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- PDB-1q3h: mouse CFTR NBD1 with AMP.PNP -

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Basic information

Entry
Database: PDB / ID: 1q3h
Titlemouse CFTR NBD1 with AMP.PNP
ComponentsCystic fibrosis transmembrane conductance regulator
KeywordsMEMBRANE PROTEIN / ABC transporter nucleotide binding domain
Function / homology
Function and homology information


RHO GTPases regulate CFTR trafficking / RHOQ GTPase cycle / positive regulation of mast cell activation / transepithelial chloride transport / positive regulation of establishment of Sertoli cell barrier / Aggrephagy / positive regulation of cyclic nucleotide-gated ion channel activity / Sec61 translocon complex binding / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity ...RHO GTPases regulate CFTR trafficking / RHOQ GTPase cycle / positive regulation of mast cell activation / transepithelial chloride transport / positive regulation of establishment of Sertoli cell barrier / Aggrephagy / positive regulation of cyclic nucleotide-gated ion channel activity / Sec61 translocon complex binding / channel-conductance-controlling ATPase / intracellularly ATP-gated chloride channel activity / water transport / positive regulation of enamel mineralization / transepithelial water transport / negative regulation of vascular associated smooth muscle cell apoptotic process / intracellular pH elevation / enamel mineralization / negative regulation of type B pancreatic cell development / amelogenesis / chloride channel inhibitor activity / Cargo recognition for clathrin-mediated endocytosis / ABC-family proteins mediated transport / Clathrin-mediated endocytosis / multicellular organismal-level water homeostasis / vesicle docking involved in exocytosis / Ub-specific processing proteases / membrane hyperpolarization / cholesterol transport / bicarbonate transport / bicarbonate transmembrane transporter activity / chloride transport / chloride transmembrane transporter activity / sperm capacitation / chloride channel activity / cholesterol biosynthetic process / positive regulation of exocytosis / positive regulation of insulin secretion involved in cellular response to glucose stimulus / microvillus / chloride channel complex / ATPase-coupled transmembrane transporter activity / sodium ion transmembrane transport / ABC-type transporter activity / cellular response to cAMP / cellular response to forskolin / isomerase activity / chloride transmembrane transport / response to endoplasmic reticulum stress / establishment of localization in cell / PDZ domain binding / lung development / recycling endosome membrane / vasodilation / protein-folding chaperone binding / early endosome membrane / basolateral plasma membrane / early endosome / response to xenobiotic stimulus / apical plasma membrane / neuronal cell body / dendrite / endoplasmic reticulum membrane / enzyme binding / cell surface / ATP hydrolysis activity / ATP binding / membrane / nucleus / plasma membrane / 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 / ABC transporters family signature. ...: / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Cystic fibrosis transmembrane conductance regulator
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLewis, H.A. / Buchanan, S.G. / Burley, S.K. / Conners, K. / Dickey, M. / Dorwart, M. / Fowler, R. / Gao, X. / Guggino, W.B. / Hendrickson, W.A.
CitationJournal: Embo J. / Year: 2004
Title: Structure of nucleotide-binding domain 1 of the cystic fibrosis transmembrane conductance regulator.
Authors: Lewis, H.A. / Buchanan, S.G. / Burley, S.K. / Conners, K. / Dickey, M. / Dorwart, M. / Fowler, R. / Gao, X. / Guggino, W.B. / Hendrickson, W.A. / Hunt, J.F. / Kearins, M.C. / Lorimer, D. / ...Authors: Lewis, H.A. / Buchanan, S.G. / Burley, S.K. / Conners, K. / Dickey, M. / Dorwart, M. / Fowler, R. / Gao, X. / Guggino, W.B. / Hendrickson, W.A. / Hunt, J.F. / Kearins, M.C. / Lorimer, D. / Maloney, P.C. / Post, K.W. / Rajashankar, K.R. / Rutter, M.E. / Sauder, J.M. / Shriver, S. / Thibodeau, P.H. / Thomas, P.J. / Zhang, M. / Zhao, X. / Emtage, S.
History
DepositionJul 29, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Cystic fibrosis transmembrane conductance regulator
D: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,75616
Polymers128,3934
Non-polymers2,36212
Water2,810156
1
A: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6894
Polymers32,0981
Non-polymers5913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6894
Polymers32,0981
Non-polymers5913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6894
Polymers32,0981
Non-polymers5913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Cystic fibrosis transmembrane conductance regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6894
Polymers32,0981
Non-polymers5913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Cystic fibrosis transmembrane conductance regulator
B: Cystic fibrosis transmembrane conductance regulator
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)261,51132
Polymers256,7878
Non-polymers4,72424
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation7_646y+1,x-1,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area26270 Å2
ΔGint-240 kcal/mol
Surface area80430 Å2
MethodPQS
Unit cell
Length a, b, c (Å)171.68, 171.68, 109.59
Angle α, β, γ (deg.)90, 90, 90
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein
Cystic fibrosis transmembrane conductance regulator / / CFTR / cAMP- dependent chloride channel


Mass: 32098.324 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: CFTR OR ABCC7 / Production host: Escherichia coli (E. coli) / References: UniProt: P26361
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 3.14 Å3/Da / Density % sol: 60.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Sodium acetate, tris buffer, sodium chloride, DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4, 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-10 mg/mlprotein1drop
23.5-4.0 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9198 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 12, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9198 Å / Relative weight: 1
ReflectionResolution: 2.5→33 Å / Num. all: 57029 / Num. obs: 57029 / % possible obs: 99.9 % / Observed criterion σ(I): 1.8 / Rsym value: 0.1
Reflection shellResolution: 2.5→2.63 Å / Rsym value: 0.408 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.5 Å / Redundancy: 14.1 % / Rmerge(I) obs: 0.122
Reflection shell
*PLUS
% possible obs: 99.6 % / Redundancy: 13.6 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
XFITdata reduction
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→33 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.257 2851 Random
Rwork0.216 --
all0.218 57024 -
obs0.218 57024 -
Refinement stepCycle: LAST / Resolution: 2.5→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8355 0 144 156 8655
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_d1.6
LS refinement shellResolution: 2.5→2.63 Å / % reflection obs: 100 %
Refinement
*PLUS
Rfactor Rfree: 0.266 / Rfactor Rwork: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_d1.9

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