SAXSdb — 9yol

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1. Structure Basics

entry_id	9yol
deposition_date	2025-10-13
title	Tra1 module of ctSAGA
keywords	ctSAGA complex, Histone Acetyl Transferase (HAT) Module, Tra1 module and Core module, TRANSCRIPTION; TRANSCRIPTION
method	ELECTRON MICROSCOPY

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Download Data

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

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2. SAXS Parameters (CRYSOL)

rg_guinier	60.74 Å
rg_electron	60.62 Å
i0	2671750000.00
molecular_weight	446890.0 kDa
excluded_volume	564180 Å³
envelope_volume	892510 Å³
shell_volume	120490 Å³
envelope_diameter	204.0 Å
shell_rg	65.21 Å
envelope_rg	58.82 Å
shape_rg	60.61 Å
total_rg	60.79 Å
total_atoms	62724
n_residues	3884
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

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3. P(r) Analysis (GNOM)

dmax	202.2 Å
rg_real	60.75 Å
rg_real_error	1.78 Å
i0_real	2.6720e+09
i0_real_error	5.8710e+07
rg_reciprocal	60.71 Å
i0_reciprocal	2671000000.0000
total_estimate	0.8623
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	70.0 Å
skewness	0.307
kurtosis	-0.456
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0001
highest_alpha	246800000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.504

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	SCA7 domain-containing protein
formula_weight	137082.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	Q
atom_count	62724

MDSRKDEEATIKVAPAKGTVLASKPHIWGKLKLKKPPVKQIKPGNWKEATLVEDKKKDKDGGAINAASPGPDVNQLDDRARDTFSNGRPLEDVLELLQCKLCRKGISRTAARDHIAKCLQIKKEKAQRKKEAREARERLKEAAREEEARRLEEEGAAKGDDDSDDDDGKEGAGKAGKKTKKTDVAGKKRKAEGELDKGKAKKKKDEPKPKVAKPKGPVDVERQCGVPLPNGQLCARSLTCKSHSMSAKRAVPGRSLPYDMLLAAYQKKNQAKQQKAALDANAPLEDEDDLNAGAVDSDEETAAVMSALANWNPQPVVPQPVFAPLKRQYQLARLHEQLQAATNGGRTNIFKVVGFGAQRLSDGHLGLYDAEDAPGEPDPVGLGSLSRRSSSIVAGEDDTTQQAQIAAVDHESQKEDAPLAEVCKKPCWKPKDRPGSVLDQEYVPMSGRSLSKVTKLKATGRAAANRQPKQSRRAASAIPESSKPLADAPVNTIVSKSSPALPTATPLYAFANLPTTDLRLQPAELAIQEMRKRLIAASSSSQSSISSTGVRAPRGRKRKEDRSMPGIHGSQPMENIHRATDGVRQTPENMAPTPKESPSDSTVEMRVLELGQLLAQEDSLAKSSPVLPNTPVVSLLGTSQNGATNGLKQGVQHIQRQMATKPTSVSRAISHSPMSSRPLFSAPSPPMMSHSLSPLTRAATPKALSSSPLVMSMLLPQQPPSHPFVSLPSGSTLSQAMQQSPIMTSMSKSGLTPAATRQPSPGVMPHSPPPRQGPGRPPKPRPADPVSPVNPTRSPNLPNASYLTTLGDLSTGMQPPQLPHMPQQQVPRVKLNQMRNQALASTFSPRPSYLPSQRLDPIREQAIKRAAERAAGLRMAQAQRQPQMQVHMNVQAQRTPQLQARTSPPTASPAETQGQMLSARAQAEDQGQNRLRMGQPQANTQLMRIDGPGMAAGMRQPIGNSQMDTMQPQRQVMNTPVVPAPQSSSPPSAERSSSQPQPVRDQIDSASVQAEAAQDETMNLDNDEMDDILREVKAQAEREAERQMAALSRTRPQAQQQAQNLRSTQNQSQMHALSPVASESSSPSLVMSASLPGLNEVNVRATVAAAAKKVAGSISPVANISSAATALSSPLDCRPYTTTSIPRPRLATTAPVPLMGATGPPAASGTTQNIGSFHVQQHRQRRQQQQLLQQHAQQHQQRLQQAAVHNNQQPFRFTYPAESMAAAVAIAGAHNLRPVVPLPPQAYLLSASQGGGRSGSRGSNIRNGSQARTQEQG

