SAXSdb — 8ixo

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Piezo-type mechanosensitive ion channel component 1

Mus musculus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 1–2547 Chain B； UniProt 1–2547 Chain F； UniProt 1–2547	Mutation：S2472E	PLX (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL × 6 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 6 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 3	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.3 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.00 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8IXO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11YE Curved structure of mPiezo1 in plasma membrane vesicles Deposited 2026-03-18	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain C 1–2547（2547 aa） Chain D 1–2547（2547 aa） Chain E 1–2547（2547 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
11ZC Flat structure of mPiezo1 in plasma membrane vesicles Deposited 2026-03-19	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–2547（2547 aa） Chain C 1–2547（2547 aa） Chain E 1–2547（2547 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.00 Å
3JAC Cryo-EM study of a channel Deposited 2015-06-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1959–2547（589 aa） Chain B 1959–2547（589 aa） Chain C 1959–2547（589 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2；25 mM NaPIPES, 140 mM NaCl, 2 mM DTT and 0.026% (w/v) C12E10 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
4RAX A regulatory domain of an ion channel Deposited 2014-09-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2214–2457（244 aa） Fragment：UNP residues 2214-2457	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.2M Magnesium chloride, 0.1M Hepes pH 7.5, 25% w/w PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K	Resolution 1.45 Å R-free 0.176
5Z10 Structure of the mechanosensitive Piezo1 channel Deposited 2017-12-22	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–2547（2547 aa） Chain B 1–2547（2547 aa） Chain C 1–2547（2547 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；After a 15 sec waiting time, the grids were blotted for 3.5 sec and plunged into liquid ethane	Resolution 3.97 Å
6B3R Structure of the mechanosensitive channel Piezo1 Deposited 2017-09-22	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–2547（2547 aa） Chain C 1–2547（2547 aa） Chain E 1–2547（2547 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot for 1 second with -1 force before plunging	Resolution 3.80 Å
6BPZ Structure of the mechanically activated ion channel Piezo1 Deposited 2017-11-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1137–1597（461 aa） Chain A 1657–2547（891 aa） Chain B 1137–1597（461 aa） Chain B 1657–2547（891 aa） Chain C 1137–1597（461 aa） Chain C 1657–2547（891 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6LQI Cryo-EM structure of the mouse Piezo1 isoform Piezo1.1 Deposited 2020-01-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–2547（2547 aa） Chain B 1–2547（2547 aa） Chain C 1–2547（2547 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
7WLT the Curved Structure of mPIEZO1 in Lipid Bilayer Deposited 2022-01-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–2547（2547 aa） Chain C 1–2547（2547 aa） Chain E 1–2547（2547 aa）	Not recorded	PLX (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL × 21 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 3 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.46 Å
7WLU The Flattened Structure of mPIEZO1 in Lipid Bilayer Deposited 2022-01-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–2547（2547 aa） Chain C 1–2547（2547 aa） Chain E 1–2547（2547 aa）	Not recorded	PLX (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.81 Å
8IMZ Cryo-EM structure of mouse Piezo1-MDFIC complex (composite map) Deposited 2023-03-07	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–2547（2547 aa） Chain B 1–2547（2547 aa） Chain C 1–2547（2547 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.66 Å
8IXN Curved structure of mPIEZO1-S2472E Deposited 2023-04-01	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–2547（2547 aa） Chain C 1–2547（2547 aa） Chain D 1–2547（2547 aa）	Mutation：S2472E Mutation：S2472E Mutation：S2472E	PLX (9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL × 6 PEE 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine × 3 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.07 Å
9VED The cryo-EM structure of mouse Piezo1-MDFI complex Deposited 2025-06-09	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1–2547（2547 aa） Chain B 1–2547（2547 aa） Chain C 1–2547（2547 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.63 Å

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PIEZ1_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–2547； UniProt 1–2547 Author chain B； PDBConstruct 1–2547； UniProt 1–2547 Author chain F； PDBConstruct 1–2547； UniProt 1–2547

