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- PDB-3wmg: Crystal structure of an inward-facing eukaryotic ABC multidrug tr... -

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Basic information

Entry
Database: PDB / ID: 3wmg
TitleCrystal structure of an inward-facing eukaryotic ABC multidrug transporter G277V/A278V/A279V mutant in complex with an cyclic peptide inhibitor, aCAP
Components
  • ATP-binding cassette, sub-family B, member 1
  • anti-CmABCB1 peptide
KeywordsTRANSPORT PROTEIN/INHIBITOR / Rec fold / Multi drug transporter / Macrocyclic peptide / TRANSPORT PROTEIN-INHIBITOR COMPLEX
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
ABC transporter transmembrane region fold / ABC transporter type 1, transmembrane domain / 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 transmembrane region fold / ABC transporter type 1, transmembrane domain / 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 / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
anti-CmABCB1 peptide / Probable ATP-dependent transporter ycf16
Similarity search - Component
Biological speciesCyanidioschyzon merolae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsKodan, A. / Yamaguchi, T. / Nakatsu, T. / Sakiyama, K. / Hipolito, C.J. / Fujioka, A. / Hirokane, R. / Ikeguchi, K. / Watanabe, B. / Hirtake, J. ...Kodan, A. / Yamaguchi, T. / Nakatsu, T. / Sakiyama, K. / Hipolito, C.J. / Fujioka, A. / Hirokane, R. / Ikeguchi, K. / Watanabe, B. / Hirtake, J. / Kimura, Y. / Suga, H. / Ueda, K. / Kato, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structural basis for gating mechanisms of a eukaryotic P-glycoprotein homolog.
Authors: Kodan, A. / Yamaguchi, T. / Nakatsu, T. / Sakiyama, K. / Hipolito, C.J. / Fujioka, A. / Hirokane, R. / Ikeguchi, K. / Watanabe, B. / Hiratake, J. / Kimura, Y. / Suga, H. / Ueda, K. / Kato, H.
History
DepositionNov 18, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1May 14, 2014Group: Non-polymer description
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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 B, member 1
B: anti-CmABCB1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0668
Polymers69,5312
Non-polymers2,5356
Water1,820101
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.490, 180.490, 153.164
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-914-

HOH

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Components

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


Mass: 67420.078 Da / Num. of mol.: 1 / Fragment: TMD and NBD domain, UNP RESIDUES 93-696 / Mutation: G277V, A278V, A279V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cyanidioschyzon merolae (eukaryote) / Gene: CYME_CMD148C / Plasmid: pABC3 / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): AD1-8u / References: UniProt: M1VAN7
#2: Protein/peptide anti-CmABCB1 peptide


Type: Cyclic peptide / Class: Inhibitor / Mass: 2111.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SELECTED by the RAPID system protocol / References: anti-CmABCB1 peptide
#3: Sugar
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.45 Å3/Da / Density % sol: 64.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 15% (w/v) PEG 2000 MME, 100mM magnesium nitrate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 21, 2012
RadiationMonochromator: double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 37184 / Num. obs: 36663 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 11.2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.4-2.499.90.575196.7
2.49-2.5910.80.426198.7
2.59-2.711.30.311199.5
2.7-2.8511.50.225199.6
2.85-3.0211.50.166199.7
3.02-3.2611.50.126199.8
3.26-3.5811.50.097199.9
3.58-4.111.40.078199.9
4.1-5.1711.40.069199.9
5.17-5010.90.049192.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
AMoREphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.4→36.47 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 13.899 / SU ML: 0.163 / SU R Cruickshank DPI: 0.2786 / Cross valid method: THROUGHOUT / ESU R: 0.29 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24607 1852 5 %RANDOM
Rwork0.21903 ---
obs0.22039 35220 98.5 %-
all-35651 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.103 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.21 Å2-0 Å2
2--0.42 Å2-0 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 2.4→36.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4540 0 99 101 4740
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0194736
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.081.9826428
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6865606
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71823.135185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.10815722
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8551531
X-RAY DIFFRACTIONr_chiral_restr0.0740.2759
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213495
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.397→2.459 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 116 -
Rwork0.305 2434 -
obs--95.54 %
Refinement TLS params.Method: refined / Origin x: 20.7196 Å / Origin y: 51.491 Å / Origin z: 34.8452 Å
111213212223313233
T0.0716 Å20.043 Å2-0.0006 Å2-0.0826 Å20.0212 Å2--0.0139 Å2
L0.167 °2-0.0579 °2-0.1056 °2-0.1201 °20.0759 °2--0.0825 °2
S-0.0531 Å °-0.0296 Å °0.0038 Å °-0.0061 Å °0.0373 Å °0.0312 Å °0.0253 Å °0.0233 Å °0.0158 Å °

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