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- PDB-6iy1: Structure of human Ras-related protein Rab11 -

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Basic information

Entry
Database: PDB / ID: 6iy1
TitleStructure of human Ras-related protein Rab11
Components(Ras-related protein Rab-11A) x 3
KeywordsTRANSPORT PROTEIN / Complex / transport / GTPase
Function / homology
Function and homology information


regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / : / regulation of endocytic recycling / early endosome to recycling endosome transport / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / positive regulation of mitotic cytokinetic process / plasma membrane to endosome transport ...regulation of early endosome to recycling endosome transport / regulation of protein localization to centrosome / : / regulation of endocytic recycling / early endosome to recycling endosome transport / postsynaptic recycling endosome / establishment of protein localization to organelle / establishment of vesicle localization / positive regulation of mitotic cytokinetic process / plasma membrane to endosome transport / exosomal secretion / regulation of cilium assembly / melanosome transport / amyloid-beta clearance by transcytosis / astral microtubule organization / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / protein transmembrane transport / regulation of vesicle-mediated transport / myosin V binding / RAB geranylgeranylation / Golgi to plasma membrane protein transport / multivesicular body assembly / protein localization to cilium / dynein light intermediate chain binding / establishment of protein localization to membrane / TBC/RABGAPs / protein localization to cell surface / syntaxin binding / mitotic metaphase chromosome alignment / positive regulation of epithelial cell migration / exocytosis / cleavage furrow / centriolar satellite / mitotic spindle assembly / phagocytic vesicle / vesicle-mediated transport / transport vesicle / Anchoring of the basal body to the plasma membrane / positive regulation of G2/M transition of mitotic cell cycle / centriole / multivesicular body / small monomeric GTPase / regulation of cytokinesis / trans-Golgi network membrane / protein localization to plasma membrane / Translocation of SLC2A4 (GLUT4) to the plasma membrane / trans-Golgi network / cytoplasmic vesicle membrane / recycling endosome / G protein activity / spindle pole / Vasopressin regulates renal water homeostasis via Aquaporins / recycling endosome membrane / endocytic vesicle membrane / neuron projection development / cytoplasmic vesicle / microtubule binding / vesicle / Golgi membrane / intracellular membrane-bounded organelle / GTPase activity / centrosome / glutamatergic synapse / GTP binding / Golgi apparatus / protein-containing complex / extracellular exosome / cytosol
Similarity search - Function
: / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases ...: / small GTPase Rab1 family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Rab-11A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsMa, P. / Li, S. / Li, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)31500632 China
CitationJournal: To Be Published
Title: Structure of human Ras-related protein Rab11
Authors: Ma, P. / Li, S. / Li, J.
History
DepositionDec 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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: Ras-related protein Rab-11A
C: Ras-related protein Rab-11A
D: Ras-related protein Rab-11A
E: Ras-related protein Rab-11A
F: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,64012
Polymers111,9816
Non-polymers2,6596
Water3,855214
1
A: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9902
Polymers18,5471
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-8 kcal/mol
Surface area8570 Å2
MethodPISA
2
B: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9902
Polymers18,5471
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-8 kcal/mol
Surface area8580 Å2
MethodPISA
3
C: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9902
Polymers18,5471
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-8 kcal/mol
Surface area8560 Å2
MethodPISA
4
D: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2822
Polymers18,8391
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-7 kcal/mol
Surface area8640 Å2
MethodPISA
5
E: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9902
Polymers18,5471
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-7 kcal/mol
Surface area8550 Å2
MethodPISA
6
F: Ras-related protein Rab-11A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3972
Polymers18,9541
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-8 kcal/mol
Surface area8740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.606, 150.762, 60.125
Angle α, β, γ (deg.)90.00, 98.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 18546.895 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11A, RAB11 / Production host: Escherichia coli (E. coli) / References: UniProt: P62491
#2: Protein Ras-related protein Rab-11A / Rab-11 / YL8


Mass: 18839.182 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11A, RAB11 / Production host: Escherichia coli (E. coli) / References: UniProt: P62491
#3: Protein Ras-related protein Rab-11A / Rab-11 / YL8


Mass: 18954.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GDP / Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11A, RAB11 / Production host: Escherichia coli (E. coli) / References: UniProt: P62491
#4: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.07 Å3/Da / Density % sol: 40.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.15M Li2SO4, 0.1M Glycine, 0.8M NaH2PO4 1.2M Na2HPO4

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 48648 / % possible obs: 91.2 % / Redundancy: 2.5 % / CC1/2: 0.945 / Rpim(I) all: 0.063 / Net I/σ(I): 8.3
Reflection shellResolution: 2.1→2.14 Å / Num. unique obs: 2190 / CC1/2: 0.945 / Rpim(I) all: 0.248

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OIV

1oiv


Resolution: 2.11→46.73 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.915 / Cross valid method: THROUGHOUT / ESU R: 0.381 / ESU R Free: 0.243
RfactorNum. reflection% reflectionSelection details
Rfree0.26108 2421 5 %RANDOM
Rwork0.21938 ---
obs0.22148 46212 91.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.154 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.11→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8009 0 0 214 8223
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0128146
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3341.66711054
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6565979
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.94621.518448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.12151391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4491566
X-RAY DIFFRACTIONr_chiral_restr0.0950.21096
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026130
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7742.5273943
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.9693.7754913
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2572.8354203
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.88434.37912711
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.107→2.161 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 154 -
Rwork0.342 3073 -
obs--82.2 %

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