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	8ixo
Deposition date deposition_date	2023-04-01
Structure title title	Intermediate structure of mPIEZO1-S2472E
Keywords keywords	Open-state structure, PIEZO1 channel, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	74.30 Å
Radius of gyration Rg (electron density) rg_electron	72.69 Å
Forward intensity I(0) i0	2546540000.00
Molecular weight molecular_weight	454390.0 kDa
Excluded volume excluded_volume	579760 Å³
Envelope volume envelope_volume	1180600 Å³
Hydration-shell volume shell_volume	138270 Å³
Envelope diameter envelope_diameter	232.8 Å
Shell Rg shell_rg	67.42 Å
Envelope Rg envelope_rg	73.18 Å
Shape Rg shape_rg	72.85 Å
Total Rg total_rg	71.96 Å
Total atoms total_atoms	32112
Residues n_residues	4185
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	215.4 Å
Rg (real space) rg_real	74.27 Å
Rg uncertainty (real space) rg_real_error	1.26 Å
I(0) (real space) i0_real	2.5450e+09
I(0) uncertainty (real space) i0_real_error	5.3210e+07
Rg (reciprocal space) rg_reciprocal	74.01 Å
I(0) (reciprocal space) i0_reciprocal	2545000000.0000
Solution quality estimate total_estimate	0.8448
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	102.6 Å
Skewness Skewness skewness	0.247
Kurtosis Kurtosis kurtosis	-0.447
Angular range angular_range	— – 0.1050 Å⁻¹
Current regularization parameter α current_alpha	0.0014
Highest regularization parameter α highest_alpha	106100000.0000
Real-space data points n_real_points	22
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.980; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.041

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Piezo-type mechanosensitive ion channel component 1
Molecular weight formula_weight	292362.7 kDa
Mutation mutation	S2472E
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,A,B
Atom count atom_count	32136

