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- PDB-4c3z: Nucleotide-free crystal structure of nucleotide-binding domain 1 ... -

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Basic information

Entry
Database: PDB / ID: 4c3z
TitleNucleotide-free crystal structure of nucleotide-binding domain 1 from human MRP1 supports a general-base catalysis mechanism for ATP hydrolysis.
ComponentsMULTIDRUG RESISTANCE-ASSOCIATED PROTEIN 1
KeywordsTRANSPORT PROTEIN / ATP-BINDING CASSETTE TRANSPORTERS / MULTIDRUG RESISTANCE PROTEIN 1 / GENERAL-BASE MECHANISM
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 / sphingolipid transporter activity / cobalamin transport / leukotriene transport / 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 / sphingolipid transporter activity / cobalamin transport / leukotriene transport / 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 / Sphingolipid de novo biosynthesis / heme catabolic process / xenobiotic transport across blood-brain barrier / transepithelial transport / export across plasma membrane / ABC-type xenobiotic transporter / ATPase-coupled lipid transmembrane transporter activity / Paracetamol ADME / xenobiotic transport / NFE2L2 regulating MDR associated enzymes / ABC-type xenobiotic transporter activity / phospholipid translocation / Heme degradation / efflux transmembrane transporter activity / xenobiotic transmembrane transporter activity / transport across blood-brain barrier / lateral plasma membrane / ATPase-coupled transmembrane transporter activity / 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 / ATP-binding cassette, ABC transporter-type domain profile. ...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
Multidrug resistance-associated protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChaptal, V. / Gueguen-Chaignon, V. / Magnard, S. / Falson, P. / Di Pietro, A. / Baubichon-Cortay, H.
CitationJournal: Biochem.Pharm. / Year: 2014
Title: Nucleotide-Free Crystal Structure of Nucleotide-Binding Domain 1 from Human Abcc1 Supports a 'General-Base Catalysis' Mechanism for ATP Hydrolysis.
Authors: Chaptal, V. / Magnard, S. / Gueguen-Chaignon, V. / Falson, P. / Di Pietro, A. / Baubichon-Cortay, H.
History
DepositionAug 28, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2015Group: Database references / Structure summary
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Dec 20, 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 / struct_site
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 / _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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)29,6097
Polymers29,0331
Non-polymers5766
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.299, 64.299, 65.491
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 / ATP-BINDING CASSETTE SUB-FAMILY C MEMBER 1 / LEUKOTRIENE C(4) TRANSPORTER / LTC4 TRANSPORTER / ...ATP-BINDING CASSETTE SUB-FAMILY C MEMBER 1 / LEUKOTRIENE C(4) TRANSPORTER / LTC4 TRANSPORTER / NUCLEOTIDE BINDING DOMAIN 1


Mass: 29032.789 Da / Num. of mol.: 1 / Fragment: NUCLEOTIDE BINDING DOMAIN, RESIDUES 628-881
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33527
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.69 Å3/Da / Density % sol: 54.91 % / Description: NONE
Crystal growpH: 5.5 / Details: 25% PEG 3.350, 0.2M AMSO4, 0.1M BISTRIS PH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→42.42 Å / Num. obs: 17692 / % possible obs: 99.9 % / Observed criterion σ(I): 1.9 / Redundancy: 3.8 % / Biso Wilson estimate: 37.73 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.7
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CBZ

2cbz


Resolution: 2.1→42.423 Å / SU ML: 0.23 / σ(F): 1.96 / Phase error: 22.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1941 865 4.9 %
Rwork0.1636 --
obs0.1651 17635 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→42.423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 30 81 1869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091814
X-RAY DIFFRACTIONf_angle_d1.1782464
X-RAY DIFFRACTIONf_dihedral_angle_d13.096655
X-RAY DIFFRACTIONf_chiral_restr0.079280
X-RAY DIFFRACTIONf_plane_restr0.005314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1002-2.23180.26951490.22062808X-RAY DIFFRACTION99
2.2318-2.40410.25981570.20032749X-RAY DIFFRACTION100
2.4041-2.6460.22751480.17522809X-RAY DIFFRACTION100
2.646-3.02870.21941210.17092801X-RAY DIFFRACTION100
3.0287-3.81550.19611500.15152815X-RAY DIFFRACTION100
3.8155-42.43140.1551400.1522788X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.59720.24920.75525.11040.71063.89840.18480.46980.1306-1.0654-0.42330.7553-0.2838-0.59510.28710.39680.1166-0.12160.3602-0.06490.2819-11.6595-21.004-18.2695
24.7013.32832.66.95992.79435.271-0.1673-0.12040.3092-0.0419-0.25070.094-0.57840.02210.19790.29640.0462-0.04180.1945-0.01360.1931-1.7923-8.48690.4595
320.38311.08246.68180.19546.31410.10480.0637-0.26780.1329-0.129-0.28210.78370.3059-0.1050.2568-0.0056-0.00250.2695-0.01250.2459-3.5728-33.5798-9.1196
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 641:712)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 713:823)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 824:871)

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