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- PDB-8cub: Crystal Structure of ABCG5/G8 in Complex with Cholesterol -

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Basic information

Entry
Database: PDB / ID: 8cub
TitleCrystal Structure of ABCG5/G8 in Complex with Cholesterol
Components
  • ATP-binding cassette sub-family G member 5
  • ATP-binding cassette sub-family G member 8
KeywordsTRANSLOCASE / ABCG5 / ABCG8 / membrane protein / cholesterol transporter
Function / homology
Function and homology information


negative regulation of intestinal phytosterol absorption / negative regulation of intestinal cholesterol absorption / Defective ABCG8 causes GBD4 and sitosterolemia / Defective ABCG5 causes sitosterolemia / sterol transport / ABC transporters in lipid homeostasis / intestinal cholesterol absorption / cholesterol transfer activity / triglyceride homeostasis / phospholipid transport ...negative regulation of intestinal phytosterol absorption / negative regulation of intestinal cholesterol absorption / Defective ABCG8 causes GBD4 and sitosterolemia / Defective ABCG5 causes sitosterolemia / sterol transport / ABC transporters in lipid homeostasis / intestinal cholesterol absorption / cholesterol transfer activity / triglyceride homeostasis / phospholipid transport / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / cholesterol efflux / response to muscle activity / bile acid signaling pathway / response to ionizing radiation / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / ATP-binding cassette (ABC) transporter complex / response to nutrient / cholesterol homeostasis / transmembrane transport / receptor complex / response to xenobiotic stimulus / apical plasma membrane / protein heterodimerization activity / ATP hydrolysis activity / ATP binding / metal ion binding / plasma membrane
Similarity search - Function
ABC transporter family G domain / ABC-2 type transporter / ABC-2 type transporter / ABC-2 type transporter / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities ...ABC transporter family G domain / ABC-2 type transporter / ABC-2 type transporter / ABC-2 type transporter / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CHOLESTEROL / ATP-binding cassette sub-family G member 8 / ATP-binding cassette sub-family G member 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.05 Å
AuthorsRezaei, F. / Farhat, D. / Lee, J.Y.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN 2018-04070 Canada
Canadian Institutes of Health Research (CIHR)PJT-180640 Canada
CitationJournal: J.Mol.Biol. / Year: 2022
Title: Structural Analysis of Cholesterol Binding and Sterol Selectivity by ABCG5/G8.
Authors: Farhat, D. / Rezaei, F. / Ristovski, M. / Yang, Y. / Stancescu, A. / Dzimkova, L. / Samnani, S. / Couture, J.F. / Lee, J.Y.
History
DepositionMay 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2022Group: Structure summary / Category: audit_author
Revision 1.2Sep 14, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: ATP-binding cassette sub-family G member 5
D: ATP-binding cassette sub-family G member 8
A: ATP-binding cassette sub-family G member 5
B: ATP-binding cassette sub-family G member 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)303,7646
Polymers302,9914
Non-polymers7732
Water0
1
C: ATP-binding cassette sub-family G member 5
D: ATP-binding cassette sub-family G member 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,8823
Polymers151,4952
Non-polymers3871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ATP-binding cassette sub-family G member 5
B: ATP-binding cassette sub-family G member 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,8823
Polymers151,4952
Non-polymers3871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.268, 230.110, 249.819
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 34 through 405 or (resid 406...
d_2ens_1(chain "C" and (resid 34 through 586 or (resid 587...
d_1ens_2(chain "B" and (resid 28 through 42 or (resid 43...
d_2ens_2chain "D"
d_1ens_3chain "E"
d_2ens_3chain "F"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLULEUC1 - 588
d_21ens_1GLULEUA1 - 588
d_11ens_2PHESERD1 - 579
d_21ens_2PHESERB1 - 579
d_11ens_3CLRCLRF
d_21ens_3CLRCLRE

NCS ensembles :
ID
ens_1
ens_2
ens_3

NCS oper:
IDCodeMatrixVector
1given(-0.948772711241, -0.248828870574, -0.194716551875), (-0.263762859224, 0.284464915288, 0.921688052469), (-0.173952569683, 0.92583146692, -0.335524363291)117.553333474, -2.2643403932, 36.3837277486
2given(-0.94997660803, -0.251058767439, -0.185779276261), (-0.257165167257, 0.291233345737, 0.921438665935), (-0.177230135546, 0.923121137025, -0.341228435849)117.064987973, -2.44283657531, 36.4460472874
3given(0.411387738439, -0.649577003175, 0.639382393883), (0.806738655944, 0.58596884882, 0.0762446668172), (-0.424184947479, 0.484448372025, 0.765099277986)32.7398163331, -20.8392552232, 7.80269604513

