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- PDB-2pzf: Minimal human CFTR first nucleotide binding domain as a head-to-t... -

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Basic information

Entry
Database: PDB / ID: 2pzf
TitleMinimal human CFTR first nucleotide binding domain as a head-to-tail dimer with delta F508
ComponentsCystic fibrosis transmembrane conductance regulator
KeywordsHYDROLASE / NBD / ABC transporter / CFTR / F508
Function / homology
Function and homology information


positive regulation of voltage-gated chloride 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 / amelogenesis / intracellular pH elevation ...positive regulation of voltage-gated chloride 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 / amelogenesis / intracellular pH elevation / chloride channel inhibitor activity / : / Golgi-associated vesicle membrane / multicellular organismal-level water homeostasis / cholesterol transport / bicarbonate transport / bicarbonate transmembrane transporter activity / vesicle docking involved in exocytosis / chloride channel regulator activity / membrane hyperpolarization / chloride transmembrane transporter activity / sperm capacitation / cholesterol biosynthetic process / RHOQ GTPase cycle / chloride channel activity / positive regulation of exocytosis / ATPase-coupled transmembrane transporter activity / chloride channel complex / positive regulation of insulin secretion involved in cellular response to glucose stimulus / ABC-type transporter activity / 14-3-3 protein binding / cellular response to forskolin / chloride transmembrane transport / response to endoplasmic reticulum stress / cellular response to cAMP / PDZ domain binding / establishment of localization in cell / clathrin-coated endocytic vesicle membrane / Defective CFTR causes cystic fibrosis / Late endosomal microautophagy / recycling endosome / ABC-family proteins mediated transport / transmembrane transport / recycling endosome membrane / Chaperone Mediated Autophagy / Aggrephagy / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / protein-folding chaperone binding / early endosome membrane / early endosome / endosome membrane / Ub-specific processing proteases / apical plasma membrane / lysosomal membrane / endoplasmic reticulum membrane / enzyme binding / cell surface / protein-containing complex / ATP hydrolysis activity / ATP binding / nucleus / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
: / CFTR regulator domain / Cystic fibrosis TM conductance regulator (CFTR), regulator domain / Cystic fibrosis transmembrane conductance regulator / : / 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 ...: / CFTR regulator domain / Cystic fibrosis TM conductance regulator (CFTR), regulator domain / Cystic fibrosis transmembrane conductance regulator / : / 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 / Cystic fibrosis transmembrane conductance regulator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAtwell, S. / Conners, K. / Emtage, S. / Gheyi, T. / Glenn, N.R. / Hendle, J. / Lewis, H.A. / Lu, F. / Rodgers, L.A. / Romero, R. ...Atwell, S. / Conners, K. / Emtage, S. / Gheyi, T. / Glenn, N.R. / Hendle, J. / Lewis, H.A. / Lu, F. / Rodgers, L.A. / Romero, R. / Sauder, J.M. / Smith, D. / Tien, H. / Wasserman, S.R. / Zhao, X.
Citation
Journal: Protein Eng.Des.Sel. / Year: 2010
Title: Structures of a minimal human CFTR first nucleotide-binding domain as a monomer, head-to-tail homodimer, and pathogenic mutant.
Authors: Atwell, S. / Brouillette, C.G. / Conners, K. / Emtage, S. / Gheyi, T. / Guggino, W.B. / Hendle, J. / Hunt, J.F. / Lewis, H.A. / Lu, F. / Protasevich, I.I. / Rodgers, L.A. / Romero, R. / ...Authors: Atwell, S. / Brouillette, C.G. / Conners, K. / Emtage, S. / Gheyi, T. / Guggino, W.B. / Hendle, J. / Hunt, J.F. / Lewis, H.A. / Lu, F. / Protasevich, I.I. / Rodgers, L.A. / Romero, R. / Wasserman, S.R. / Weber, P.C. / Wetmore, D. / Zhang, F.F. / Zhao, X.
#1: Journal: Pediatr.Pulmonol.Suppl. / Year: 2007
Title: Structure of the human CFTR NBD1 domain as a homodimer: insights and applications
Authors: Atwell, S. / Conners, K. / Emtage, S. / Gheyi, T. / Lewis, H. / Lu, F. / Romero, R. / Zhao, X.
History
DepositionMay 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Jun 14, 2017Group: Database references / Refinement description ...Database references / Refinement description / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / software / struct_ref_seq_dif
Item: _entity.pdbx_ec / _entity.pdbx_fragment ..._entity.pdbx_ec / _entity.pdbx_fragment / _entity_name_com.name / _software.name / _struct_ref_seq_dif.align_id / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.pdbx_seq_db_seq_num / _struct_ref_seq_dif.seq_num
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cystic fibrosis transmembrane conductance regulator
B: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8196
Polymers50,7562
Non-polymers1,0634
Water2,342130
1
A: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9103
Polymers25,3781
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9103
Polymers25,3781
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-41 kcal/mol
Surface area18650 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.152, 92.662, 106.471
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cystic fibrosis transmembrane conductance regulator / CFTR / ATP-binding cassette sub-family C member 7 / Channel conductance-controlling ATPase / cAMP- ...CFTR / ATP-binding cassette sub-family C member 7 / Channel conductance-controlling ATPase / cAMP-dependent chloride channel


