SAXSdb — 9qt9

▼

1. Structure Basics

entry_id	9qt9
deposition_date	2025-04-08
title	Cryo-EM structure of the core of the Arabidopsis thaliana UBR4/DI19/CALM1 complex
keywords	Ubiquitin ligase, Protein quality control, LIGASE; LIGASE
method	ELECTRON MICROSCOPY

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	48.83 Å
rg_electron	48.72 Å
i0	402706000.00
molecular_weight	135240.0 kDa
excluded_volume	156080 Å³
envelope_volume	345650 Å³
shell_volume	61388 Å³
envelope_diameter	153.0 Å
shell_rg	49.79 Å
envelope_rg	47.14 Å
shape_rg	48.71 Å
total_rg	48.78 Å
total_atoms	9662
n_residues	1948
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	153.8 Å
rg_real	48.67 Å
rg_real_error	1.61 Å
i0_real	4.0270e+08
i0_real_error	8.2440e+06
rg_reciprocal	48.83 Å
i0_reciprocal	402800000.0000
total_estimate	0.8935
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	57.7 Å
skewness	0.138
kurtosis	-0.636
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	26990000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.967; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.714

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (3)

Entity 1 polymer

description	Auxin transport protein (BIG)
formula_weight	572672.2 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	9662

MADDLANLCRFLFDDTAFPSLSSSASSDLFSRRLRSDDSIKRGLRSFYLLLRWGVAPIGGDDADSSGKLRFETWSDSQLQALVSISQAILLLSRSLLVDQLEPIVLGVIQEVMEFSLSFLEKSSFRQNDLKMEINMEILLEIASFDGSEKQYDILPDFSPAEVAELWPAFSGEHDNMDAQSLVKCTFQGGRCSNEEKPVDRLLITLMSECIESDVQAQSVVKSPFQQDCGDLNPFTRHLAVVHLRCVCRLIMVCKELVQLPNMLDEKTVDQAVLDKLSFCLRILKLLGSLSKDVQSIENDGSLLQAVASFTDAFPKLFRVFFEFTNHTATEGNIESLSLALVEGFLNLVQLIFGKSSVFQNVQACVAASIVSNLDSSVWRYDGSSCNLTPPLAYFPRSVIYTLKLIQDLKRQPYHIHDLRVLESEVTYEDVSSTVDSVYFHLRQEKIPLLKCFTVEDIMRVIFPSSSQWMDNFFHLVYFLHREGVKLRPKVERTYSSLRSNSFAEVESQISHDDEALFGNLFSEGSRSLCSIEPNDQPPVSVSSNLLLQAAKELLNFLRACILCQEWVPSIYEDGCKKLDTGHIDILLNIVGCSIEDKASDGGCMLQDEGRPGHVAFELLLNLLRSRALSDFLESYLFQQILVVENSDFNYNDKTLALLAHTLLCRPGLAGAQLRAKIYDGFVSFVTERARGICAEALSLKELTACLPSAFHIEILLMAFHLSNEAEKAKFSNLIASCLHKVDTPAGICDGPQLSSWAMLISRLLVLLHHMLLHPNTCPTSLMLDLRSKLREVRSCGSNLHVTVGDHLSSWASLVARGITDSWAEDESVSHLMSQMIDFSPHPPTFQNDVSTAKTLNLDYGDLSASLCRVLGLWKGKKAGKVEDLLVERYIFMLSSDIARINCALDSQPSLHVNYQNVDISNSVDLISTSHLLVGDINVVGRNIELRNILIGVLNQLQAAPEQVVEDLGWDYIREGAWLSLLLYFLDGGVWDYCNKNSCSEIDPFWKECTSVDAKYVAAAEGVVSYLMKTGDIAELLRMLSSLVGKYLRVYKKAFLATFSDWNHHGHSSPSLLLLKHTQFGKSLQGEYAKIGDNSLHLQCIFYLSKLDSLGDGRGSGVLWKVFWEFMVHGFPTSLQTSSAILLSCILSIRCIVLTINGLLKLGNSKEKFGVDTSVLHQLLDSIMIIKFDQVFESFHGKCEEIHQNICAVLQLPDLTELFLMKDMEGFVRDISAEQIDRSQVLEGVITKIVDVMDSLSKDSSKSDIFKFYLGVDAVSEHTREFYELQRGDLSVFIDSLDYCSLEPVNIKVLNFLVDLLSVAQSPDLRRRVQQKFIDMDLISLSGWLERRLLGSFVEEIDGKKTAKGNSLPFREAAMNFINCLVSSTNDLQTRELQNHLFEALLISLDTAFLSFDIHMSMSYFHFVLQLAREDNLMKMVLKRTIMLMEKLAAEEKLLPGLKFIFGVIGTLLSNRSPSHGESLCGKSLASYKNTATGPLVPKLSGTTKKSDTLALPVDQEGSSISLECDVTSVDEDEDDGTSDGEVASLDKEDEEDANSERYLASKVCTFTSSGSNFMEQHWYFCYTCDLTVSKGCCSVCAKVCHRGHRVVYSRSSRFFCDCGAGGVRGSSCQCLKPRKYNGNGSAPARGTNNFQSFLPLSEDADQLGESDSDVEEDGFGEENHVVLYIPKETQYKMSLLLEELGIEDRVLELFSSLLPSITSKRDSGLSKEKQVNLGKDKVLSFDTDLLQLKKAYKSGSLDLKIKADYTNSKDLKSLLANGSLVKSLLSVSVRGRLAVGEGDKVAIFDVGQLIGQATIAPINADKANVKPLSRNIVRFEIVHLSFNPVVENYLAVAGLEDCQILTLNHRGEVIDRLAVELALQGAFIRRIDWVPGSQVQLMVVTNKFVKIYDLSQDSISPTQYFTLPNDMIVDATLFVASRGRVFLLVLSEQGNLYRFELSWGGNAGATPLKEIVQIMGKDVTGKGSSVYFSPTYRLLFISYHDGSSFMGRLSSDATSLTDTSGMFEEESDCKQRVAGLHRWKELLAGSGLFICFSSVKSNAVLAVSLRGDGVCAQNLRHPTGSSSPMVGITAYKPLSKDNVHCLVLHDDGSLQIYSHVRSGVDTDSNFTAEKVKKLGSKILNNKTYAGAKPEFPLDFFERAFCITADVRLGSDAIRNGDSEGAKQSLASEDGFIESPSPVGFKISVSNPNPDIVMVGIRMHVGTTSASSIPSEVTIFQRSIKMDEGMRCWYDIPFTVAESLLADEDVVISVGPTTSGTALPRIDSLEVYGRAKDEFGWKEKMDAVLDMEARVLGHGLLLPGSSKKRALAQSASMEEQVIADGLKLLSIYYSVCRPRQEVVLSELKCKQLLETIFESDRETLLQTTACRVLQSVFPRKEIYYQVKDTMRLLGVVKVTSILSSRLGILGTGGSIVEEFNAQMRAVSKVALTRKSNFSVFLEMNGSEVVDNLMQVLWGILESEPLDTPTMNNVVMSSVELIYSYAECLASQGKDTGVHSVAPAVQLLKALMLFPNESVQTSSSLAISSRLLQVPFPKQTMLTTDDLVDNVTTPSVPIRTAGGNTHVMIEEDSITSSVQYCCDGCSTVPILRRRWHCTVCPDFDLCEACYEVLDADRLPPPHTRDHPMTAIPIEVESLGADTNEIQFSADEVGISNMLPVVTSSIPQASTPSIHVLEPGESAEFSASLTDPISISASKRAVNSLILSEFLQELSGWMETVSGVQAIPVMQLFYRLSSAIGGAFMDSSKPEEISLDKLIKWLLGEINLSKPFAASTRSSLGEIVILVFMFFTLMLRSWHQPGSDGSSSKLGGSTDVHDRRIVQSSTVVATQSSLHVQERDDFASQLVRACSCLRNQEFVNYLMNILQQLVHVFKSRAANVEARGSSSGSGCGAMLTVRRDLPAGNYSPFFSDSYAKAHRADIFVDYHRLLLENVFRLVYTLVRPEKQEKMGEKEKVYRNASSKDLKLDGFQDVLCSYINNPHTAFVRRYARRLFLHLCGSKTQYYSVRDSWQFSNEVKNLYKHVEKSGGFENNVSYERSVKIVKSLSTIAEVAVARPRNWQKYCLRHGDFLSFLLNGVFHFAEESVIQTLKLLNLAFYQGKDVSSSVQKAEATEVVTGSNRSGSQSVDSKKKKKGEDGHDSGLEKLYVDMEGVVDIFSANCGDLLRQFIDFFLLEWNSSSVRTEAKSVIYGLWHHGRHSFKESLLAALLQKVRYLPAYGQNIVEYTELVSLLLDKAPENNSKQAINELVDRCLNPDVIRCFFETLHSQNELIANHPNSRIYSTLGNLVEFDGYYLESEPCVACSSPDVPYSKMKLESLKSETKFTDNRIIVKCTGSYTIQSVTMNVHDARKSKSVKVLNLYYNNRPVSDLSELKNNWSLWKRAKSCHLSFNQTELKVEFPIPITACNFMIELDSFYENLQALSLEPLQCPRCSRPVTDKHGICSNCHENAYQCRQCRNINYENLDSFLCNECGYSKYGRFEFNFMAKPSFIFDNMENDEDMKKGLAAIESESENAHKRYQQLLGFKKPLLKIVSSIGETEMDSQHKDTVQQMMASLPGPSCKINRKIALLGVLYGEKCKAAFDSVSKSVQTLQGLRRVLMSYLHQKNSNFSSGASRCVVSKTPNNCYGCATTFVTQCLEILQVLSKHPRSRKQLVAAGILSELFENNIHQGPKTARAQARAALSTFSEGDLSAVNELNNLVQKKIMYCLEHHRSMDIALATREEMLLLSEVCSLTDEFWESRLRLVFQLLFSSIKLGAKHPAISEHIILPCLKIISVACTPPKPDTAEKEQTMGKSAPAVQEKDENAAGVIKYSSESEENNLNVSQKTRDIQLVSYLEWEKGASYLDFVRRQYKASQSIRGASQKSRTHRSDFLALKYTLRWKRRSSRTSKGGLQAFELGSWVTELILSACSQSIRSEMCTLISLLAAQSSPRRYRLINLLIGLLPATLAAGESSAEYFELLFKMIETQDALLFLTVRGCLTTICKLISQEVGNIESLERSLQIDISQGFTLHKLLELLGKFLEVPNIRSRFMRDNLLSHVLEALIVIRGLIVQKTKLINDCNRRLKDLLDGLLLESSENKRQFIRACVSGLQTHAEENKGRTCLFILEQLCNLICPSKPEAVYMLILNKSHTQEEFIRGSMTKNPYSSAEIGPLMRDVKNKICQQLDLLGLLEDDYGMELLVAGNIISLDLSIAQVYELVWKKSNQSSTSLTNSALLASNAAPSRDCPPMTVTYRLQGLDGEATEPMIKELEEDREESQDPEIEFAIAGAVREYGGLEILLDMIKSLQDDFKSNQEEMVAVLDLLNHCCKIRENRRALLRLGALSLLLETARRAFSVDAMEPAEGILLIVESLTLEANESDSISAAQSALTVSNEETGTWEQAKKIVLMFLERLSHPSGLKKSNKQQRNTEMVARILPYLTYGEPAAMEALIEHFSPYLQNWSEFDQLQQRHEEDPKDDSIAQQAAKQRFTVENFVRVSESLKTSSCGERLKDIVLENGIIAVAVKHIKEIFAITGQTGFKSSKEWLLALKLPSVPLILSMLRGLSMGHLPTQTCIDEGGILTLLHALEGVSGENDIGARAENLLDTLADKEGKGDGFLGEKVRALRDATKDEMRRRALRKREELLQGLGMRQELSSDGGERIVVSQPILEGFEDVEEEEDGLACMVCREGYKLRPSDLLGVYSYSKRVNLGVGNSGSARGECVYTTVSYFNIIHFQCHQEAKRADAALKNPKKEWEGAMLRNNESLCNSLFPVKGPSVPLAQYLRYVDQYWDNLNALGRADGSRLRLLTYDIVLMLARFATGASFSADCRGGGRDSNSRFLPFMFQMARHLLDQGGPVQRTNMARSVSSYISSSSTSTATAPSSDSRPLTPGSQLSSTGTEETVQFMMVNSLLSESYESWLQHRRVFLQRGIYHTFMQHAHGRVASRAAEPTSSGGKTQDAETLTGDELLSIVKPMLVYTGMIEQLQQLFKPKKPVHIEPIKKEGTSSGVELEPWEIVMKEKLLNVKEMIGFSKELISWLDEINSATDLQEAFDIVGVLADVLSEGVTQCDQFVRSAIDKDGSLEVLFQGPAEAAAKEAAAKEAAAKEAAAKALEAEAAAKEAAAKEAAAKEAAAKAHHHHHHHH

