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- PDB-5do7: Crystal Structure of the Human Sterol Transporter ABCG5/ABCG8 -

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Basic information

Entry
Database: PDB / ID: 5do7
TitleCrystal Structure of the Human Sterol Transporter ABCG5/ABCG8
Components
  • ATP-binding cassette sub-family G member 5
  • ATP-binding cassette sub-family G member 8
KeywordsTRANSPORT PROTEIN / ATP-binding cassette transporter / ABCG / Sterol efflux / Sitosterolemia
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
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 / SAD / Resolution: 3.93 Å
AuthorsLee, J.-Y. / Kinch, L.N. / Borek, D.M. / Urbatsch, I.L. / Xie, X.-S. / Grishin, N.V. / Cohen, J.C. / Otwinowski, Z. / Hobbs, H.H. / Rosenbaum, D.M.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL72304 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P01-HL20948 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM113050 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM053163 United States
American Heart Association0825285F United States
American Heart Association0463130Y United States
CitationJournal: Nature / Year: 2016
Title: Crystal structure of the human sterol transporter ABCG5/ABCG8.
Authors: Lee, J.Y. / Kinch, L.N. / Borek, D.M. / Wang, J. / Wang, J. / Urbatsch, I.L. / Xie, X.S. / Grishin, N.V. / Cohen, J.C. / Otwinowski, Z. / Hobbs, H.H. / Rosenbaum, D.M.
History
DepositionSep 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
Revision 1.2Jun 8, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)302,9914
Polymers302,9914
Non-polymers00
Water0
1
A: ATP-binding cassette sub-family G member 5
B: ATP-binding cassette sub-family G member 8


Theoretical massNumber of molelcules
Total (without water)151,4952
Polymers151,4952
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5070 Å2
ΔGint-28 kcal/mol
Surface area49250 Å2
MethodPISA
2
D: ATP-binding cassette sub-family G member 8
C: ATP-binding cassette sub-family G member 5


Theoretical massNumber of molelcules
Total (without water)151,4952
Polymers151,4952
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-32 kcal/mol
Surface area48390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.552, 224.804, 253.304
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISILEILEAA36 - 64936 - 649
21HISHISILEILECD36 - 64936 - 649
12GLNGLNPROPROBB24 - 66926 - 671
22GLNGLNPROPRODC24 - 66926 - 671

NCS ensembles :
ID
1
2

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Components

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


Mass: 74509.445 Da / Num. of mol.: 2 / Mutation: G2E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCG5 / Production host: Komagataella pastoris (fungus) / References: UniProt: Q9H222
#2: Protein ATP-binding cassette sub-family G member 8 / Sterolin-2


Mass: 76985.844 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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.08 Å3/Da / Density % sol: 69.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: Bicelle, ammonium sulfate, PEG 400, MES, TCEP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1801
2801
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID11
SYNCHROTRONAPS 23-ID-D21
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDNov 26, 2013
MARMOSAIC 300 mm CCD2CCDOct 18, 2013
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
21
ReflectionResolution: 3.9→50 Å / Num. obs: 46342 / % possible obs: 99.4 % / Redundancy: 18.9 % / Net I/σ(I): 8.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 3.93→25 Å / Cor.coef. Fo:Fc: 0.851 / Cor.coef. Fo:Fc free: 0.731 / SU B: 65.732 / SU ML: 0.853 / Cross valid method: THROUGHOUT / ESU R Free: 1.011
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: SAD with tungstate for initial phase determination. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32871 1845 5 %RANDOM
Rwork0.24532 ---
obs0.24951 34889 82.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.196 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å2-0 Å20 Å2
2---3.4 Å2-0 Å2
3---1.86 Å2
Refinement stepCycle: 1 / Resolution: 3.93→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18151 0 0 0 18151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01918543
X-RAY DIFFRACTIONr_bond_other_d0.0040.0218216
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.9725094
X-RAY DIFFRACTIONr_angle_other_deg1.178341693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.98652283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.83922.668776
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.664153223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.84115137
X-RAY DIFFRACTIONr_chiral_restr0.0920.22881
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02120659
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024458
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_it28.6866.2279174
X-RAY DIFFRACTIONr_mcbond_other28.6676.2269173
X-RAY DIFFRACTIONr_mcangle_it42.0629.20911443
X-RAY DIFFRACTIONr_mcangle_other42.0619.2111444
X-RAY DIFFRACTIONr_scbond_it33.8937.6189369
X-RAY DIFFRACTIONr_scbond_other33.8917.6189370
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other48.15310.74713652
X-RAY DIFFRACTIONr_long_range_B_refined56.37759.10678465
X-RAY DIFFRACTIONr_long_range_B_other56.37759.10778466
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A325070.16
12C325070.16
21B295700.18
22D295700.18
LS refinement shellResolution: 3.93→4.029 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.571 15 -
Rwork0.379 268 -
obs--8.91 %

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