Entity 2 polymer

description	Spt20-like SEP domain-containing protein
formula_weight	128449.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MAPTVTAAAPPVNPPSATKVKRPIPPGIQTNGVAPSRSSPSPSMAAKRAPSAVRQPSNPPSAGGTTPGATRPTIRIRRDPGPGPPLGRGQRSAGLRSASIATDPVTSPTFDAPPYVITPEYILKKFAGHPPSLIVHLYQNHFRFDQQEGMFQYKSPMRIFIEHLRNRTVPHEIMEYLIQGGVPFYEGCLIVQVFDHRTVNQTKEAAKPSSESSKTVPFSIHNHNPYITPSPYVPYPKEDTPADGSQTPASEKPSEDKDKENMPAPPVPADGQKAKGEPAKPTVYTVVLMPTAQALHTDLLLKTVTPRGASDSGGPPPTPHTAGPPPTPTAAGMPPPAKKQKRDHMELDPKNIYEVEAKILLATYPKLDLEPTKNAEETIAKLEKLAHPEHSHKPPEPKVRKRTVAEVAHDEALAAEQERYMLTLDERLSSKLAGAQAGANGADGDGQAPSASWEPRFERFKLIENIKQEHAEKKEQERIKQAEQERKLLQQKQEAAILQARQQQAEMERKRQEQIVLQQRQEAQRRLQQAQAAPVAQAQAQAQAQAQAQAQAQAQAQARAQARAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAQAAQAQAQAQAQAQAQAQAQAQAQAQAQAQQAATAATMGQTPHAHPMQPSPLPAGMTAGMPVSMAQQAQARFSQVSQPQQMSSPIVQQGTPQAASSPMPPMAAVAMQHSNSNMGQAGSPPRPPSVVQNHPMGVPMAPSMSARGSQQSHAAGTPRVPSATPNIPHATPITRPQVVPTPRMTQASPPAGVMTPTPQQMGQAMLMNNQGIAQMPNVNINSLAAAQQMAAQQRLIQQYQQQLQQSGMVPGNVQANMLQQQLAARQQMMIQQQLLAQQQQRAGQMMNPNIQAQLAAQYQQSLNNMQQQQLAQMNPMQAAHMRQLLAAQQAQRQGMMGVNVNVNGMTPQQLAVMQQQIQLQQQAQLIQQQQQQQQQLQQQQQQQQQQQQQQQQQQQQQQQQQAAQQQPQPGMPGHPPQAAVAPTAPQVPIAQLQPPQNQLAALMMNPAVQNQIRNHSNALYSKNLPALAERFGGNAQNIPPEALAEFRQKCLNQAKVQVLSMLQQQQAGGRLAAGLPPQVQAAQVQAMQQQAQALAVAQAQVQAAQQAAAAQAAQQQGGMGQGM

Entity 3 polymer

description	Chains: C
formula_weight	48541.5 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MALSDNNPEEVDGMFLSNLRSDLELEEIWRMLQSGVTSPEDSQPTVSLDASSSGDKTMSSESQVALQDDADDELLVSILAGKVPLSELLANDNELLQSDGLSSAVCSADSDQEEDDNNDAGYGEEPDPRDVIANWFELCQMMYVSGETGEPSLETTGIIEDIVRQQVIEIIRHDAPKVSRLRTFLAWKDVRKNVKDSDDKGADADIAPGDDPVGAVVPGATVDDTARKTKKSRVGLPWEPASFYSVEVPEREDEEDEEEEEMNYITLQRLRKADERTKAMTKEEYVTWSEFRQASFTYRKGKRFREWAGFGLVTDSKPSDDIIDILGFLTFEMVQTLTEEALKIKEQEDLHRERTGENQSNANNPNGSANSSLSKKRKLTGGGGLFDPPNEGRTPVEPRHIQEAFRRLQQRPKKARAMLNGTKLQQRTQLKLF

Entity 4 polymer

description	Putative transcriptional coactivator HFI1 protein
formula_weight	52133.4 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

