / molecular adaptor activity / vesicle / endosome / cilium / ciliary basal body / Golgi membrane / cell division / intracellular membrane-bounded organelle / GTPase activity / calcium ion binding / centrosome / GTP binding
Similarity search - Function
: / Rab11-FIP3-like domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2440 / GDP/GTP exchange factor Sec2, N-terminal / Rab-binding domain FIP-RBD / FIP-RBD, C-terminal domain superfamily / Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2 / GDP/GTP exchange factor Sec2p / FIP domain / FIP-RBD domain profile. ...: / Rab11-FIP3-like domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2440 / GDP/GTP exchange factor Sec2, N-terminal / Rab-binding domain FIP-RBD / FIP-RBD, C-terminal domain superfamily / Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2 / GDP/GTP exchange factor Sec2p / FIP domain / FIP-RBD domain profile. / : / Small GTPase Rab domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / EF-hand domain pair / Rab subfamily of small GTPases / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Rab11 family-interacting protein 3 / Ras-related protein Rab-11A / Rab-3A-interacting protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsVetter, M. / Lorentzen, E.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Structure of Rab11-Fip3-Rabin8 Reveals Simultaneous Binding of Fip3 and Rabin8 Effectors to Rab11.
Authors: Vetter, M. / Stehle, R. / Basquin, C. / Lorentzen, E.
History
DepositionApr 8, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Sep 16, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAS-RELATED PROTEIN RAB-11A
B: RAB-3A-INTERACTING PROTEIN
C: RAB11 FAMILY-INTERACTING PROTEIN 3
D: RAS-RELATED PROTEIN RAB-11A
E: RAB-3A-INTERACTING PROTEIN
F: RAB11 FAMILY-INTERACTING PROTEIN 3
G: RAS-RELATED PROTEIN RAB-11A
H: RAB-3A-INTERACTING PROTEIN
I: RAB11 FAMILY-INTERACTING PROTEIN 3
J: RAS-RELATED PROTEIN RAB-11A
K: RAB-3A-INTERACTING PROTEIN
L: RAB11 FAMILY-INTERACTING PROTEIN 3
M: RAS-RELATED PROTEIN RAB-11A
N: RAB-3A-INTERACTING PROTEIN
O: RAB11 FAMILY-INTERACTING PROTEIN 3
P: RAS-RELATED PROTEIN RAB-11A
Q: RAB-3A-INTERACTING PROTEIN
R: RAB11 FAMILY-INTERACTING PROTEIN 3
S: RAS-RELATED PROTEIN RAB-11A
T: RAB-3A-INTERACTING PROTEIN
U: RAB11 FAMILY-INTERACTING PROTEIN 3
V: RAS-RELATED PROTEIN RAB-11A
W: RAB-3A-INTERACTING PROTEIN
X: RAB11 FAMILY-INTERACTING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)409,48942
Polymers404,82724
Non-polymers4,66218
Water1,946108
1
A: RAS-RELATED PROTEIN RAB-11A
B: RAB-3A-INTERACTING PROTEIN
C: RAB11 FAMILY-INTERACTING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1505
Polymers50,6033
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-20.9 kcal/mol
Surface area23760 Å2
MethodPQS
2
D: RAS-RELATED PROTEIN RAB-11A
E: RAB-3A-INTERACTING PROTEIN
F: RAB11 FAMILY-INTERACTING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1505
Polymers50,6033
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-21.8 kcal/mol
Surface area23930 Å2
MethodPQS
3
G: RAS-RELATED PROTEIN RAB-11A
H: RAB-3A-INTERACTING PROTEIN
I: RAB11 FAMILY-INTERACTING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1505
Polymers50,6033
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-21.6 kcal/mol
Surface area23120 Å2
MethodPQS
4
J: RAS-RELATED PROTEIN RAB-11A
K: RAB-3A-INTERACTING PROTEIN
L: RAB11 FAMILY-INTERACTING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1505
Polymers50,6033
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-23 kcal/mol
Surface area23120 Å2
MethodPQS
5
M: RAS-RELATED PROTEIN RAB-11A
N: RAB-3A-INTERACTING PROTEIN
O: RAB11 FAMILY-INTERACTING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,2466
Polymers50,6033
Non-polymers6433
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-23.4 kcal/mol
Surface area23230 Å2
MethodPQS
6
P: RAS-RELATED PROTEIN RAB-11A
Q: RAB-3A-INTERACTING PROTEIN
R: RAB11 FAMILY-INTERACTING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1505
Polymers50,6033
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-21.8 kcal/mol
Surface area22970 Å2
MethodPQS
7
S: RAS-RELATED PROTEIN RAB-11A
T: RAB-3A-INTERACTING PROTEIN
U: RAB11 FAMILY-INTERACTING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1505
Polymers50,6033
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-22.3 kcal/mol
Surface area23170 Å2
MethodPQS
8
V: RAS-RELATED PROTEIN RAB-11A
W: RAB-3A-INTERACTING PROTEIN
X: RAB11 FAMILY-INTERACTING PROTEIN 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,3446
Polymers50,6033
Non-polymers7413
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-20.1 kcal/mol
Surface area21830 Å2
MethodPQS
Unit cell
Length a, b, c (Å)67.498, 165.374, 218.687
Angle α, β, γ (deg.)90.00, 95.93, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
/ NCS ensembles :
ID
1
2
3