MEPHVLGAGLYWLLLPCTLLAASLLRFNALSLVYLLFLLLLPWLPGPSRHSIPGHTGRLLRALLCLSLLFLVAHLAFQICLHTVPHLDQFLGQNGSLWVKVSQHIGVTRLDLKDIFNTTRLVAPDLGVLLASSLCLGLCGRLTRKAGQSRRTQELQDDDDDDDDDDEDIDAAPAVGLKGAPALATKRRLWLASRFRVTAHWLLMTSGRTLVIVLLALAGIAHPSAFSSIYLVVFLAICTWWSCHFPLSPLGFNTLCVMVSCFGAGHLICLYCYQTPFIQDMLPPGNIWARLFGLKNFVDLPNYSSPNALVLNTKHAWPIYVSPGILLLLYYTATSLLKLHKSCPSELRKETPREDEEHELELDHLEPEPQARDATQGEMPMTTEPDLDNCTVHVLTSQSPVRQRPVRPRLAELKEMSPLHGLGHLIMDQSYVCALIAMMVWSIMYHSWLTFVLLLWACLIWTVRSRHQLAMLCSPCILLYGLTLCCLRYVWAMELPELPTTLGPVSLHQLGLEHTRYPCLDLGAMLLYLLTFWLLLRQFVKEKLLKKQKVPAALLEVTVADTEPTQTQTLLRSLGELVTGIYVKYWIYVCAGMFIVVSFAGRLVVYKIVYMFLFLLCLTLFQVYYTLWRKLLRVFWWLVVAYTMLVLIAVYTFQFQDFPTYWRNLTGFTDEQLGDLGLEQFSVSELFSSILIPGFFLLACILQLHYFHRPFMQLTDLEHVPPPGTRHPRWAHRQDAVSEAPLLEHQEEEEVFREDGQSMDGPHQATQVPEGTASKWGLVADRLLDLAASFSAVLTRIQVFVRRLLELHVFKLVALYTVWVALKEVSVMNLLLVVLWAFALPYPRFRPMASCLSTVWTCIIIVCKMLYQLKIVNPHEYSSNCTEPFPNNTNLQPLEINQSLLYRGPVDPANWFGVRKGYPNLGYIQNHLQILLLLVFEAVVYRRQEHYRRQHQQAPLPAQAVCADGTRQRLDQDLLSCLKYFINFFFYKFGLEICFLMAVNVIGQRMNFMVILHGCWLVAILTRRRREAIARLWPNYCLFLTLFLLYQYLLCLGMPPALCIDYPWRWSKAIPMNSALIKWLYLPDFFRAPNSTNLISDFLLLLCASQQWQVFSAERTEEWQRMAGINTDHLEPLRGEPNPIPNFIHCRSYLDMLKVAVFRYLFWLVLVVVFVAGATRISIFGLGYLLACFYLLLFGTTLLQKDTRAQLVLWDCLILYNVTVIISKNMLSLLSCVFVEQMQSNFCWVIQLFSLVCTVKGYYDPKEMMTRDRDCLLPVEEAGIIWDSICFFFLLLQRRIFLSHYFLHVSADLKATALQASRGFALYNAANLKSINFHRQIEEKSLAQLKRQMKRIRAKQEKYRQSQASRGQLQSKDPQDPSQEPGPDSPGGSSPPRRQWWRPWLDHATVIHSGDYFLFESDSEEEEEALPEDPRPAAQSAFQMAYQAWVTNAQTVLRQRRERARQERAEQLASGGDLNPDVEPVDVPEDEMAGRSHMMQRVLSTMQFLWVLGQATVDGLTRWLRAFTKHHRTMSDVLCAERYLLTQELLRVGEVRRGVLDQLYVGEDEATLSGPVETRDGPSTASSGLGAEEPLSSMTDDTSSPLSTGYNTRSGSEEIVTDAGDLQAGTSLHGSQELLANARTRMRTASELLLDRRLHIPELEEAERFEAQQGRTLRLLRAGYQCVAAHSELLCYFIIILNHMVTASAASLVLPVLVFLWAMLTIPRPSKRFWMTAIVFTEVMVVTKYLFQFGFFPWNSYVVLRRYENKPYFPPRILGLEKTDSYIKYDLVQLMALFFHRSQLLCYGLWDHEEDRYPKDHCRSSVKDREAKEEPEAKLESQSETGTGHPKEPVLAGTPRDHIQGKGSIRSKDVIQDPPEDLKPRHTRHISIRFRRRKETPGPKGTAVMETEHEEGEGKETTERKRPRHTQEKSKFRERMKAAGRRLQSFCVSLAQSFYQPLQRFFHDILHTKYRAATDVYALMFLADIVDIIIIIFGFWAFGKHSAATDIASSLSDDQVPQAFLFMLLVQFGTMVIDRALYLRKTVLGKLAFQVVLVVAIHIWMFFILPAVTERMFSQNAVAQLWYFVKCIYFALSAYQIRCGYPTRILGNFLTKKYNHLNLFLFQGFRLVPFLVELRAVMDWVWTDTTLSLSNWMCVEDIYANIFIIKCSRETEKKYPQPKGQKKKKIVKYGMGGLIILFLIAIIWFPLLFMSLIRSVVGVVNQPIDVTVTLKLGGYEPLFTMSAQQPSIVPFTPQAYEELSQQFDPYPLAMQFISQYSPEDIVTAQIEGSSGALWRISPPSRAQMKQELYNGTADITLRFTWNFQRDLAKGGTVEYTNEKHTLELAPNSTARRQLAQLLEGRPDQSVVIPHLFPKYIRAPNGPEANPVKQLQPDEEEDYLGVRIQLRREQVGTGASGEQAGTKASDFLEWWVIELQDCKADCNLLPMVIFSDKVSPPSLGFLAGYGIVGLYVEIVLVVGKFVRGFFSEISHSIMFEELPCVDRILKLCQDIFLVRETRELELEEELYAKLIFLYRSPETMIKWTRERE

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	;(9R,11S)-9-({[(1S)-1-HYDROXYHEXADECYL]OXY}METHYL)-2,2-DIMETHYL-5,7,10-TRIOXA-2LAMBDA~5~-AZA-6LAMBDA~5~-PHOSPHAOCTACOSANE-6,6,11-TRIOL ;
Molecular weight formula_weight	767.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
Molecular weight formula_weight	792.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	1,2-dioleoyl-sn-glycero-3-phosphoethanolamine
Molecular weight formula_weight	744.0 kDa
Source method src_method	syn
Copy count entity_count	3

▶

8. Citations (1)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	4.00 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	434112

fit	/app/data/saxs_computation/ix/8ixo/8ixo.fit
pddf	/app/data/pr_computation/ix/8ixo/8ixo.pr.out
profile	/app/data/saxs_computation/ix/8ixo/8ixo.dat

Intermediate structure of mPIEZO1-S2472E

1. Protein Identity and Related Structures Protein Identity & Related Structures

Piezo-type mechanosensitive ion channel component 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D