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9ujt

RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome)

Method: ELECTRON MICROSCOPY D_max: 214.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9ujt
deposition_date	2025-04-17
title	RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome)
keywords	RNAPII, subnucleosome, H3-H4 tetrasome, TRANSCRIPTION, TRANSCRIPTION-RNA-DNA complex; TRANSCRIPTION/RNA/DNA
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	60.45 Å
rg_electron	58.97 Å
i0	5001500000.00
molecular_weight	546680.0 kDa
excluded_volume	664520 Å³
envelope_volume	1025900 Å³
shell_volume	143600 Å³
envelope_diameter	209.8 Å
shell_rg	63.36 Å
envelope_rg	58.40 Å
shape_rg	58.90 Å
total_rg	59.31 Å
total_atoms	38099
n_residues	4438
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	214.8 Å
rg_real	60.58 Å
rg_real_error	2.29 Å
i0_real	5.0020e+09
i0_real_error	1.0800e+08
rg_reciprocal	60.33 Å
i0_reciprocal	4999000000.0000
total_estimate	0.8316
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	66.1 Å
skewness	0.472
kurtosis	-0.133
angular_range	— – 0.1300 Å⁻¹
current_alpha	0.0001
highest_alpha	524700000.0000
n_real_points	27
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.692; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.750

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4. Crystallography & Experiment

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5. Entities & Polymer Info (17)

Entity 1 polymer

description	DNA (198-MER)
formula_weight	61372.9 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	N
atom_count	38099

GCTTACGTCAGTCTGGCCATCTTTGTGTTTGGTGTGTTTGGGTGGTGGCCGTTTTCGTTGTTTTTTTCTGTCTCGTGCCTGGTGTCTTGGGTGTTTACCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTGAT

Entity 2 polymer

description	DNA (198-MER)
formula_weight	60879.0 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	T

ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGTAAACACCCAAGACACCAGGCACGAGACAGAAAAAAACAACGAAAACGGCCACCACCCAAACACACCAAACACAAGAGCTAATTGACTGACGTAAGC

Entity 3 polymer

description	DNA-directed RNA polymerase subunit
formula_weight	194107.4 kDa
ec_number	2.7.7.6
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A

MSQFPYSSAPLRSVKEVQFGLLSPEEIRAISVVKIEYPEIMDESRQRPREGGLNDPKLGSIDRNFKCQTCGEGMAECPGHFGHMELAKPVFHIGFIPKIKKVCECICMNCGKLLLDETNPTMAQAIRIRDPKKRFNAVWQLCKTKMVCEADAPVDEYSEQKVVSRGGCGNTQPVVRKDGMKLWGTWKKSGFSDRDAQPERKLLTPGEILNVFKHISPEDCFRLGFNEDYARPEWMIITVLPVPPPQVRPSIAMDETTQGQDDLTHKLSDILKANINVQKLEMDGSPQHIINEVEQLLQFHVATYMDNDIAGQPQALQKSGRPVKAIRARLKGKEGRLRGNLMGKRVDFSARTVISGDPNLELDQVGVPISIAKTLSYPETVTQYNIHRLTEYVRNGPNEHPGAKYVIRDNGDRIDLRYHKRAGDIVLQYGWKVERHLMDDDPVLFNRQPSLHKMSMMAHRVKVMPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPVMGIVQDTLCGVRKMTLRDTFIEYEQVMNMLFWVPSWDGVVPQPAILKPKPLWTGKQLLSIAIPSGIHLQRTDGGNSLLSPKDNGMLIVDGKVMFGVVDKKTVGSGGGGLIHTVMREKGPKICAELFGNIQKVVNYWLLHNGFSIGIGDAIADASTMKEITHAISSAKEQVQEIIYKAQHNELELKPGMTLRESFEGEVSRTLNDARDSAGRSAEMNLKDLNNVKQMVSAGSKGSFINIAQMSACVGQQMVEGKRIAFGFADRSLPHFTKDDFSPESKGFVENSYLRGLTPQEFFFHAMAGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDGTTRNSLGDIIQFLYGEDGLDGTQVERQTIDTIPGSDKAFHKRYYVDLMDEKNSIKPDVIEYAADILGDVELQKELNSEYEQLVSDRKFLREIVFVNGDHNWPLPVNLRRIIQNAQQIFHLDRAKASDLTIPEIIHGVRDLCKKLFVLRGENELIKEAQQNATSLFQCLVRARLATRRILEEFRLNRDAFEWVLGTIEAQFQRSLVHPGEMVGVIAAQSIGEPATQMTLNTFHYAGVSSKNVTLGVPRLKEILNVAKNIKTPALTVYLDREIALDIEKAKVIQSSIEYTTLKNVTSATEIYYDPDPTSTVIEEDFDTVEAYFSIPDEKVEETIDKQSPWLLRLELDRARMLDKQLTMNQVADKISEVFSDDLFVMWSEDNADKLIIRCRVIRDPKAMDEELEAEEDQMLKRIEAHMLDLIALRGIPGISKVYMVKHKVSVPDESGEYKNEELWALETDGINLAEVMAVPGVDSSRTYSNSFVEILSVLGIEATRSSLYKEILNVIAFDGSYVNYRHMALLVDVMTSRGYLMAITRHGINRADTGALMRCSFEETVEILFEAGAAAELDDCRGVSENVMLGQLAPMGTGAFDVMIDEKLLTSLPADYAPTMPLFKGKATQGSATPYDNNAQYDDEFNHDDVADVMFSPMAETGSGDDRSGGLTEYAGIQSPYQPTSPGLSATSPGFAPTSPGFAPTSPRYSPTSPGYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPTSPQYSPASPQYSPSRHSPNGESKEGE

