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- PDB-4f4c: The Crystal Structure of the Multi-Drug Transporter -

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Basic information

Entry
Database: PDB / ID: 4f4c
TitleThe Crystal Structure of the Multi-Drug Transporter
ComponentsMultidrug resistance protein pgp-1Multiple drug resistance
KeywordsHYDROLASE / PROTEIN TRANSPORT / ABC transporter / ATPase / multi-drug transporter / exporter / ATP binding
Function / homology
Function and homology information


response to nematicide / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ABC-type xenobiotic transporter / ABC-type xenobiotic transporter activity / response to metal ion / efflux transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / transmembrane transport / defense response to Gram-negative bacterium / membrane => GO:0016020 ...response to nematicide / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ABC-type xenobiotic transporter / ABC-type xenobiotic transporter activity / response to metal ion / efflux transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / transmembrane transport / defense response to Gram-negative bacterium / membrane => GO:0016020 / apical plasma membrane / innate immune response / ATP hydrolysis activity / ATP 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-0SA / Multidrug resistance protein pgp-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsJin, M.S. / Oldham, M.L. / Zhang, Q. / Chen, J.
CitationJournal: Nature / Year: 2012
Title: Crystal structure of the multidrug transporter P-glycoprotein from Caenorhabditis elegans.
Authors: Jin, M.S. / Oldham, M.L. / Zhang, Q. / Chen, J.
History
DepositionMay 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multidrug resistance protein pgp-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,9914
Polymers145,2171
Non-polymers1,7743
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)96.896, 155.360, 162.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Multidrug resistance protein pgp-1 / Multiple drug resistance / P-glycoprotein A / P-glycoprotein-related protein 1


Mass: 145217.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: pgp-1, K08E7.9 / Production host: Pichia pastoris (fungus) / References: UniProt: P34712, xenobiotic-transporting ATPase
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-0SA / undecyl 4-O-alpha-D-glucopyranosyl-1-thio-beta-D-glucopyranoside


Mass: 512.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H44O10S

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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: 4.21 Å3/Da / Density % sol: 70.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG MME 2000, 100M sodium Hepes pH 6.5, 200mM malonate , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 3, 2011 / Details: K-B pair of biomorph mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.4→50 Å / Num. all: 33973 / Num. obs: 33973 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 3.4→3.52 Å / % possible all: 95.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HYD and 3G5U

2hyd

3g5u


Resolution: 3.4→46.43 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1656341.09 / Data cutoff low absF: 0 / Isotropic thermal model: individual / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1654 4.9 %RANDOM
Rwork0.25 ---
all0.25 33973 --
obs0.25 33973 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 93.778 Å2 / ksol: 0.28 e/Å3
Displacement parametersBiso mean: 145.9 Å2
Baniso -1Baniso -2Baniso -3
1-23.11 Å20 Å20 Å2
2---15.83 Å20 Å2
3----7.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.52 Å0.46 Å
Luzzati d res low-5 Å
Luzzati sigma a0.77 Å0.74 Å
Refinement stepCycle: LAST / Resolution: 3.4→46.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9423 0 118 0 9541
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.9
X-RAY DIFFRACTIONc_improper_angle_d0.91
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 3.4→3.61 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.36 265 4.8 %
Rwork0.342 5231 -
obs--97.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION6

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