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Components

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Protein , 3 types, 24 molecules ADGJMPSVBEHKNQTWCFILORUX

#1: Protein
RAS-RELATED PROTEIN RAB-11A / RAB-11 / YL8 / RAB11A


Mass: 21116.736 Da / Num. of mol.: 8 / Fragment: GTPASE DOMAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P62491
#2: Protein
RAB-3A-INTERACTING PROTEIN / RAB3A-INTERACTING PROTEIN / RABIN-3 / SSX2-INTERACTING PROTEIN / RABIN8


Mass: 22217.479 Da / Num. of mol.: 8 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q96QF0
#3: Protein
RAB11 FAMILY-INTERACTING PROTEIN 3 / FIP3-RAB11 / RAB11-FIP3 / ARFOPHILIN-1 / EF HANDS-CONTAINING RAB-INTERACTING PROTEIN / EFERIN / MU- ...FIP3-RAB11 / RAB11-FIP3 / ARFOPHILIN-1 / EF HANDS-CONTAINING RAB-INTERACTING PROTEIN / EFERIN / MU-MB-17.148 / FIP3


Mass: 7269.180 Da / Num. of mol.: 8 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75154

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Non-polymers , 5 types, 126 molecules

#4: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growpH: 5.6
Details: 50MM MES PH 5.6, 0.2M AMMONIUM SULFATE AND 12% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 92398 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19
Reflection shellResolution: 2.97→3.14 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1.8 / % possible all: 94

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: DEV_1647)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YZK

1yzk


Resolution: 3→48.543 Å / SU ML: 0.48 / σ(F): 1.33 / Phase error: 27.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2504 9297 5 %
Rwork0.1979 --
obs0.2005 92398 98.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→48.543 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22924 0 282 108 23314
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523670
X-RAY DIFFRACTIONf_angle_d0.9932136
X-RAY DIFFRACTIONf_dihedral_angle_d13.5928472
X-RAY DIFFRACTIONf_chiral_restr0.0393692
X-RAY DIFFRACTIONf_plane_restr0.0044055
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.03410.37563140.3545970X-RAY DIFFRACTION100
3.0341-3.06980.39493180.3416024X-RAY DIFFRACTION100
3.0698-3.10720.37463050.33335822X-RAY DIFFRACTION100
3.1072-3.14650.38343140.31865914X-RAY DIFFRACTION100
3.1465-3.18790.38963230.31556093X-RAY DIFFRACTION100
3.1879-3.23160.36933080.30585905X-RAY DIFFRACTION100
3.2316-3.27780.3353070.29155861X-RAY DIFFRACTION100
3.2778-3.32670.33453140.28355960X-RAY DIFFRACTION100
3.3267-3.37860.3283210.25096024X-RAY DIFFRACTION99
3.3786-3.4340.31273140.24785894X-RAY DIFFRACTION100
3.434-3.49320.31933050.23445832X-RAY DIFFRACTION100
3.4932-3.55670.29963220.22946097X-RAY DIFFRACTION100
3.5567-3.62510.28443080.22745811X-RAY DIFFRACTION99
3.6251-3.69910.30013120.21975915X-RAY DIFFRACTION99
3.6991-3.77950.25983100.21725875X-RAY DIFFRACTION99
3.7795-3.86740.26323030.20645814X-RAY DIFFRACTION98
3.8674-3.9640.27973140.2095938X-RAY DIFFRACTION97
3.964-4.07120.27073040.20625693X-RAY DIFFRACTION98
4.0712-4.19090.2673110.18135861X-RAY DIFFRACTION97
4.1909-4.32610.21852980.16935741X-RAY DIFFRACTION97
4.3261-4.48060.21623180.16775954X-RAY DIFFRACTION98
4.4806-4.65990.21463050.15855713X-RAY DIFFRACTION98
4.6599-4.87170.2253100.1565905X-RAY DIFFRACTION98
4.8717-5.12830.21683120.16225853X-RAY DIFFRACTION98
5.1283-5.44920.23773070.16855787X-RAY DIFFRACTION98
5.4492-5.86930.23992980.18255833X-RAY DIFFRACTION98
5.8693-6.45880.21833060.17985838X-RAY DIFFRACTION98
6.4588-7.39050.22723030.17065791X-RAY DIFFRACTION97
7.3905-9.30060.17422930.14385674X-RAY DIFFRACTION95
9.3006-48.5490.19823200.17985902X-RAY DIFFRACTION99

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