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- PDB-6nlo: Human ABCC6 NBD1 H812A in Apo state -

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Basic information

Entry
Database: PDB / ID: 6nlo
TitleHuman ABCC6 NBD1 H812A in Apo state
ComponentsMultidrug resistance-associated protein 6
KeywordsTRANSPORT PROTEIN / ABCC6 / NBD1 / Apo state / ATP-Binding Cassette transporter C6 / nucleotide binding domain 1
Function / homology
Function and homology information


Defective ABCC6 causes PXE / inorganic diphosphate transport / inhibition of non-skeletal tissue mineralization / ATP transport / leukotriene transport / ABC-type glutathione-S-conjugate transporter / ABC-type glutathione S-conjugate transporter activity / response to sodium phosphate / intracellular phosphate ion homeostasis / ATPase-coupled inorganic anion transmembrane transporter activity ...Defective ABCC6 causes PXE / inorganic diphosphate transport / inhibition of non-skeletal tissue mineralization / ATP transport / leukotriene transport / ABC-type glutathione-S-conjugate transporter / ABC-type glutathione S-conjugate transporter activity / response to sodium phosphate / intracellular phosphate ion homeostasis / ATPase-coupled inorganic anion transmembrane transporter activity / phosphate ion homeostasis / Translocases; Catalysing the translocation of other compounds; Linked to the hydrolysis of a nucleoside triphosphate / response to magnesium ion / ATPase-coupled transmembrane transporter activity / calcium ion homeostasis / ATP metabolic process / visual perception / basal plasma membrane / ABC-family proteins mediated transport / transmembrane transport / gene expression / basolateral plasma membrane / response to xenobiotic stimulus / endoplasmic reticulum membrane / ATP hydrolysis activity / extracellular region / nucleoplasm / ATP binding / membrane / plasma membrane
Similarity search - Function
Multi drug resistance-associated protein / : / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain ...Multi drug resistance-associated protein / : / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / 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. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ATP-binding cassette sub-family C member 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.85021981416 Å
AuthorsZheng, A. / Thibodeau, P.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122091 United States
CitationJournal: To be published
Title: Structures of human ABCC6 NBD1 and NBD2
Authors: Zheng, A. / Thibodeau, P.H.
History
DepositionJan 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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: Multidrug resistance-associated protein 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3382
Polymers25,2421
Non-polymers961
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.600, 92.600, 45.510
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Multidrug resistance-associated protein 6 / ATP-binding cassette sub-family C member 6 / Anthracycline resistance-associated protein / Multi- ...ATP-binding cassette sub-family C member 6 / Anthracycline resistance-associated protein / Multi-specific organic anion transporter E / MOAT-E


Mass: 25241.824 Da / Num. of mol.: 1 / Fragment: nucleotide binding domain 1, residues 622-859 / Mutation: M848V, H812A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABCC6, ARA, MRP6 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O95255
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 2.34 Å3/Da / Density % sol: 47.47 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 2.1-2.4M Ammonium Sulfate 0.1M HEPES pH 6.8-8.2 / PH range: 6.8-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jul 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.85→39.581 Å / Num. obs: 5467 / % possible obs: 99.9 % / Redundancy: 19.41 % / Biso Wilson estimate: 53.6577065481 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.047 / Rrim(I) all: 0.209 / Net I/σ(I): 15.32
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 10.66 % / Rmerge(I) obs: 1.474 / Mean I/σ(I) obs: 2 / Num. unique obs: 541 / CC1/2: 0.765 / Rpim(I) all: 0.474 / Rrim(I) all: 1.55 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
Coot0.8.8model building
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BZS

6bzs


Resolution: 2.85021981416→39.5805684083 Å / SU ML: 0.356837989154 / Cross valid method: FREE R-VALUE / σ(F): 1.47636511379 / Phase error: 25.2360877641
RfactorNum. reflection% reflection
Rfree0.259750519508 544 9.97798972854 %
Rwork0.229303242172 --
obs0.232547704813 5452 99.8900696226 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 53.1407473374 Å2
Refinement stepCycle: LAST / Resolution: 2.85021981416→39.5805684083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1696 0 5 0 1701
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004566432059781733
X-RAY DIFFRACTIONf_angle_d0.7660257737682364
X-RAY DIFFRACTIONf_chiral_restr0.0489093270488279
X-RAY DIFFRACTIONf_plane_restr0.00553225835177305
X-RAY DIFFRACTIONf_dihedral_angle_d10.2357732791027
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8502-3.13690.3306400854941330.2986309197491211X-RAY DIFFRACTION100
3.1369-3.59060.3145862158131340.2500396819111209X-RAY DIFFRACTION99.9255952381
3.5906-4.52280.2533862059881370.211031000661224X-RAY DIFFRACTION100
4.5228-39.58440.2169178071311400.2125093605561264X-RAY DIFFRACTION99.645138396

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