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- PDB-6l6i: hASIC1a co-crystallized with Mamb-1 -

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Basic information

Entry
Database: PDB / ID: 6l6i
TitlehASIC1a co-crystallized with Mamb-1
ComponentsAcid-sensing ion channel 1
KeywordsTRANSPORT PROTEIN / Ion channel / complex
Function / homology
Function and homology information


monoatomic ion-gated channel activity / sensory perception of sour taste / pH-gated monoatomic ion channel activity / ligand-gated sodium channel activity / cellular response to pH / negative regulation of neurotransmitter secretion / neurotransmitter secretion / response to acidic pH / sodium ion transport / protein homotrimerization ...monoatomic ion-gated channel activity / sensory perception of sour taste / pH-gated monoatomic ion channel activity / ligand-gated sodium channel activity / cellular response to pH / negative regulation of neurotransmitter secretion / neurotransmitter secretion / response to acidic pH / sodium ion transport / protein homotrimerization / associative learning / sodium ion transmembrane transport / behavioral fear response / response to amphetamine / regulation of membrane potential / calcium ion transmembrane transport / Stimuli-sensing channels / memory / presynapse / Golgi apparatus / cell surface / plasma membrane
Similarity search - Function
Epithelial sodium channel, chordates / Epithelial sodium channel, conserved site / Amiloride-sensitive sodium channels signature. / Epithelial sodium channel / Amiloride-sensitive sodium channel
Similarity search - Domain/homology
Acid-sensing ion channel 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.24 Å
AuthorsLei, F. / Jian, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: To Be Published
Title: hASIC1a co-crystallized with Mamb-1
Authors: Lei, F. / Jian, S.
History
DepositionOct 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acid-sensing ion channel 1
B: Acid-sensing ion channel 1
C: Acid-sensing ion channel 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,7696
Polymers155,1063
Non-polymers6643
Water1629
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14980 Å2
ΔGint-87 kcal/mol
Surface area58840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.920, 146.620, 207.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERALAALAAA35 - 45725 - 447
21SERSERALAALABB35 - 45725 - 447
12ALAALAGLUGLUAA44 - 45234 - 442
22ALAALAGLUGLUCC44 - 45234 - 442
13ALAALAGLUGLUBB44 - 45234 - 442
23ALAALAGLUGLUCC44 - 45234 - 442

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Acid-sensing ion channel 1 / ASIC1 / Amiloride-sensitive cation channel 2 / neuronal / Brain sodium channel 2 / BNaC2


Mass: 51701.871 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASIC1, ACCN2, BNAC2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P78348
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.97 Å3/Da / Density % sol: 69.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M magnesium formate dehydrate, 14% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.24→49.581 Å / Num. obs: 40093 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.07 / Rrim(I) all: 0.181 / Net I/σ(I): 9.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
3.24-3.376.51.47644630.4890.6230.01604100
11.68-49.535.40.049010.9980.0190.04593

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Processing

Software
NameVersionClassification
Aimless0.7.3data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S3W

3s3w


Resolution: 3.24→49.581 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.902 / SU B: 23.362 / SU ML: 0.365 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.43
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2499 2031 5.1 %RANDOM
Rwork0.2142 ---
obs0.216 38004 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 276.02 Å2 / Biso mean: 94.465 Å2 / Biso min: 27.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å2-0 Å2-0 Å2
2---2.94 Å20 Å2
3---3.3 Å2
Refinement stepCycle: final / Resolution: 3.24→49.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10270 0 42 9 10321
Biso mean--129.66 46.79 -
Num. residues----1281
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01310577
X-RAY DIFFRACTIONr_bond_other_d0.0020.0179568
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.65114323
X-RAY DIFFRACTIONr_angle_other_deg1.2211.57822262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.75251278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.2823.019573
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.688151810
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9461555
X-RAY DIFFRACTIONr_chiral_restr0.0670.21335
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211826
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022271
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A12428
12B12428
21A11937
22C11937
31B11906
32C11906
LS refinement shellResolution: 3.24→3.324 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.421 154 -
Rwork0.35 2730 -
obs--99.97 %

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