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Components

#1: Protein ATP-binding cassette sub-family G member 5 / Sterolin-1


Mass: 74249.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCG5 / Production host: Komagataella pastoris (fungus)
References: UniProt: Q9H222, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate
#2: Protein ATP-binding cassette sub-family G member 8 / Sterolin-2


Mass: 77246.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCG8 / Production host: Komagataella pastoris (fungus)
References: UniProt: Q9H221, Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate
#3: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 4.17 Å3/Da / Density % sol: 70.49 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8-2.0 M ammonium sulfate, 100 mM MES, pH 6.5, 2-5% PEG400, 1 mM TCEP

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 4.05→30.91 Å / Num. obs: 50917 / % possible obs: 83.96 % / Redundancy: 11.2 % / Biso Wilson estimate: 26.55 Å2 / CC1/2: 0.377 / CC star: 0.74 / Net I/σ(I): 5.9
Reflection shellResolution: 4.051→4.195 Å / Rmerge(I) obs: 5.094 / Mean I/σ(I) obs: 1.41 / Num. unique obs: 915 / CC1/2: 0.137 / CC star: 0.491 / % possible all: 22.75

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7JR7

7jr7


Resolution: 4.05→30.91 Å / SU ML: 0.6448 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.2978
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3029 2999 5.89 %
Rwork0.2459 47918 -
obs0.2492 50917 64.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.45 Å2
Refinement stepCycle: LAST / Resolution: 4.05→30.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18442 0 56 0 18498
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004718900
X-RAY DIFFRACTIONf_angle_d0.930425593
X-RAY DIFFRACTIONf_chiral_restr0.05082949
X-RAY DIFFRACTIONf_plane_restr0.00683204
X-RAY DIFFRACTIONf_dihedral_angle_d6.41152599
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2CX-RAY DIFFRACTIONTorsion NCS1.10881542453
ens_2d_2DX-RAY DIFFRACTIONTorsion NCS1.20219597621
ens_3d_2CX-RAY DIFFRACTIONTorsion NCS0.826369178865
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.05-4.120.2476120.2613183X-RAY DIFFRACTION5.27
4.12-4.190.3421360.2875562X-RAY DIFFRACTION16.1
4.19-4.260.34630.26651032X-RAY DIFFRACTION29.32
4.26-4.340.3466820.26941260X-RAY DIFFRACTION35.61
4.34-4.430.3157900.2591416X-RAY DIFFRACTION40.09
4.43-4.530.2876900.2611499X-RAY DIFFRACTION43.1
4.53-4.630.3371100.2581626X-RAY DIFFRACTION46.23
4.63-4.750.25621020.24811744X-RAY DIFFRACTION49.72
4.75-4.880.28681240.24291881X-RAY DIFFRACTION53.81
4.88-5.020.30681380.24882078X-RAY DIFFRACTION58.98
5.02-5.180.32831270.24532316X-RAY DIFFRACTION65.99
5.18-5.370.32551640.25582553X-RAY DIFFRACTION72.92
5.37-5.580.36031790.27822838X-RAY DIFFRACTION80.39
5.58-5.830.3311970.27973092X-RAY DIFFRACTION88.8
5.83-6.140.37812110.29173353X-RAY DIFFRACTION94.56
6.14-6.520.31881960.293384X-RAY DIFFRACTION96.55
6.52-7.020.33572270.27563433X-RAY DIFFRACTION97.47
7.02-7.710.31882160.24643429X-RAY DIFFRACTION97.93
7.71-8.80.29212040.21063423X-RAY DIFFRACTION97.19
8.8-11.010.19832110.16963406X-RAY DIFFRACTION96.63
11.01-30.910.28482200.23153410X-RAY DIFFRACTION96.75
Refinement TLS params.Method: refined / Origin x: 47.7562520145 Å / Origin y: 52.6862507304 Å / Origin z: 57.0740364902 Å
111213212223313233
T-0.276075618827 Å20.123144023607 Å2-0.133221468857 Å2--0.135561150073 Å20.122908660872 Å2--0.0433360928816 Å2
L0.451740985837 °20.481166217948 °2-0.108518088531 °2-2.034378428 °2-0.655423403396 °2--1.72426291086 °2
S-0.0930079824011 Å °0.00284828514951 Å °-0.125097541634 Å °0.0497694197483 Å °0.113092048612 Å °-0.408847727094 Å °0.319534591787 Å °-0.0646873009236 Å °0.0154763912301 Å °
Refinement TLS groupSelection details: all

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