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- PDB-3gd7: Crystal structure of human NBD2 complexed with N6-Phenylethyl-ATP... -

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Basic information

Entry
Database: PDB / ID: 3gd7
TitleCrystal structure of human NBD2 complexed with N6-Phenylethyl-ATP (P-ATP)
ComponentsFusion complex of Cystic fibrosis transmembrane conductance regulator, residues 1193-1427 and Maltose/maltodextrin import ATP-binding protein malK, residues 219-371
KeywordsHYDROLASE / CFTR / ABC transporter / nucleotide binding domain / NBD / ATP / P-ATP / N6-Phenylethyl-ATP / ATP-binding / Chloride channel / Ion transport / Ionic channel / Transport / Cell inner membrane / Cell membrane / Sugar transport
Function / homology
Function and homology information


ABC-type maltose transporter / ABC-type maltose transporter activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / positive regulation of voltage-gated chloride channel activity / positive regulation of cyclic nucleotide-gated ion channel activity / Sec61 translocon complex binding / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity ...ABC-type maltose transporter / ABC-type maltose transporter activity / negative regulation of maltose transport / enzyme IIA-maltose transporter complex / negative regulation of transmembrane transport / positive regulation of voltage-gated chloride channel activity / positive regulation of cyclic nucleotide-gated ion channel activity / Sec61 translocon complex binding / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / positive regulation of enamel mineralization / transepithelial water transport / RHO GTPases regulate CFTR trafficking / intracellular pH elevation / amelogenesis / chloride channel inhibitor activity / ATPase-coupled inorganic anion transmembrane transporter activity / Golgi-associated vesicle membrane / multicellular organismal-level water homeostasis / cholesterol transport / membrane hyperpolarization / vesicle docking involved in exocytosis / bicarbonate transport / bicarbonate transmembrane transporter activity / chloride channel regulator activity / chloride transmembrane transporter activity / sperm capacitation / chloride channel activity / cholesterol biosynthetic process / maltose transport complex / RHOQ GTPase cycle / positive regulation of insulin secretion involved in cellular response to glucose stimulus / positive regulation of exocytosis / maltose transport / maltodextrin transmembrane transport / chloride channel complex / ATPase-coupled transmembrane transporter activity / ABC-type transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / cellular response to forskolin / cellular response to cAMP / chloride transmembrane transport / response to endoplasmic reticulum stress / ATP-binding cassette (ABC) transporter complex / isomerase activity / establishment of localization in cell / PDZ domain binding / Defective CFTR causes cystic fibrosis / Late endosomal microautophagy / clathrin-coated endocytic vesicle membrane / ABC-family proteins mediated transport / transmembrane transport / recycling endosome / Aggrephagy / Chaperone Mediated Autophagy / recycling endosome membrane / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / protein-folding chaperone binding / early endosome membrane / DNA-binding transcription factor binding / early endosome / endosome membrane / Ub-specific processing proteases / apical plasma membrane / lysosomal membrane / endoplasmic reticulum membrane / enzyme binding / cell surface / ATP hydrolysis activity / protein-containing complex / ATP binding / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Maltose/Maltodextrin import ATP-binding protein malK family profile. / Transport-associated OB, type 2 / TOBE domain / MalK OB fold domain / ABC transporter, maltose/maltodextrin import, MalK-like / : / : / CFTR regulator domain / Cystic fibrosis TM conductance regulator (CFTR), regulator domain / Cystic fibrosis transmembrane conductance regulator ...Maltose/Maltodextrin import ATP-binding protein malK family profile. / Transport-associated OB, type 2 / TOBE domain / MalK OB fold domain / ABC transporter, maltose/maltodextrin import, MalK-like / : / : / CFTR regulator domain / Cystic fibrosis TM conductance regulator (CFTR), regulator domain / Cystic fibrosis transmembrane conductance regulator / Molybdate/tungstate binding, C-terminal / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / : / 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 / Nucleic acid-binding proteins / 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. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / Beta Barrel / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-B44 / Cystic fibrosis transmembrane conductance regulator / Maltose/maltodextrin import ATP-binding protein MalK
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsAtwell, S. / Antonysamy, S. / Conners, K. / Emtage, S. / Gheyi, T. / Lewis, H.A. / Lu, F. / Sauder, J.M. / Wasserman, S.R. / Zhao, X.
CitationJournal: To be Published
Title: Crystal structure of human NBD2 complexed with N6-Phenylethyl-ATP (P-ATP)
Authors: Atwell, S. / Antonysamy, S. / Guggino, W.B. / Conners, K. / Emtage, S. / Gheyi, T. / Hunt, J.F. / Lewis, H.A. / Lu, F. / Sauder, J.M. / Weber, P.C. / Wetmore, D. / Zhao, X.
History
DepositionFeb 23, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion complex of Cystic fibrosis transmembrane conductance regulator, residues 1193-1427 and Maltose/maltodextrin import ATP-binding protein malK, residues 219-371
B: Fusion complex of Cystic fibrosis transmembrane conductance regulator, residues 1193-1427 and Maltose/maltodextrin import ATP-binding protein malK, residues 219-371
C: Fusion complex of Cystic fibrosis transmembrane conductance regulator, residues 1193-1427 and Maltose/maltodextrin import ATP-binding protein malK, residues 219-371
D: Fusion complex of Cystic fibrosis transmembrane conductance regulator, residues 1193-1427 and Maltose/maltodextrin import ATP-binding protein malK, residues 219-371
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,5208
Polymers174,0754
Non-polymers2,4454
Water4,576254
1
D: Fusion complex of Cystic fibrosis transmembrane conductance regulator, residues 1193-1427 and Maltose/maltodextrin import ATP-binding protein malK, residues 219-371
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1302
Polymers43,5191
Non-polymers6111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Fusion complex of Cystic fibrosis transmembrane conductance regulator, residues 1193-1427 and Maltose/maltodextrin import ATP-binding protein malK, residues 219-371
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1302
Polymers43,5191
Non-polymers6111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Fusion complex of Cystic fibrosis transmembrane conductance regulator, residues 1193-1427 and Maltose/maltodextrin import ATP-binding protein malK, residues 219-371
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1302
Polymers43,5191
Non-polymers6111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
C: Fusion complex of Cystic fibrosis transmembrane conductance regulator, residues 1193-1427 and Maltose/maltodextrin import ATP-binding protein malK, residues 219-371
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,1302
Polymers43,5191
Non-polymers6111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-39 kcal/mol
Surface area63650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.837, 173.725, 82.574
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Fusion complex of Cystic fibrosis transmembrane conductance regulator, residues 1193-1427 and Maltose/maltodextrin import ATP-binding protein malK, residues 219-371 / CFTR / cAMP-dependent chloride channel / ATP-binding cassette transporter sub-family C member 7


