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- PDB-5u9i: Crystal structure of the FKBP domain of human aryl hydrocarbon re... -

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Basic information

Entry
Database: PDB / ID: 5u9i
TitleCrystal structure of the FKBP domain of human aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) complexed with S-farnesyl-L-cysteine methyl ester
ComponentsAryl hydrocarbon receptor-interacting protein-like 1 (AIPL1)
KeywordsSIGNALING PROTEIN / AIPL1 / FKBP / chaperone / PDE6 / photoreceptor / LCA / isoprenyl
Function / homology
Function and homology information


farnesylated protein binding / regulation of opsin-mediated signaling pathway / protein farnesylation / phototransduction, visible light / retina homeostasis / photoreceptor inner segment / visual perception / peptidyl-prolyl cis-trans isomerase activity / unfolded protein binding / nuclear speck ...farnesylated protein binding / regulation of opsin-mediated signaling pathway / protein farnesylation / phototransduction, visible light / retina homeostasis / photoreceptor inner segment / visual perception / peptidyl-prolyl cis-trans isomerase activity / unfolded protein binding / nuclear speck / apoptotic process / negative regulation of apoptotic process / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
AIP/AIPL1 / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
FARNESYL / Aryl-hydrocarbon-interacting protein-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYadav, R.P. / Gakhar, L. / Liping, Y. / Artemyev, N.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY-10843 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Unique structural features of the AIPL1-FKBP domain that support prenyl lipid binding and underlie protein malfunction in blindness.
Authors: Yadav, R.P. / Gakhar, L. / Yu, L. / Artemyev, N.O.
History
DepositionDec 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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

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Assembly

Deposited unit
A: Aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5332
Polymers19,3271
Non-polymers2061
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.970, 66.180, 106.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1)


Mass: 19327.109 Da / Num. of mol.: 1 / Fragment: UNP residues 2-161
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AIPL1, AIPL2 / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9NZN9
#2: Chemical ChemComp-FAR / FARNESYL / Farnesol


Mass: 206.367 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H26

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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: 2.52 Å3/Da / Density % sol: 51.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM Na-Citrate 20% (W/V) PEG 4000 20% (V/V) 2-Propanol
PH range: 5-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Sep 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→42.29 Å / Num. obs: 8993 / % possible obs: 99.9 % / Redundancy: 13.3 % / Biso Wilson estimate: 39.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.115 / Net I/σ(I): 15.6
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 13.1 % / Rmerge(I) obs: 1.06 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1272 / CC1/2: 0.97 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Blu-Icedata collection
XDSdata scaling
PHASERphasing
Cootmodel building
SCALAdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U9A

5u9a


Resolution: 2.3→42.286 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.04 / Phase error: 36.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2663 419 4.72 %
Rwork0.2346 --
obs0.2362 8914 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→42.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1205 0 15 0 1220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111249
X-RAY DIFFRACTIONf_angle_d1.1911692
X-RAY DIFFRACTIONf_dihedral_angle_d14.653735
X-RAY DIFFRACTIONf_chiral_restr0.059187
X-RAY DIFFRACTIONf_plane_restr0.008218
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.44410.39231290.35312627X-RAY DIFFRACTION99
2.4441-2.63280.3191320.30232628X-RAY DIFFRACTION99
2.6328-2.89770.31061200.27922653X-RAY DIFFRACTION99
2.8977-3.31680.33711340.2712658X-RAY DIFFRACTION100
3.3168-4.17830.31241120.21952651X-RAY DIFFRACTION99
4.1783-42.29280.19021580.18672640X-RAY DIFFRACTION100

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