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- PDB-5u9j: Crystal structure of the FKBP domain of human aryl hydrocarbon re... -

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Basic information

Entry
Database: PDB / ID: 5u9j
TitleCrystal structure of the FKBP domain of human aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) complexed with geranyl geranyl pyrophoshate
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
GERAN-8-YL GERAN / ISOPROPYL ALCOHOL / Aryl-hydrocarbon-interacting protein-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 2.0Nov 22, 2017Group: Atomic model / Refinement description / Category: atom_site / software
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _software.classification
Revision 2.1Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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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)
B: Aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2866
Polymers38,6542
Non-polymers6324
Water2,540141
1
A: Aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6854
Polymers19,3271
Non-polymers3583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6022
Polymers19,3271
Non-polymers2741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.340, 51.170, 106.970
Angle α, β, γ (deg.)90.00, 93.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-447-

HOH

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Components

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


Mass: 19327.109 Da / Num. of mol.: 2 / 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-GER / GERAN-8-YL GERAN


Mass: 274.484 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C20H34
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 141 / 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: 2.45 Å3/Da / Density % sol: 49.82 %
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: Oct 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→41.152 Å / Num. obs: 17642 / % possible obs: 98.1 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 20.4
Reflection shellResolution: 2.1→2.37 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 5.3 / CC1/2: 0.957 / % possible all: 95.5

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Processing

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

5u9a


Resolution: 2.1→41.152 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0.82 / Phase error: 32.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.294 972 4.47 %
Rwork0.2376 --
obs0.24 20398 92.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→41.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2402 0 41 141 2584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142498
X-RAY DIFFRACTIONf_angle_d1.293385
X-RAY DIFFRACTIONf_dihedral_angle_d14.8981467
X-RAY DIFFRACTIONf_chiral_restr0.065377
X-RAY DIFFRACTIONf_plane_restr0.009435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15680.40241400.35142994X-RAY DIFFRACTION94
2.1568-2.22030.44431210.42742548X-RAY DIFFRACTION82
2.2203-2.29190.5375990.48182219X-RAY DIFFRACTION71
2.2919-2.37390.35411360.28853024X-RAY DIFFRACTION95
2.3739-2.46890.35881620.272943X-RAY DIFFRACTION95
2.4689-2.58120.30341460.24713006X-RAY DIFFRACTION96
2.5812-2.71730.32181680.23483066X-RAY DIFFRACTION97
2.7173-2.88750.28561310.23273114X-RAY DIFFRACTION98
2.8875-3.11040.28981310.24213100X-RAY DIFFRACTION99
3.1104-3.42330.29231500.22013036X-RAY DIFFRACTION97
3.4233-3.91830.26291580.20982814X-RAY DIFFRACTION89
3.9183-4.93530.19971190.17482931X-RAY DIFFRACTION93
4.9353-41.15940.24941080.19983001X-RAY DIFFRACTION94

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