SAXSdb — 9r8o

▼

1. Structure Basics

entry_id	9r8o
deposition_date	2025-05-16
title	Primed-state RyR1 in 0.05% POPC micelles, in complex with a nanobody and FKBP
keywords	Ion channel, Ca2+, tetramer, TRANSPORT PROTEIN; TRANSPORT PROTEIN
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	— Å
rg_electron	106.80 Å
i0	57894700000.00
molecular_weight	2070700.0 kDa
excluded_volume	2594900 Å³
envelope_volume	4745500 Å³
shell_volume	368790 Å³
envelope_diameter	377.9 Å
shell_rg	104.50 Å
envelope_rg	102.90 Å
shape_rg	106.90 Å
total_rg	106.60 Å
total_atoms	145532
n_residues	18224
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	274.1 Å
rg_real	102.50 Å
rg_real_error	0.73 Å
i0_real	5.5550e+10
i0_real_error	1.0320e+09
rg_reciprocal	106.70 Å
i0_reciprocal	57790000000.0000
total_estimate	0.9136
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	127.9 Å
skewness	0.121
kurtosis	-0.691
angular_range	— – 0.0750 Å⁻¹
current_alpha	0.3069
highest_alpha	5933000000.0000
n_real_points	16
gnom_version	4.1.3
quality_criteria	AN1: 0.001; Oscil: 0.999; Stabil: 0.974; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.000

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (8)

Entity 1 polymer

description	Nanobody 9657
formula_weight	13783.1 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	K,A,D,G
atom_count	145532

QVQLQESGGGLMQAGGSLRLSCTASGSIFSINSMGWYRQAPGKQRELVATITSGNSINYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCNADRVPNGYNPWGTPNDEYDYWGQGTQVTVS

Source

organism	Lama glama
ncbi_taxonomy_id	9844
host_organism	Escherichia coli

Entity 2 polymer

description	Peptidyl-prolyl cis-trans isomerase FKBP1B
formula_weight	11667.3 kDa
ec_number	5.2.1.8
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	L,B,E,H

GVEIETISPGDGRTFPKKGQTCVVHYTGMLQNGKKFDSSRDRNKPFKFRIGKQEVIKGFEEGAAQMSLGQRAKLTCTPDVAYGATGHPGVIPPNATLIFDVELLNLE

Entity 3 polymer

description	Ryanodine receptor 1
formula_weight	564931.8 kDa
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	J,C,F,I

