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- PDB-6s8x: Crystal structure of the Rab-binding domain of FIP2 -

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Basic information

Entry
Database: PDB / ID: 6s8x
TitleCrystal structure of the Rab-binding domain of FIP2
ComponentsRab11 family-interacting protein 2
KeywordsSIGNALING PROTEIN / membrane trafficking / Rab small GTPases / effector protein / Rab-binding domain / endosomal trafficking
Function / homology
Function and homology information


TRAM-dependent toll-like receptor 4 signaling pathway / regulated exocytosis / insulin secretion involved in cellular response to glucose stimulus / establishment of cell polarity / positive regulation of GTPase activity / phagocytosis / phagocytic cup / cytoplasmic vesicle membrane / positive regulation of protein localization to plasma membrane / cell projection ...TRAM-dependent toll-like receptor 4 signaling pathway / regulated exocytosis / insulin secretion involved in cellular response to glucose stimulus / establishment of cell polarity / positive regulation of GTPase activity / phagocytosis / phagocytic cup / cytoplasmic vesicle membrane / positive regulation of protein localization to plasma membrane / cell projection / small GTPase binding / recycling endosome membrane / Vasopressin regulates renal water homeostasis via Aquaporins / endosome / intracellular membrane-bounded organelle / protein kinase binding / protein homodimerization activity / nucleoplasm / identical protein binding
Similarity search - Function
Rab11-family interacting protein class I / Rab-binding domain FIP-RBD / FIP-RBD, C-terminal domain superfamily / FIP domain / FIP-RBD domain profile. / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily
Similarity search - Domain/homology
HEXANE-1,6-DIOL / Rab11 family-interacting protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.29 Å
AuthorsKearney, A.M. / Khan, A.R.
Funding support Ireland, 1items
OrganizationGrant numberCountry
Science Foundation Ireland12/IA/1239 Ireland
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Crystal structure of the Rab-binding domain of Rab11 family-interacting protein 2.
Authors: Kearney, A.M. / Khan, A.R.
History
DepositionJul 10, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 5, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Rab11 family-interacting protein 2
B: Rab11 family-interacting protein 2
D: Rab11 family-interacting protein 2
E: Rab11 family-interacting protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6035
Polymers36,4854
Non-polymers1181
Water1,11762
1
A: Rab11 family-interacting protein 2


Theoretical massNumber of molelcules
Total (without water)9,1211
Polymers9,1211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rab11 family-interacting protein 2


Theoretical massNumber of molelcules
Total (without water)9,1211
Polymers9,1211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Rab11 family-interacting protein 2


Theoretical massNumber of molelcules
Total (without water)9,1211
Polymers9,1211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Rab11 family-interacting protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2392
Polymers9,1211
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.538, 68.430, 172.086
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-609-

HOH

21B-601-

HOH

31D-612-

HOH

41E-705-

HOH

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Components

#1: Protein
Rab11 family-interacting protein 2 / Rab11-FIP2 / NRip11


Mass: 9121.314 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAB11FIP2, KIAA0941 / Production host: Escherichia coli #1/H766 (bacteria) / References: UniProt: Q7L804
#2: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.75 Å3/Da / Density % sol: 67.17 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: 0.01M cobat chloride 0.1M NaOAc, pH 4.7 1M 1,6 hexanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.29→46.16 Å / Num. all: 72768 / Num. obs: 16934 / % possible obs: 99.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 35.97 Å2 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.059 / Rrim(I) all: 0.126 / Net I/σ(I): 8.8
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.872 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1611 / CC1/2: 0.712 / Rpim(I) all: 0.483 / Rrim(I) all: 1.048 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimlessdata scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.29→43.02 Å / SU ML: 0.2621 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.3366
RfactorNum. reflection% reflection
Rfree0.2739 824 4.88 %
Rwork0.246 --
obs0.2473 16885 99.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 45.36 Å2
Refinement stepCycle: LAST / Resolution: 2.29→43.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 8 62 1791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611747
X-RAY DIFFRACTIONf_angle_d0.77782346
X-RAY DIFFRACTIONf_chiral_restr0.0375276
X-RAY DIFFRACTIONf_plane_restr0.0039294
X-RAY DIFFRACTIONf_dihedral_angle_d3.58761103
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.430.30461260.29492653X-RAY DIFFRACTION99.32
2.43-2.620.28711420.26362635X-RAY DIFFRACTION99.43
2.62-2.890.28481410.25492645X-RAY DIFFRACTION99.22
2.89-3.30.29591470.26172653X-RAY DIFFRACTION99.19
3.3-4.160.25231250.22032696X-RAY DIFFRACTION98.98
4.16-43.020.26521430.24182779X-RAY DIFFRACTION98.65
Refinement TLS params.Method: refined / Origin x: 24.7894067103 Å / Origin y: 38.4361092945 Å / Origin z: 66.7265682416 Å
111213212223313233
T0.248082351707 Å2-0.0569023185143 Å2-0.0127727145403 Å2-0.319367225943 Å2-0.025287672378 Å2--0.309258497226 Å2
L-0.0159109853575 °2-0.24996827729 °2-0.304008932237 °2-0.196314696246 °2-0.179800225754 °2--1.17990599898 °2
S-0.0259890336313 Å °-0.0167918759754 Å °-0.0207674395659 Å °-0.0281689470671 Å °-0.0330745426324 Å °0.00495586782159 Å °0.0168297173492 Å °-0.00463020378326 Å °-0.000881897147311 Å °
Refinement TLS groupSelection details: all

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