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- PDB-2cbz: Structure of the human Multidrug Resistance Protein 1 Nucleotide ... -

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Basic information

Entry
Database: PDB / ID: 2cbz
TitleStructure of the human Multidrug Resistance Protein 1 Nucleotide Binding Domain 1
ComponentsMULTIDRUG RESISTANCE-ASSOCIATED PROTEIN 1
KeywordsTRANSPORT / ABC PROTEINS / MRP1/ABCC1 / NUCLEOTIDE-BINDING DOMAIN / ATP-BINDING / HYDROLYSIS
Function / homology
Function and homology information


sphingolipid translocation / cyclic nucleotide transport / Transport of RCbl within the body / ABC-type vitamin B12 transporter activity / carboxylic acid transmembrane transport / carboxylic acid transmembrane transporter activity / leukotriene transport / cobalamin transport / sphingolipid transporter activity / glutathione transmembrane transport ...sphingolipid translocation / cyclic nucleotide transport / Transport of RCbl within the body / ABC-type vitamin B12 transporter activity / carboxylic acid transmembrane transport / carboxylic acid transmembrane transporter activity / leukotriene transport / cobalamin transport / sphingolipid transporter activity / glutathione transmembrane transport / glutathione transmembrane transporter activity / ABC-type glutathione-S-conjugate transporter / ABC-type glutathione S-conjugate transporter activity / leukotriene metabolic process / ATPase-coupled inorganic anion transmembrane transporter activity / Synthesis of Leukotrienes (LT) and Eoxins (EX) / sphingolipid biosynthetic process / heme catabolic process / Sphingolipid de novo biosynthesis / xenobiotic transport across blood-brain barrier / transepithelial transport / ATPase-coupled lipid transmembrane transporter activity / export across plasma membrane / ABC-type xenobiotic transporter / Paracetamol ADME / NFE2L2 regulating MDR associated enzymes / ABC-type xenobiotic transporter activity / phospholipid translocation / Heme degradation / xenobiotic transport / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / transport across blood-brain barrier / lateral plasma membrane / ABC-type transporter activity / xenobiotic metabolic process / basal plasma membrane / cell chemotaxis / ABC-family proteins mediated transport / Cytoprotection by HMOX1 / transmembrane transport / positive regulation of inflammatory response / cellular response to amyloid-beta / cellular response to oxidative stress / basolateral plasma membrane / response to xenobiotic stimulus / apical plasma membrane / ATP hydrolysis activity / extracellular exosome / 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
ADENOSINE-5'-TRIPHOSPHATE / Multidrug resistance-associated protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsRamaen, O. / Leulliot, N. / Sizun, C. / Ulryck, N. / Pamlard, O. / Lallemand, J.-Y. / van Tilbeurgh, H. / Jacquet, E.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure of the Human Multidrug Resistance Protein 1 Nucleotide Binding Domain 1 Bound to Mg(2+)/ATP Reveals a Non-Productive Catalytic Site.
Authors: Ramaen, O. / Leulliot, N. / Sizun, C. / Ulryck, N. / Pamlard, O. / Lallemand, J.-Y. / Van Tilbeurgh, H. / Jacquet, E.
History
DepositionJan 10, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MULTIDRUG RESISTANCE-ASSOCIATED PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4333
Polymers25,9021
Non-polymers5312
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)65.560, 65.560, 64.612
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein MULTIDRUG RESISTANCE-ASSOCIATED PROTEIN 1 / MRP1 / ATP-BINDING CASSETTE SUB- FAMILY C MEMBER 1


Mass: 25901.539 Da / Num. of mol.: 1 / Fragment: NBD1 DOMAIN, RESIDUES 642-871
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33527
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O
Compound detailsMAY PARTICIPATE DIRECTLY IN THE ACTIVE TRANSPORT OF DRUGS INTO SUBCELLULAR ORGANELLES OR INFLUENCE ...MAY PARTICIPATE DIRECTLY IN THE ACTIVE TRANSPORT OF DRUGS INTO SUBCELLULAR ORGANELLES OR INFLUENCE DRUG DISTRIBUTION INDIRECTLY.
Sequence detailsASN642 TO SER871 DOMAIN, 6X HIS C-TERMINAL TAG

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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: 2.77 Å3/Da / Density % sol: 55.23 %
Crystal growpH: 8 / Details: 8% PEG1000, 0.1M MG ACETATE PH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 49722 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 14.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.1
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XMI

1xmi


Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.145 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.065 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.187 2490 5 %RANDOM
Rwork0.16 ---
obs0.161 47194 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20.03 Å20 Å2
2--0.06 Å20 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 32 284 2068
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221817
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1941.9922472
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9125229
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.12124.45974
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.59615302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.741510
X-RAY DIFFRACTIONr_chiral_restr0.0730.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021350
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.2842
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21269
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2219
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9151.51167
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.4521834
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2353733
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5134.5638
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: 1.5→1.54 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.324 203
Rwork0.25 3489

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