Entity 4 polymer

description	DNA-directed RNA polymerase subunit beta
formula_weight	139746.1 kDa
ec_number	2.7.7.6
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MSYDPYSIDDTITTEDCWTVISAFFEEKGLVSQQLDSFDEFMETSIQDLVWEEPRLILDQPAQHTNEKDNINKRYEIRFGKIYLSRPTMTEADGTTHAMFPQEARLRNLTYSSPVYLDMEKSMFTSIDDEGNPNATLDWQQVHEPIKDGVEEGNKVHIGKVPIMLRSKFCSLRTLDEVDLYKMKECPYDMGGYFVINGSEKVLIAQERSAANIVQVFKKAAPSPISHVAEIRSALEKGSRLISTMQIKLYGREDKGTGRTIKATLPYVKQDIPIVIVFRALGVVPDGEILQHICYDENDWQMLEMLKPCIEEGFVIQDKEVALDFIGRRGSAALGIRREKRIQYAKDILQKELLPHITQEEGFETRKTFFLGYMVNRLLLCALERKDQDDRDHFGKKRLDLAGPLLANLFRILFRKLTREIYRYMQRCIETDRDFNLNLAVKSTTITSGLKYSLATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLLSGISIGSPSEPIINFLEEWGMEPLEDYDPAQHTKSTRIFVNGVWTGIHRDPSMLVSTMRDLRRSGAISPEVSIIRDIREREFKIFTDVGRVYRPLFIVEDDESKDNKGELRITKEHIRKIQQGYDDDAMNDDSEEQEQDVYGWSSLVTSGVIEYVDGEEEETIMIAMTPEDLQTRSLEQKEIDLNDTAKRIKPEMSTSSHHTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLAKTQAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKRFGISIVEEFEKPTRATTLRLKHGTYEKLDEDGLIAPGVRVSGDDIIIGKTTPIPPDTEELGQRTKYHTKRDASTPLRSTENGIVDQVLLTTNQEGLKFVKVRMRTTKVPQIGDKFASRHGQKGTIGVTYRHEDMPFSAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVGSIRGYEGDATPFTDLTVDAVSNLLRDNGYQSRGFEVMYNGHTGKKLMAQVFFGPTYYQRLRHMVDDKIHARARGPVQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAAGFLKERLMEASDAFRVHVCGICGLMSVIANLKKNQFECRSCKNKTNIYQLHIPYAAKLLFQELMAMNIAPRLYTERSGVSMRS

Entity 5 polymer

description	RNA polymerase II third largest subunit B44, part of central core
formula_weight	34216.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MSKEPKVNIINAQDDEVELMLSDVNLSLANSLRRTMLAEVPTLAIDLVEIKMNTSVLADEFISHRLGLIPLVSEDVEEMKYSRDCTCEDYCDECSVVLELSARHEGEEGTTDVYSSSLIKVSGPGNLNVGEPVRRDDYDQGILLCKLRNHQELNIRCIAKKGIAKEHAKWSPCSAIAFEYDPHNKLKHTDFWFEVDAKKEWPDSKYATWEEPPKPGEVFDYKAKPNRFYMTVETTGSLKANQVFSRGIKTLQEKLANVLFELENSRPANTTAYGGATAYGGQTVYGRETSYGGNTNYGDYNAPY

Entity 6 polymer

description	RNA polymerase II subunit B32
formula_weight	20623.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MNVSTSTVGARRRRAKQQVDDEENATLLRLGPEFALKQYDHDGNEHDLIALSLSESRLLIREALKARSRARNGGVDIESSNGEIDDDELAKVTSGAVANGVVKKTLDYLNTFARFKDEETCTAVDQLLHNSSDCSVLHPFEIAQLSSLGCEDVDEAITLIPSLAAKKEVNLQRILDELNRLEDPYK