VQFLRTDDEVVLQCSATVLKEQLKLCLAAEGFGNRLCFLEPTSNAQNVPPDLAICCFTLEQSLSVRALQEMLANTVEAGVESSQGGGHRTLLYGHAILLRHAHSRMYLSCLTTSRSMTDKLAFDVGLQEDATGEACWWTMHPASKQRSEGEKVRVGDDLILVSVSSERYLHLSTASGELQVDASFMQTLWNMNPICSCCEEGYVTGGHVLRLFHGHMDECLTISAADSDDQRRLVYYEGGAVCTHARSLWRLEPLRISWSGSHLRWGQPLRIRHVTTGRYLALTEDQGLVVVDACKAHTKATSFCFRVSKEKLDTAPKRDVEGMGPPEIKYGESLCFVQHVASGLWLTYAAPDPKALRLGVLKKKAILHQEGHMDDALFLTRCQQEESQAARMIHSTAGLYNQFIKGLDSFSGKPRGSGPPAGPALPIEAVILSLQDLIGYFEPPSEELQHEEKQSKLRSLRNRQSLFQEEGMLSLVLNCIDRLNVYTTAAHFAEYAGEEAAESWKEIVNLLYELLASLIRGNRANCALFSTNLDWVVSKLDRLEASSGILEVLYCVLIESPEVLNIIQENHIKSIISLLDKHGRNHKVLDVLCSLCVCNGVAVRSNQDLITENLLPGRELLLQTNLINYVTSIRPNIFVGRAEGSTQYGKWYFEVMVDEVVPFLTAQATHLRVGWALTEGYSPYPGGGEGWGGNGVGDDLYSYGFDGLHLWTGHVARPVTSPGQHLLAPEDVVSCCLDLSVPSISFRINGCPVQGVFEAFNLDGLFFPVVSFSAGVKVRFLLGGRHGEFKFLPPPGYAPCHEAVLPRERLRLEPIKEYRREGPRGPHLVGPSRCLSHTDFVPCPVDTVQIVLPPHLERIREKLAENIHELWALTRIEQGWTYGPVRDDNKRLHPCLVNFHSLPEPERNYNLQMSGETLKTLLALGCHVGMADEKAEDNLKKTKLPKTYMMSNGYKPAPLDLSHVRLTPAQTTLVDRLAENGHNVWARDRVAQGWSYSAVQDIPARRNPRLVPYRLLDEATKRSNRDSLCQAVRTLLGYGYNIEPPDQEPSQVENQSRWDRVRIFRAEKSYTVQSGRWYFEFEAVTTGEMRVGWARPELRPDVELGADELAYVFNGHRGQRWHLGSEPFGRPWQSGDVVGCMIDLTENTIIFTLNGEVLMSDSGSETAFREIEIGDGFLPVCSLGPGQVGHLNLGQDVSSLRFFAICGLQEGFEPFAINMQRPVTTWFSKSLPQFEPVPPEHPHYEVARMDGTVDTPPCLRLAHRTWGSQNSLVEMLFLRLSLPVQFHQHFRCTAGATPLAPPGLQPPAEDEARAAEPDPDYENLRRSAGGWGEAEGGKEGTAKEGTPGGTPQPGVEAQPVRAENEKDATTEKNKKRGFLFKAKKAAMMTQPPATPALPRLPHDVVPADNRDDPEIILNTTTYYYSVRVFAGQEPSCVWVGWVTPDYHQHDMNFDLSKVRAVTVTMGDEQGNVHSSLKCSNCYMVWGGDFVSPGQQGRISHTDLVIGCLVDLATGLMTFTANGKESNTFFQVEPNTKLFPAVFVLPTHQNVIQFELGKQKNIMPLSAAMFLSERKNPAPQCPPRLEVQMLMPVSWSRMPNHFLQVETRRAGERLGWAVQCQDPLTMMALHIPEENRCMDILELSERLDLQRFHSHTLRLYRAVCALGNNRVAHALCSHVDQAQLLHALEDAHLPGPLRAGYYDLLISIHLESACRSRRSMLSEYIVPLTPETRAITLFPPGRKGGNARRHGLPGVGVTTSLRPPHHFSPPCFVAALPAAGVAEAPARLSPAIPLEALRDKALRMLGEAVRDGGQHARDPVGGSVEFQFVPVLKLVSTLLVMGIFGDEDVKQILKMIEPEVFTEEEEEEEEEEEEEEEEEEDEEEKEEDEEEEEKEDAEKEEEEAPEGEKEDLEEGLLQMKLPESVKLQMCNLLEYFCDQELQHRVESLAAFAERYVDKLQANQRSRYALLMRAFTMSAAETARRTREFRSPPQEQINMLLHFKDEADEEDCPLPEDIRQDLQDFHQDLLAHCGIQLEGEEEEPEEETSLSSRLRSLLETVRLVKKKEEKPEEELPAEEKKPQSLQELVSHMVVRWAQEDYVQSPELVRAMFSLLHRQYDGLGELLRALPRAYTISPSSVEDTMSLLECLGQIRSLLIVQMGPQEENLMIQSIGNIMNNKVFYQHPNLMRALGMHETVMEVMVNVLGGGETKEIRFPKMVTSCCRFLCYFCRISRQNQRSMFDHLSYLLENSGIGLGMQGSTPLDVAAASVIDNNELALALQEQDLEKVVSYLAGCGLQSCPMLLAKGYPDIGWNPCGGERYLDFLRFAVFVNGESVEENANVVVRLLIRKPECFGPALRGEGGSGLLAAIEEAIRISEDPARDGPGVRRDRRREHFGEEPPEENRVHLGHAIMSFYAALIDLLGRCAPEMHLIQAGKGEALRIRAILRSLVPLDDLVGIISLPLQIPTLGKDGALVQPKMSASFVPDHKASMVLFLDRVYGIENQDFLLHVLDVGFLPDMRAAASLDTATFSTTEMALALNRYLCLAVLPLITKCAPLFAGTEHRAIMVDSMLHTVYRLSRGRSLTKAQRDVIEDCLMALCRYIRPSMLQHLLRRLVFDVPILNEFAKMPLKLLTNHYERCWKYYCLPTGWANFGVTSEEELHLTRKLFWGIFDSLAHKKYDQELYRMAMPCLCAIAGALPPDYVDASYSSKAEKKATVDAEGNFDPRPVETLNVIIPEKLDSFINKFAEYTHEKWAFDKIQNNWSYGENVDEELKTHPMLRPYKTFSEKDKEIYRWPIKESLKAMIAWEWTIEKAREGEEERTEKKKTRKISQTAQTYDPREGYNPQPPDLSGVTLSRELQAMAEQLAENYHNTWGRKKKQELEAKGGGTHPLLVPYDTLTAKEKARDREKAQELLKFLQMNGYAVTRGLKDMELDTSSIEKRFAFGFLQQLLRWMDISQEFIAHLEAVVSSGRVEKSPHEQEIKFFAKILLPLINQYFTNHCLYFLSTPAKVLGSGGHASNKEKEMITSLFCKLAALVRHRVSLFGTDAPAVVNCLHILARSLDARTVMKSGPEIVKAGLRSFFESASEDIEKMVENLRLGKVSQARTQVKGVGQNLTYTTVALLPVLTTLFQHIAQHQFGDDVILDDVQVSCYRTLCSIYSLGTTKNTYVEKLRPALGECLARLAAAMPVAFLEPQLNEYNACSVYTTKSPRERAILGLPNSVEEMCPDIPVLDRLMADIGGLAESGARYTEMPHVIEITLPMLCSYLPRWWERGPEAPPPALPAGAPPPCTAVTSDHLNSLLGNILRIIVNNLGIDEATWMKRLAVFAQPIVSRARPELLHSHFIPTIGRLRKRAGKVVAEEEQLRLEAKAEAEEGELLVRDEFSVLCRDLYALYPLLIRYVDNNRAHWLTEPNANAEELFRMVGEIFIYWSKSHNFKREEQNFVVQNEINNMSFLTADSKSKMAKAGDAQSGGSDQERTKKKRRGDRYSVQTSLIVATLKKMLPIGLNMCAPTDQDLIMLAKTRYALKDTDEEVREFLQNNLHLQGKVEGSPSLRWQMALYRGLPGREEDADDPEKIVRRVQEVSAVLYHLEQTEHPYKSKKAVWHKLLSKQRRRAVVACFRMTPLYNLPTHRACNMFLESYKAAWILTEDHSFEDRMIDDLSKAGEQEEEEEEVEEKKPDPLHQLVLHFSRTALTEKSKLDEDYLYMAYADIMAKSCHLEEGGENGEAEEEEVEVSFEEKEMEKQRLLYQQSRLHTRGAAEMVLQMISACKGETGAMVSSTLKLGISILNGGNAEVQQKMLDYLKDKKEVGFFQSIQALMQTCSVLDLNAFERQNKAEGLGMVNEDGTVINRQNGEKVMADDEFTQDLFRFLQLLCEGHNNDFQNYLRTQTGNTTTINIIICTVDYLLRLQESISDFYWYYSGKDVIEEQGKRNFSKAMSVAKQVFNSLTEYIQGPCTGNQQSLAHSRLWDAVVGFLHVFAHMMMKLAQDSSQIELLKELLDLQKDMVVMLLSLLEGNVVNGMIARQMVDMLVESSSNVEMILKFFDMFLKLKDIVGSEAFQDYVTDPRGLISKKDFQKAMDSQKQFTGPEIQFLLSCSEADENEMINFEEFANRFQEPARDIGFNVAVLLTNLSEHVPHDPRLRNFLELAESILEYFRPYLGRIEIMGASRRIERIYFEISETNRAQWEMPQVKESKRQFIFDVVNEGGEAEKMELFVSFCEDTIFEMQIAAQISEPEGEPEADEDEGMGEAAAEGAEEGAAGAEGAAGTVAAGATARLAAAAARALRGLSYRSLRRRVRRLRRLTAREAATALAALLWAVVARAGAAGAGAAAGALRLLWGSLFGGGLVEGAKKVTVTELLAGMPDPTSDEVHGEQPAGPGGDADGAGEGEGEGDAAEGDGDEEVAGHEAGPGGAEGVVAVADGGPFRPEGAGGLGDMGDTTPAEPPTPEGSPILKRKLGVDGEEEELVPEPEPEPEPEPEKADEENGEKEEVPEAPPEPPKKAPPSPPAKKEEAGGAGMEFWGELEVQRVKFLNYLSRNFYTLRFLALFLAFAINFILLFYKVSDSPPGEDDMEGSAAGDLAGAGSGGGSGWGSGAGEEAEGDEDENMVYYFLEESTGYMEPALWCLSLLHTLVAFLCIIGYNCLKVPLVIFKREKELARKLEFDGLYITEQPGDDDVKGQWDRLVLNTPSFPSNYWDKFVKRKVLDKHGDIFGRERIAELLGMDLASLEITAHNERKPDPPPGLLTWLMSIDVKYQIWKFGVIFTDNSFLYLGWYMVMSLLGHYNNFFFAAHLLDIAMGVKTLRTILSSVTHNGKQLVMTVGLLAVVVYLYTVVAFNFFRKFYNKSEDEDEPDMKCDDMMTCYLFHMYVGVRAGGGIGDEIEDPAGDEYELYRVVFDITFFFFVIVILLAIIQGLIIDAFGELRDQQEQVKEDMETKCFICGIGSDYFDTTPHGFETHTLEEHNLANYMFFLMYLINKDETEHTGQESYVWKMYQERCWDFFPAGDCFRKQYEDQLS

Entity 4 non-polymer

description	ADENOSINE-5'-TRIPHOSPHATE
formula_weight	507.2 kDa
src_method	syn
entity_count	4

Entity 5 non-polymer

description	CAFFEINE
formula_weight	194.2 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	4

Entity 7 non-polymer

description	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
formula_weight	760.1 kDa
src_method	syn
entity_count	40

Entity 8 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	4

▶

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	triclinic

resolution	3.30 Å
resolution_method	—
num_particles	39983

fit	/app/data/saxs_computation/r8/9r8o/9r8o.fit
pddf	/app/data/pr_computation/r8/9r8o/9r8o.pr.out
profile	/app/data/saxs_computation/r8/9r8o/9r8o.dat

Primed-state RyR1 in 0.05% POPC micelles, in complex with a nanobody and FKBP

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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)