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- PDB-4uj4: Crystal structure of human Rab11-Rabin8-FIP3 -

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Basic information

Entry
Database: PDB / ID: 4uj4
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 / RABIN8 / RAB11 / FIP3
Function / homology
Function and homology information


Golgi to plasma membrane transport vesicle / ciliary basal body-plasma membrane docking / regulation of multivesicular body size / proximal dendrite / postsynaptic recycling endosome / establishment of protein localization to organelle / negative regulation of filopodium assembly / protein localization to organelle / plasma membrane to endosome transport / establishment of vesicle localization ...Golgi to plasma membrane transport vesicle / ciliary basal body-plasma membrane docking / regulation of multivesicular body size / proximal dendrite / postsynaptic recycling endosome / establishment of protein localization to organelle / negative regulation of filopodium assembly / protein localization to organelle / plasma membrane to endosome transport / establishment of vesicle localization / negative regulation of adiponectin secretion / BBSome-mediated cargo-targeting to cilium / exosomal secretion / melanosome transport / astral microtubule organization / VxPx cargo-targeting to cilium / amyloid-beta clearance by transcytosis / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein localization to cilium / regulation of vesicle-mediated transport / Golgi to plasma membrane transport / myosin V binding / dynein light intermediate chain binding / RAB geranylgeranylation / multivesicular body assembly / RAB GEFs exchange GTP for GDP on RABs / protein targeting to membrane / endocytic recycling / establishment of protein localization to membrane / protein localization to cell surface / TBC/RABGAPs / mitotic metaphase plate congression / intercellular bridge / syntaxin binding / positive regulation of epithelial cell migration / cleavage furrow / exocytosis / mitotic spindle assembly / cilium assembly / centriolar satellite / endocytic vesicle / phagocytic vesicle / Vasopressin regulates renal water homeostasis via Aquaporins / G protein activity / transport vesicle / Anchoring of the basal body to the plasma membrane / small monomeric GTPase / positive regulation of G2/M transition of mitotic cell cycle / multivesicular body / centriole / guanyl-nucleotide exchange factor activity / ciliary basal body / vesicle-mediated transport / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of cytokinesis / protein localization to plasma membrane / microtubule organizing center / GTPase binding / trans-Golgi network / cytoplasmic vesicle membrane / recycling endosome / small GTPase binding / spindle pole / recycling endosome membrane / neuron projection development / midbody / lamellipodium / microtubule binding / cytoplasmic vesicle / vesicle / endosome / cell cycle / GTPase activity / axon / cell division / centrosome / glutamatergic synapse / intracellular membrane-bounded organelle / GTP binding / calcium ion binding / perinuclear region of cytoplasm / Golgi apparatus / protein homodimerization activity / protein-containing complex / mitochondrion / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Rab11 family-interacting protein 3 / Rab-binding domain FIP-RBD / FIP-RBD domain profile. / GDP/GTP exchange factor Sec2, N-terminal / FIP-RBD, C-terminal domain superfamily / Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2 / GDP/GTP exchange factor Sec2p / FIP domain / small GTPase Rab1 family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases ...Rab11 family-interacting protein 3 / Rab-binding domain FIP-RBD / FIP-RBD domain profile. / GDP/GTP exchange factor Sec2, N-terminal / FIP-RBD, C-terminal domain superfamily / Guanine nucleotide exchange factor RAB3IL/RAB3IP/Sec2 / GDP/GTP exchange factor Sec2p / FIP domain / small GTPase Rab1 family profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Small GTPase / Ras family / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ras-related protein Rab-11A / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / Rab11 family-interacting protein 3 / Rab-3A-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.2 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 1.3Jun 6, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_name_com / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity.pdbx_description / _entity_name_com.name / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_seq_type / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.seq_align_beg

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,96720
Polymers201,78112
Non-polymers2,1868
Water0
1
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,98310
Polymers100,8906
Non-polymers1,0934
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
J: Ras-related protein Rab-11A
K: Rab-3A-interacting protein
L: Rab11 family-interacting protein 3
hetero molecules

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)101,98310
Polymers100,8906
Non-polymers1,0934
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
MethodPISA
3
A: Ras-related protein Rab-11A
B: Rab-3A-interacting protein
C: Rab11 family-interacting protein 3
hetero molecules

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)101,98310
Polymers100,8906
Non-polymers1,0934
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.120, 161.701, 192.762
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Ras-related protein Rab-11A / Rab-11 / YL8 / RAB11A


Mass: 20958.578 Da / Num. of mol.: 4 / Fragment: GTPASE DOMAIN, RESIDUES 4-186 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11A, RAB11 / Plasmid: PET / Production host: Escherichia coli BL21(DE3) (unknown) / References: UniProt: P62491
#2: Protein
Rab-3A-interacting protein / Rab3A-interacting protein / Rabin-3 / SSX2-interacting protein


Mass: 22217.479 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN, UNP RESIDUES 286-476
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB3IP, RABIN8 / Plasmid: PET / Production host: Escherichia coli BL21(DE3) (unknown) / References: UniProt: Q96QF0
#3: Protein
Rab11 family-interacting protein 3 / Rab11-FIP3 / Arfophilin-1 / EF hands-containing Rab-interacting protein / Eferin / MU-MB-17.148


Mass: 7269.180 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN, RESIDUES 695-756
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11FIP3, ARFO1, KIAA0665 / Plasmid: PET / Production host: Escherichia coli BL21(DE3) (unknown) / References: UniProt: O75154
#4: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 4 / 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.: 4 / Source method: obtained synthetically / Formula: Mg
Sequence detailsQ70L POINT MUTATION

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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: 2.56 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 5.8
Details: 50MM MES PH 5.8, 0.2M AMMONIUM SULFATE AND 14% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4.2→50 Å / Num. obs: 15003 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 149.24 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 11
Reflection shellResolution: 4.2→4.4 Å / Redundancy: 3 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 1.6 / % possible all: 61

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4UJ3
Resolution: 4.2→49.469 Å / SU ML: 0.51 / σ(F): 1.35 / Phase error: 29.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2655 829 5.3 %
Rwork0.2521 --
obs0.2529 15708 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.2→49.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11540 0 132 0 11672
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711924
X-RAY DIFFRACTIONf_angle_d1.15116186
X-RAY DIFFRACTIONf_dihedral_angle_d13.9314292
X-RAY DIFFRACTIONf_chiral_restr0.0481858
X-RAY DIFFRACTIONf_plane_restr0.0052044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.2001-4.46310.32941570.31512393X-RAY DIFFRACTION100
4.4631-4.80740.33331130.27872459X-RAY DIFFRACTION100
4.8074-5.29070.27271220.27532459X-RAY DIFFRACTION100
5.2907-6.05510.31091340.2832486X-RAY DIFFRACTION100
6.0551-7.62430.23711560.25292458X-RAY DIFFRACTION100
7.6243-49.47270.23181470.21552624X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 20.7022 Å / Origin y: -25.0956 Å / Origin z: -39.0344 Å
111213212223313233
T1.2042 Å2-0.2318 Å20.0425 Å2-1.219 Å20.1051 Å2--1.393 Å2
L0.5523 °2-0.2415 °20.0931 °2-0.7108 °20.5122 °2--1.0941 °2
S-0.0687 Å °0.1246 Å °0.1412 Å °0.0228 Å °0.0559 Å °-0.054 Å °0.0042 Å °0.054 Å °0 Å °
Refinement TLS groupSelection details: ALL

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