Entity 7 polymer

description	RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III
formula_weight	24962.7 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MEDNNRIISRLWRSFRTVKEMAADRGYFISQEEMDQSLEEFRSKICDSMGNPQRKLMSFLANPTPEALEKYSDLGTLWVEFCDEPSVGIKTMRNFCLRIQEKNFSTGIFIYQNNITPSANKMIPTVSPAIIETFQESDLVVNITHHELVPKHIRLSDGEKSQLLQRYKLKESQLPRIQREDPVARYLGLKRGQVVKIIRRSETSGRYASYRICL

Entity 8 polymer

description	RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III
formula_weight	17803.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MSEDEAFNEQTENFENFEDEHFSDDNFEDRSTQPEDYAVGVTADGRQIINGDGIQEVNGTIKAHRKRSNKELAILKEERTTTPYLTKYERARILGTRALQISMNAPVLVDIEGETDPLQIAMKELSQRKIPLVIRRYLPDGSYEDWGCDELIVDN

Entity 9 polymer

description	RNA polymerase II subunit
formula_weight	18802.6 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

MFFLKDLSLILTLHPSYFGPQMNQYLREKLLTDVEGTCTGQFGYIVTVLDGMNIDVGKGRIIPGSGSAEFEVKYRAVVWKPFKGEVVDAIVSNVSPIGFFADVGPLNVFVSTRLIPDNLVYNPSNSPPAYMSNDELITKGSKVRLKVVGTRTDVNEIYAIGSIKEDFLGAI

Entity 10 polymer

description	DNA-directed RNA polymerases I, II, and III subunit RPABC3
formula_weight	16249.2 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	H

MSSALFDDIFTVQTVDNGRYNKVSRIIGISTTNSAIKLTLDINNEMFPVSQDDSLTVTLANSLSLDGEDESANFSKSWRPPKPTDKSLADDYDYVMFGTVYKFEEGDEDKIKVYVSFGGLLMCLEGGYKSLASLKQDNLYILIRR

Entity 11 polymer

description	DNA-directed RNA polymerase subunit
formula_weight	13612.3 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	I

MASFRFCLECNNMLYPKEDKENQRLLYSCRNCDYTELAEDPKVYRHELITNIGETAGIVDDIGQDPTLPRSDKECPECHSRDCVFFQSQQRRKDTNMTLFYVCLNCKKTFRDESE

Entity 12 polymer

description	RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III
formula_weight	8554.1 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	J

MIIPVRCFSCGKVVGDKWDAYLRLLEEGKQEGDALDELKLKRYCCRRMVLTHVDLIEKFLRYNPLEKKDFDS

Entity 13 polymer

description	RNA polymerase II subunit B12.5
formula_weight	13832.9 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	K

MNAPDRFELFILPDDVPKLKITPDSRVPNCIIIKFEREDHTLANLLREELALYPDVTFVAYKVEHPLFANFVMRLQTEEGTRPKQALERACASIINKLKTLDHKFNEEWNIKNFSLND

Entity 14 polymer

description	RNA polymerase subunit ABC10-alpha
formula_weight	7862.0 kDa
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

MSREGFVAPSGTDLAAAASGVAPNKHYGVKYTCGACAHNFSLNKSDPVRCKECGHRVIYKARTKRMIQFDAR

Entity 15 polymer

description	;RNA (5'-R(PCPUPUPGPGPGPUPGPUPUP*U)-3') ;
formula_weight	3478.0 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	P

CUUGGGUGUUU

Entity 16 polymer

description	Histone H3.1
formula_weight	15719.4 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	e,g

GSHMARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 17 polymer

description	Histone H4
formula_weight	11676.7 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	f,h

GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

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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	—

resolution	6.540 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	6.54 Å
resolution_method	—
num_particles	5000

fit	/app/data/saxs_computation/uj/9ujt/9ujt.fit
pddf	/app/data/pr_computation/uj/9ujt/9ujt.pr.out
profile	/app/data/saxs_computation/uj/9ujt/9ujt.dat

RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome)

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 (17)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

Entity 8 polymer

Polymer

Entity 9 polymer

Polymer

Entity 10 polymer

Polymer

Entity 11 polymer

Polymer

Entity 12 polymer

Polymer

Entity 13 polymer

Polymer

Entity 14 polymer

Polymer

Entity 15 polymer

Polymer

Entity 16 polymer

Polymer

Source

Entity 17 polymer

Polymer

Source

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)