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Trichoplusia ni

Entity 2 polymer

description	Calmodulin-1
formula_weight	20042.9 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	E,F

MDYKDHDGDYKDHDIDYKDDDDKGGSGGMADQLTDEQISEFKEAFSLFDKDGDGCITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLNLMAKKMKDTDSEEELKEAFRVFDKDQNGFISAAELRHVMTNLGEKLTDEEVEEMIREADVDGDGQINYEEFVKIMMAK

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Trichoplusia ni

Entity 3 polymer

description	Protein DEHYDRATION-INDUCED 19
formula_weight	24828.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

MDADSKRFLATLRSRSEMLMGFEEIDGDDDFQEEFACPFCAESYDIIGLCCHIDDEHTLESKNAVCPVCSLKVGVDIVAHITLHHGSLFKLQRKRKSRKSGTNSTLSLLRKELREGDLQRLLGFTSRNGSVASSVTPDPLLSSFISPTRSQSSPAPRQTKNVSEDKQIERKRQVFISPVSLKDREERRHKSEFVQRLLSSAIFDEVGGSGGSAWSHPQFEK

Source

organism	Arabidopsis thaliana
common_name	thale cress
ncbi_taxonomy_id	3702
host_organism	Trichoplusia ni

▶

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	3.900 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.90 Å
resolution_method	—
num_particles	67226

fit	/app/data/saxs_computation/qt/9qt9/9qt9.fit
pddf	/app/data/pr_computation/qt/9qt9/9qt9.pr.out
profile	/app/data/saxs_computation/qt/9qt9/9qt9.dat

Cryo-EM structure of the core of the Arabidopsis thaliana UBR4/DI19/CALM1 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

Refinement

EM 3D

5. Entities & Polymer Info (3)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)