SAXSdb — 9ved

▼

1. Structure Basics

entry_id	9ved
deposition_date	2025-06-09
title	The cryo-EM structure of mouse Piezo1-MDFI complex
keywords	Piezo1, mechanosensitive channel, MDFI, MEMBRANE PROTEIN; MEMBRANE PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	63.54 Å
rg_electron	62.17 Å
i0	2172660000.00
molecular_weight	416420.0 kDa
excluded_volume	530570 Å³
envelope_volume	934260 Å³
shell_volume	123440 Å³
envelope_diameter	193.9 Å
shell_rg	65.20 Å
envelope_rg	60.76 Å
shape_rg	62.23 Å
total_rg	62.03 Å
total_atoms	29400
n_residues	3732
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

▼

3. P(r) Analysis (GNOM)

dmax	200.4 Å
rg_real	63.17 Å
rg_real_error	1.67 Å
i0_real	2.1730e+09
i0_real_error	4.5250e+07
rg_reciprocal	63.82 Å
i0_reciprocal	2175000000.0000
total_estimate	0.8478
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	88.2 Å
skewness	0.024
kurtosis	-0.560
angular_range	— – 0.1250 Å⁻¹
current_alpha	0.0001
highest_alpha	214200000.0000
n_real_points	26
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.850; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.489

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

Entity 1 polymer

description	Piezo-type mechanosensitive ion channel component 1,Green fluorescent protein
formula_weight	322403.8 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	A,C,B
atom_count	29400