MVDINPAALSRPSIGLSTPSFPGKSGSINVSVPSSASASASASSAHSKPQKTSLVPPRIDLEPIYTALKAAIGAEQWPVYKETLTNFLIGRLNQAELSERIDPILASQDGQKEHLHNQLIAAIYANVTREMPDPGLAPWVSANDKPTTAQTKPVTGDANERRLKGEVMQLPARDRRRIKELAHNDFDPYDALANVLMEHARAKPPKIAEPPASAGGLKMNFDLEIRKRYAQPLAVESGEFPDTSNIESRMLPFCYEAGLSSGHAPDAAQFMSIATETFIKEVMSAIFSRTRSNGPGDSGSAGFGLGSGWIQTHRYRKQLAKEEEAFQRGEISRDKMGLLPVEAKAASERGPLGMADVRLALEMGDCGLAGFPVIVKSVIYGWREGELENWEDYTYVDPSRPDGIAIPSRGDGDVEMGGVGVNGVVKGEPEPQQQPLANGVHDVDAMDIDGVSVAGGAANEIWWEGAEPETSDLLNAVLDSCLAVN

Entity 5 polymer

description	Transcription initiation factor TFIID subunit 12
formula_weight	83091.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

MNQTPAQGQGQGQPGQGMANRPPNAPSAANVAAPGGAPRQQGTPMYRPEMMRNIPLLSDEEKTKYERGLQQLWLMHDNTAPGSAENIEAKKKIAEFGRVLLTKLQQRRQQQQLQQQRQQQQQQQQQQQQQQQQQQQVQQQMQQQAQQPQTQPQQGQPQQQLQQAQVQQQVQQQQQIPQQQQQAPQQQQQQQQPQQLGQPGQQVQMMPQNQQPQVAQNVQPVAPTTVPQQQPAPATQTAPNQMGAPNSAAAQLRSLPAHIVSHVKDVTFLAPNNVVDKAGWIDQLKLQYAQKLFVMDSAGRQIKQIAASLADQSLPPEERKKLEEKKQTLEKQYNDAISFANTVRKQYMQKPAQNGAAVQNAANVARPQSAQGASAMTQPGAGVGNGTPVAAPVNPMQSSAAAINTAIETAKKQQMAAGRMAGAVNAMAAQVQSPATPVQAQVSPATQVHATQQSVPQQPQQIQQAQPTQQPQAQVKIEPGTAPHPAPLNTTMAGPTGVPSAAAPAQNAARMQTPTSATPTSANPNIRPLTHAAAMNLASQQRPGMPAVPTAASGAAPGTPMGIMGAAQQQQQQQPGHSHAHPPQPTQAPPPHSTNPKLPIPKVLHDKAIQMPQPVPNIGGAGSGRPTYTSGVMNQPALPKTPAFQLEGEGERVLNKKKLDELVRQVCGGTAEGQDGNMLTPEVEESVLNMADAFVDNVLHQACRNAKERGSKVLEIRDIQLVLERVYNIRIPGYASEELRTVRKVQPNSNWIKKMSAVQAAKVVPGKGDI

