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- PDB-6l6p: hASIC2a co-crystallized with Mamb-1 -

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Basic information

Entry
Database: PDB / ID: 6l6p
TitlehASIC2a co-crystallized with Mamb-1
ComponentsAcid-sensing ion channel 2
KeywordsTRANSPORT PROTEIN / Ion channel / complex
Function / homology
Function and homology information


regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback / monoatomic ion-gated channel activity / sensory perception of sour taste / detection of mechanical stimulus involved in sensory perception / protein localization to synapse / peripheral nervous system development / regulation of monoatomic ion transmembrane transport / cellular response to acidic pH / positive regulation of synapse assembly / inorganic cation transmembrane transport ...regulation of systemic arterial blood pressure by aortic arch baroreceptor feedback / monoatomic ion-gated channel activity / sensory perception of sour taste / detection of mechanical stimulus involved in sensory perception / protein localization to synapse / peripheral nervous system development / regulation of monoatomic ion transmembrane transport / cellular response to acidic pH / positive regulation of synapse assembly / inorganic cation transmembrane transport / ligand-gated sodium channel activity / voltage-gated sodium channel activity / phototransduction / regulation of vasoconstriction / synapse assembly / sodium ion transmembrane transport / central nervous system development / regulation of membrane potential / establishment of localization in cell / sensory perception of sound / Stimuli-sensing channels / cellular response to xenobiotic stimulus / chemical synaptic transmission / dendritic spine / neuronal cell body / negative regulation of apoptotic process / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.08 Å
AuthorsLei, F. / Jian, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: To Be Published
Title: hASIC2a 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 20, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Assembly

Deposited unit
A: Acid-sensing ion channel 2
B: Acid-sensing ion channel 2
C: Acid-sensing ion channel 2


Theoretical massNumber of molelcules
Total (without water)156,7643
Polymers156,7643
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16040 Å2
ΔGint-68 kcal/mol
Surface area59150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.863, 155.664, 156.644
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: _ / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEAA20 - 45822 - 460
21PHEPHEBB20 - 45822 - 460
12PHEPHEAA20 - 45822 - 460
22PHEPHECC20 - 45822 - 460
13ILEILEBB19 - 45821 - 460
23ILEILECC19 - 45821 - 460

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Acid-sensing ion channel 2 / ASIC2 / Amiloride-sensitive brain sodium channel / Amiloride-sensitive cation channel 1 / neuronal ...ASIC2 / Amiloride-sensitive brain sodium channel / Amiloride-sensitive cation channel 1 / neuronal / Amiloride-sensitive cation channel neuronal 1 / Brain sodium channel 1 / BNaC1 / Mammalian degenerin homolog / MDEG


Mass: 52254.723 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ASIC2, ACCN, ACCN1, BNAC1, MDEG / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q16515
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.27 Å3/Da / Density % sol: 71.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 4% Tascimate pH 8.0, 12% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3.08→49.33 Å / Num. obs: 50203 / % possible obs: 99.6 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.045 / Rrim(I) all: 0.117 / Net I/σ(I): 12.6 / Num. measured all: 329259 / Scaling rejects: 38
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.08-3.186.31.2942851745430.6440.5571.4121.599.6
12.32-49.335.70.03146868240.9980.0150.03545.693

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.08→49.23 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.828 / SU B: 27.73 / SU ML: 0.426 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.968 / ESU R Free: 0.415
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2822 2474 5 %RANDOM
Rwork0.2312 ---
obs0.2337 47331 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 230.7 Å2 / Biso mean: 100.171 Å2 / Biso min: 35.19 Å2
Baniso -1Baniso -2Baniso -3
1--6 Å2-0 Å2-0 Å2
2---3.99 Å20 Å2
3---9.99 Å2
Refinement stepCycle: final / Resolution: 3.08→49.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10363 0 0 6 10369
Biso mean---43.79 -
Num. residues----1297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01310632
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179782
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.64414415
X-RAY DIFFRACTIONr_angle_other_deg1.1781.56722749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.73351289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48223.109534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.18151816
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8941545
X-RAY DIFFRACTIONr_chiral_restr0.0680.21363
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211749
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022230
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A127200.12
12B127200.12
21A125790.12
22C125790.12
31B123740.13
32C123740.13
LS refinement shellResolution: 3.08→3.16 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 166 -
Rwork0.409 3451 -
all-3617 -
obs--98.56 %

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