MEPHVLGAGLYWLLLPCTLLAASLLRFNALSLVYLLFLLLLPWLPGPSRHSIPGHTGRLLRALLCLSLLFLVAHLAFQICLHTVPHLDQFLGQNGSLWVKVSQHIGVTRLDLKDIFNTTRLVAPDLGVLLASSLCLGLCGRLTRKAGQSRRTQELQDDDDDDDDDDEDIDAAPAVGLKGAPALATKRRLWLASRFRVTAHWLLMTSGRTLVIVLLALAGIAHPSAFSSIYLVVFLAICTWWSCHFPLSPLGFNTLCVMVSCFGAGHLICLYCYQTPFIQDMLPPGNIWARLFGLKNFVDLPNYSSPNALVLNTKHAWPIYVSPGILLLLYYTATSLLKLHKSCPSELRKETPREDEEHELELDHLEPEPQARDATQGEMPMTTEPDLDNCTVHVLTSQSPVRQRPVRPRLAELKEMSPLHGLGHLIMDQSYVCALIAMMVWSIMYHSWLTFVLLLWACLIWTVRSRHQLAMLCSPCILLYGLTLCCLRYVWAMELPELPTTLGPVSLHQLGLEHTRYPCLDLGAMLLYLLTFWLLLRQFVKEKLLKKQKVPAALLEVTVADTEPTQTQTLLRSLGELVTGIYVKYWIYVCAGMFIVVSFAGRLVVYKIVYMFLFLLCLTLFQVYYTLWRKLLRVFWWLVVAYTMLVLIAVYTFQFQDFPTYWRNLTGFTDEQLGDLGLEQFSVSELFSSILIPGFFLLACILQLHYFHRPFMQLTDLEHVPPPGTRHPRWAHRQDAVSEAPLLEHQEEEEVFREDGQSMDGPHQATQVPEGTASKWGLVADRLLDLAASFSAVLTRIQVFVRRLLELHVFKLVALYTVWVALKEVSVMNLLLVVLWAFALPYPRFRPMASCLSTVWTCIIIVCKMLYQLKIVNPHEYSSNCTEPFPNNTNLQPLEINQSLLYRGPVDPANWFGVRKGYPNLGYIQNHLQILLLLVFEAVVYRRQEHYRRQHQQAPLPAQAVCADGTRQRLDQDLLSCLKYFINFFFYKFGLEICFLMAVNVIGQRMNFMVILHGCWLVAILTRRRREAIARLWPNYCLFLTLFLLYQYLLCLGMPPALCIDYPWRWSKAIPMNSALIKWLYLPDFFRAPNSTNLISDFLLLLCASQQWQVFSAERTEEWQRMAGINTDHLEPLRGEPNPIPNFIHCRSYLDMLKVAVFRYLFWLVLVVVFVAGATRISIFGLGYLLACFYLLLFGTTLLQKDTRAQLVLWDCLILYNVTVIISKNMLSLLSCVFVEQMQSNFCWVIQLFSLVCTVKGYYDPKEMMTRDRDCLLPVEEAGIIWDSICFFFLLLQRRIFLSHYFLHVSADLKATALQASRGFALYNAANLKSINFHRQIEEKSLAQLKRQMKRIRAKQEKYRQSQASRGQLQSKDPQDPSQEPGPDSPGGSSPPRRQWWRPWLDHATVIHSGDYFLFESDSEEEEEALPEDPRPAAQSAFQMAYQAWVTNAQTVLRQRRERARQERAEQLASGGDLNPDVEPVDVPEDEMAGRSHMMQRVLSTMQFLWVLGQATVDGLTRWLRAFTKHHRTMSDVLCAERYLLTQELLRVGEVRRGVLDQLYVGEDEATLSGPVETRDGPSTASSGLGAEEPLSSMTDDTSSPLSTGYNTRSGSEEIVTDAGDLQAGTSLHGSQELLANARTRMRTASELLLDRRLHIPELEEAERFEAQQGRTLRLLRAGYQCVAAHSELLCYFIIILNHMVTASAASLVLPVLVFLWAMLTIPRPSKRFWMTAIVFTEVMVVTKYLFQFGFFPWNSYVVLRRYENKPYFPPRILGLEKTDSYIKYDLVQLMALFFHRSQLLCYGLWDHEEDRYPKDHCRSSVKDREAKEEPEAKLESQSETGTGHPKEPVLAGTPRDHIQGKGSIRSKDVIQDPPEDLKPRHTRHISIRFRRRKETPGPKGTAVMETEHEEGEGKETTERKRPRHTQEKSKFRERMKAAGRRLQSFCVSLAQSFYQPLQRFFHDILHTKYRAATDVYALMFLADIVDIIIIIFGFWAFGKHSAATDIASSLSDDQVPQAFLFMLLVQFGTMVIDRALYLRKTVLGKLAFQVVLVVAIHIWMFFILPAVTERMFSQNAVAQLWYFVKCIYFALSAYQIRCGYPTRILGNFLTKKYNHLNLFLFQGFRLVPFLVELRAVMDWVWTDTTLSLSNWMCVEDIYANIFIIKCSRETEKKYPQPKGQKKKKIVKYGMGGLIILFLIAIIWFPLLFMSLIRSVVGVVNQPIDVTVTLKLGGYEPLFTMSAQQPSIVPFTPQAYEELSQQFDPYPLAMQFISQYSPEDIVTAQIEGSSGALWRISPPSRAQMKQELYNGTADITLRFTWNFQRDLAKGGTVEYTNEKHTLELAPNSTARRQLAQLLEGRPDQSVVIPHLFPKYIRAPNGPEANPVKQLQPDEEEDYLGVRIQLRREQVGTGASGEQAGTKASDFLEWWVIELQDCKADCNLLPMVIFSDKVSPPSLGFLAGYGIVGLYVSIVLVVGKFVRGFFSEISHSIMFEELPCVDRILKLCQDIFLVRETRELELEEELYAKLIFLYRSPETMIKWTRERESNSLEVLFQGPTAAAAVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEKRDHMVLLEFVTAAGITLGMDELYKSGGGHHHHHHHHHH

Source

organism	Aequorea victoria
ncbi_taxonomy_id	6100
host_organism	Homo sapiens

Entity 2 polymer

description	Isoform I-mfA of MyoD family inhibitor
formula_weight	27539.6 kDa
src_method	man
entity_count	3

Polymer

type	polypeptide(L)
strand_id	F,D,E

MDYKDDDDKGGGGSSTTNGSSATMSQVSGQCPSRCDAPHGVPSAALDPAQTMSLLPGLEVARSTHPVEASSEEGFPEEAAPSMPHDSGLRAQQALNSIDLDVPTEAVTCQPQGNPQGCTPLLPNGSSHDHLSEPGSAGHAGNGALGGSKAHRKLQTHPSLGSQAGRKSRGSARSASQVPLQAQEDCCVHCILSCLFCEFLTLCNILLDCATCGSCSSEDSCLCCCCCGSGECADCDLPCDLDCGIVDACCESADCLEICMECCGLCFSS

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

▶

6. Citations (1)

▶

length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	3.63 Å
resolution_method	—
num_particles	56377

fit	/app/data/saxs_computation/ve/9ved/9ved.fit
pddf	/app/data/pr_computation/ve/9ved/9ved.pr.out
profile	/app/data/saxs_computation/ve/9ved/9ved.dat

The cryo-EM structure of mouse Piezo1-MDFI complex

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

EM 3D

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)