Entity 6 polymer

description	Non-specific serine/threonine protein kinase
formula_weight	444670.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MATSLIEDVVKKLSVAETGTGNSLSERSLLVLPLMQVSCYTELKVKAEAACALRDSLDHYTAGPAYPAFLKKVMPVFIHILRQQPVFQTTGEQGHMQKLRNCILEILHRLPTSQTPPEHFEPYAHEIVDLLLELVRTDNEDNVILCVKILSDIMRHQHKIMSGKVQTFLNLIQELFEQLDKVVRDQLDNTSTTGPPGPPSTPGSTQSSFLPHQQSPRPGSPVTTGVTDFGADANQQANRLLPRGMYSFKVLAECPIIVVSIFQVHRSAVTPNVKAFVPLIKSALLCQAKAQDQAHREAAARGTIHIGVSPNIKNRAAFGDFITAQVKTMSFLAYLLRQYSSQLSDFLPHLPDIIVRLLRDCPRDKSSARKELFVAIRHIINFNFRKIFLPKIDELLDERTLVGDGLTVHETMRPLAYSMLADLIHHVRDQLSPEQIRKTVEVYTRNLQDNFPGTSFQTMSAKLLLNMAECIARLPNKVDARHYLIMILNAIADKFAAMNRQYPNAVKLSKQYAQQAAKNVPETYLADKENPPDWDEIDIFNATPIKISNPRDRAADPVVDNKFLFRNLMTGLKNTFYQLKSCNIPGAVDLTGAPAHWTDVAYGFTAEEVKVIAKLFREGAYVFRYYEIEKPAAESPYSSPVEYMANFYMVSSSKEEKELLETFATVFHCIDPATFHEVFQQEIPRLYEMIHEHTALLHIPQFFLASEATSPSFCGILLRFLMERIEDVGSADIKKSSILLRLFKLAFMAVTLFANQNEQVLLPHVVDIVTKSIELSTKAEEPMNYFLLLRSLFRSIGGGKFEHLYKQILPLLEMLLDVLNNLLMAARKPAERDLYVELCLTVPARLSNLLPHLSFLMRPLVVALRAGTELVGQGLRTLELCVDNLTADYLDPIMAPVIDELMTALFDHLKPHPYSHFHAHTTLRILGKLGGRNRKFMTEALPVTFQQYVDDRASFDLRLIGSKRDRAFPAHLGIDLAIQKLTEIPKPVKGGVPQLSRQYDPYYKRQALNLIIAQTKLRVGFDSVPEDLPRLVRLQVEDLVKKNRDVDISLFEVSDKERSIAKKNEEQALLKRLLKALLYAESIPEFKQEVDALLVNLARHFTLIEIGRSVIDMKKAYTPFDTKSGEGPLFIDNRVLSEAILESLANENLEVREAAKRLIKEMHNAAVTVFGSPMHVPRMTFWSSLASTFCHGCYEEEWFTKQGGALGIQTLLTEIDLGDLWVAAKQIEFVRALMYVVKDMPQDLPEKTRRTAQVTLEQLLARITRNAKKQDCLPPPPPPAPPGSHPPQPPPRPPRLAQLVMMLNSELAHMNRHVRATARRSIEAIAAAAQAEVWELLEPHKKHILGPIYAKPLRALPFAIQIGYIDAVTYYMSLKRDFVPFDENLNRLLMESLALADASDESLAGKTLEFRTHDFIVNLRVSCIKILSRAMSFEEFGSGSNNPTRPKVVSVFFKCLYSDSQPTIDAANDALKAVLQHTTKLPKDLLQSGLRPVLASLQDAKRLTVHSLDNLGRLLRLLTTYFKVEIGTRLLEHVKQIADPNFLQQLSFTFFEQNNAMKVIAAVFNIFHLLPDAARQFKERVIDNVLDLEQKLRRTHHSPFRLPLYKYLNKYPSDIWAFTLQKLEDLRYGRFLAQVLRHPDSQVLRDYGAANVEFIIKTCNTVVVSGKETKFIAIINTINMLDALCQFPTANSQSWLDNKEHIEWLKTVGKELELQQKKNSLTPNLRLPAHQASEQLMNILTKALDRNPNDLDALFSLVEGITSDDFRETPALLSHIYNKIIRSDSIDFWRITILRCLDIYSGKTASQRMKWYLLHNIVNPIIAMDVMRTWDDPNKASRLLDRTVIDSINTKIWKVNLPDPQEDLLQPRVDHTRMEVLQLSAMLVKYRHALLQDARKDFIKFAWTYIRLDDVINKHAAYVVIGYFIAHYETPAKIVSQIYFSLLKTNQNEGRALVTQALELMAPVMPKRCPFPPGDRNPVWALAPRRILAEESQNVQQMTAIFHYLVRHPDLFYDTRDKFAMLIIQCLRKVASPPNPSNDNRKLALNMMWLIWQWEQRRVESKLSEPLRAPSESPNSNKRKLDEQQGLSPSATRQAEFQIPSVGRHKMIRYLVEFIAQLNERYPLPSARPSDPPTTTSFLLPSPSNELCKKATALLYNLLQPQYWGDLVEEMDLFPNVTDLVLAGEKSATLLSADPSDPEKCDDKLITSIINTLQVVRIVLHFKSDRWILDNMPQIQKILEKCLKSANPEIQDCLHMADRKYDGDRDVKPTIKRILDAVPEDIPMEDADGDIEPESQTSELIAWLSGIATESMAAGNYVSGINILWSLGHRKPSIIDQHIPAIMRSLQSKLARDHVSHYAALGHQASGLRPQADPNAPTEMKAYDLEIQTNLILKAIEVTAMRMEILGDNRRPFLSVLATIVEKSLHIPLCEKILEMVEGWVFRSEGTWPTLKEKTAVLHKMISFEHRTDPTMLHKFLNLVLRIYEDPKITRTELTVRMEHAFLIGTRAQDVEMRNKFMSIFDKCLSKTASARLAYVILGQNWDTLADSYWLAQASQLLLGAVDMNPTIQLHQDDFRTLPISQLVAPYAKDSREPSVMIDDKFEAFMANHRRFLAELGDVRARDVLEPLMQLQHIDANFAHELWVALFPMFWSAVPKEDRPDLERGLVTLLTKDYHSRQMDKRPNVVQSLMAGAVKTWPHCKIPPHVLKFEAKTYDAWYTALHQLENAAIKPEIDSAAVRESNLDALVDLYSTLGEDDLFYGTWRRRCQFVETNAGLSYEQHGMWEKAQRMYESAQIKARTGVIPFSEAEYMLWEDHWVLCAQKLQQWEILQDFAKHENFQDLLLECAWRNTEYWQNQENRDQLDTVIKGVMDAPTPRRYFFQAFMSLLKLHNKQETPQDFNRVVDEAIQLSIRKWHQLPKRLTAAHVPLLQNFQQLVELHDASVICQSLAQTNASNLDVKSGELKLLLGSWRDRLPNMWDDIVAWQDLVTWRQHVFGLINATYLQLIPQQAQNAGGASFAYRGYHETAWIINRFAHVARKHALPEVCISQLSRIYTLPNIEIQEAFLKLREQAKCHYQNPDELTSGLDVINNTNLNYFSAPQKAEFYTLKGMFLEKLGQKEEADTAFGTALYFDITAAKAWAEWGYFNDRKFKENPSDLPSAKQALTSYLQAASSYKNHKSRKLIARILWLLSLDDANGTIAAGFDDFKGEIYVWWWIIFIPQLLVGLGYKEAPRVQAILLKIAKTYPQALYFLLRTNREDMLTIKKNQEAKERARQRAAQAAIPNKPNGSPQLTKKDGAAGAADGRPPTANGETPKPPEIKIEGAAPNAPTAATPQAAANAPQVPGAAPAEQQTGGVQKKPPWELTEEIMSVLKTAFPLLALSMETMVDQIQKHFKCPPDEDAYRLIVALLNDGLSYVSRMPASYAKDVKLPAATENNITRFAETILPNHIRPTFEADFVKVKPTMYEYIHNLRKWRDKFEEKLDRRASPAPLESFAHYSPHLSEFRYQKFDDVEIPGQYLQHKDKNQDFIRIDRFLPNVDLVRTIGASHRRLRIRGHDGSVHAFAVQHPAARHCRREERVLQLFRQLNQTLANKKESRRRDLQFTLPLMVPLAPHIRIVQEDTSYITLQSVYEDHCRRHGMNKDEPILFTMEKLRGLMDAKALQKPEQAVTAKLEVYRAIQEKFVDHTIVLEYFQGAYPNFADFWLFRRRFSYQLAALTFMTYTMHIDKRYPHKMNIARGSGNIWGSEAVSYMAPSRPLFQNTEPVPFRLTPNLQTLMGPLATEGIFAASVMAIARCLTEPEQHLEHALTLFVRDEMMFWFTNSHRTMSLTENQLRETVQANCDMIVKKALALAQTPQGNLPAHQTVTDLIAKATNPMNLALCDALWMPYL

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6. Citations (1)

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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	2.60 Å
resolution_method	—
num_particles	1886619

fit	/app/data/saxs_computation/yo/9yol/9yol.fit
pddf	/app/data/pr_computation/yo/9yol/9yol.pr.out
profile	/app/data/saxs_computation/yo/9yol/9yol.dat

Tra1 module of ctSAGA

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 (6)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)