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- PDB-6a6m: Crystal structure of an outward-open nucleotide-bound state of th... -

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Basic information

Entry
Database: PDB / ID: 6a6m
TitleCrystal structure of an outward-open nucleotide-bound state of the eukaryotic ABC multidrug transporter CmABCB1
ComponentsATP-binding cassette, sub-family B, member 1
KeywordsTRANSPORT PROTEIN / TRANSPORT PROTEIN ALPHA-HELICAL
Function / homology
Function and homology information


oligopeptide export from mitochondrion / ABC-type oligopeptide transporter activity / mitochondrial inner membrane / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Type 1 protein exporter / 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. ...Type 1 protein exporter / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / NITRATE ION / Probable ATP-dependent transporter ycf16
Similarity search - Component
Biological speciesCyanidioschyzon merolae strain 10D (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsKato, H. / Nakatsu, T. / Kodan, A.
CitationJournal: Nat Commun / Year: 2019
Title: Inward- and outward-facing X-ray crystal structures of homodimeric P-glycoprotein CmABCB1.
Authors: Kodan, A. / Yamaguchi, T. / Nakatsu, T. / Matsuoka, K. / Kimura, Y. / Ueda, K. / Kato, H.
History
DepositionJun 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ATP-binding cassette, sub-family B, member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0877
Polymers66,0471
Non-polymers2,0406
Water7,837435
1
A: ATP-binding cassette, sub-family B, member 1
hetero molecules

A: ATP-binding cassette, sub-family B, member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,17414
Polymers132,0932
Non-polymers4,08012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation22_564z+1/4,-y+5/4,x-1/41
Buried area21850 Å2
ΔGint-132 kcal/mol
Surface area46640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)174.340, 174.340, 174.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-1091-

HOH

21A-1185-

HOH

31A-1228-

HOH

41A-1244-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules A

#1: Protein ATP-binding cassette, sub-family B, member 1


Mass: 66046.609 Da / Num. of mol.: 1 / Mutation: Q147A, T381A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanidioschyzon merolae strain 10D (eukaryote)
Strain: 10D / Gene: CYME_CMD148C / Details (production host): pABC3 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): AD1-8u- / References: UniProt: M1VAN7
#4: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 4 types, 438 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 3.37 Å3/Da / Density % sol: 63.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 21% PEG 2000 MME, 50 mM potassium nitrate and 50 mM magnesium nitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 9, 2014
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→43.62 Å / Num. obs: 72007 / % possible obs: 99.8 % / Redundancy: 21.1 % / Rsym value: 0.152 / Net I/σ(I): 13
Reflection shellResolution: 1.9→1.95 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→43.62 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.925 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20764 3606 5.1 %RANDOM
Rwork0.16526 ---
obs0.16747 67507 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.61 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.9→43.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4488 0 103 435 5026
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0144732
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174364
X-RAY DIFFRACTIONr_angle_refined_deg1.5371.6696424
X-RAY DIFFRACTIONr_angle_other_deg1.1591.65310178
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7745604
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.2520.726234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48115767
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.641539
X-RAY DIFFRACTIONr_chiral_restr0.1650.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025340
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02907
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_it4.4446.1332380
X-RAY DIFFRACTIONr_mcbond_other4.4396.1322379
X-RAY DIFFRACTIONr_mcangle_it6.2729.1722981
X-RAY DIFFRACTIONr_mcangle_other6.2759.1742982
X-RAY DIFFRACTIONr_scbond_it4.2996.3172350
X-RAY DIFFRACTIONr_scbond_other4.3016.3222348
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6589.3813436
X-RAY DIFFRACTIONr_long_range_B_refined7.48773.4785703
X-RAY DIFFRACTIONr_long_range_B_other7.54373.6055579
X-RAY DIFFRACTIONr_rigid_bond_restr3.30739092
X-RAY DIFFRACTIONr_sphericity_free12.1985215
X-RAY DIFFRACTIONr_sphericity_bonded20.02259222
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 258 -
Rwork0.289 4685 -
obs--95.39 %

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