Mass: 43518.781 Da / Num. of mol.: 4
Mutation: Q1280E, Y1307N, E1308A, Q1309A, W1310H, H1402A, Q1411D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Escherichia coli K-12 (bacteria)
Gene: CFTR,malK / Plasmid: pET26 / Production host: Escherichia coli (E. coli)
Strain (production host): BL21(DE3)RIL with chaperone coexpression
References: UniProt: P13569, UniProt: P68187
#2: Chemical
ChemComp-B44 / N-(2-phenylethyl)adenosine 5'-(tetrahydrogen triphosphate)


Mass: 611.330 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H24N5O13P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.84 Å3/Da / Density % sol: 56.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 1.1-1.25 M tri-sodium citrate, pH 5.5-8, sitting drop, temperature 277K, VAPOR DIFFUSION
PH range: 5.5-8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 11, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1158 Å / Relative weight: 1
ReflectionResolution: 2.7→54 Å / Num. obs: 55240 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.121 / Rsym value: 0.121 / Net I/σ(I): 6.4
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.7 / Num. unique all: 7974 / Rsym value: 0.566 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
d*TREKdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q12

1q12


Resolution: 2.7→54 Å / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: FREE R-VALUE
RfactorNum. reflectionSelection details
Rfree0.308 2768 RANDOM
Rwork0.247 --
obs-55240 -
Displacement parametersBiso max: 106.7 Å2 / Biso mean: 59.261 Å2 / Biso min: 19.12 Å2
Refinement stepCycle: LAST / Resolution: 2.7→54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11424 0 156 254 11834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02211820
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9481.97916118
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.67451501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.5622.257491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.715151873
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9371571
X-RAY DIFFRACTIONr_chiral_restr0.060.21867

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