Mass: 25378.232 Da / Num. of mol.: 2 / Fragment: CFTR NBD1 387-646 / Mutation: del405-436, delF508
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CFTR, ABCC7 / Plasmid: modified pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon+RIL / References: UniProt: P13569, EC: 3.6.3.49
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.1 Å3/Da / Density % sol: 41.33 %
Crystal growTemperature: 281 K / Method: vapor diffusion / pH: 8.5
Details: Protein: 9.5mg/ml NBD1, 0.15M NaCl, 0.01M methionine, 0.01M HEPES pH 7.5, 10% glycerol, 0.001M TCEP, 0.002M ATP; Well: 0.1M Tris pH 8.5, 35% PEG 4K, 0.2M NaAcetate; Cryo: 25% DMSO, vapor ...Details: Protein: 9.5mg/ml NBD1, 0.15M NaCl, 0.01M methionine, 0.01M HEPES pH 7.5, 10% glycerol, 0.001M TCEP, 0.002M ATP; Well: 0.1M Tris pH 8.5, 35% PEG 4K, 0.2M NaAcetate; Cryo: 25% DMSO, vapor diffusion, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9797 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 18, 2007 / Details: mirrors
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2→25.583 Å / Num. all: 29245 / Num. obs: 29245 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.127 / Rsym value: 0.127 / Net I/σ(I): 4.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.116.30.7860.92578541120.78696.9
2.11-2.246.30.5441.32452338890.54496.9
2.24-2.396.20.3681.72328737410.36898.1
2.39-2.586.40.2632.82230034900.26398.7
2.58-2.836.50.1853.82131632670.18599.8
2.83-3.166.90.13452048829890.134100
3.16-3.6570.10261864926510.102100
3.65-4.4770.0896.71581122720.089100
4.47-6.326.80.086.71225218010.08100
6.32-25.586.20.0657.8637110330.06597.9

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345data collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PZE

2pze


Resolution: 2→25.118 Å / Isotropic thermal model: isotropic / Cross valid method: FREE R-VALUE / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 1493 -RANDOM
Rwork0.2107 ---
all0.213 29187 --
obs0.213 29187 98.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: Mask bulk solvent correction
Displacement parametersBiso mean: 29.015 Å2
Baniso -1Baniso -2Baniso -3
1-0.913 Å20 Å20 Å2
2--0.587 Å20 Å2
3----1.499 Å2
Refinement stepCycle: LAST / Resolution: 2→25.118 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3254 0 64 130 3448
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d1.326
X-RAY DIFFRACTIONr_planar_tor5.626
X-RAY DIFFRACTIONr_chiral_restr0.083
X-RAY DIFFRACTIONr_plane_restr0.005
X-RAY DIFFRACTIONr_mcbond_it1.081
X-RAY DIFFRACTIONr_mcangle_it1.927
X-RAY DIFFRACTIONr_scbond_it2.693
X-RAY DIFFRACTIONr_scangle_it3.827

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