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9upw

CryoEM structure of the T.thermophilus transcription initiation complex in the presence of Gp4A, -1 dC in the template DNA strand

Method: ELECTRON MICROSCOPY D_max: 186.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9upw
deposition_date	2025-04-29
title	CryoEM structure of the T.thermophilus transcription initiation complex in the presence of Gp4A, -1 dC in the template DNA strand
keywords	Complex, 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	49.53 Å
rg_electron	49.32 Å
i0	4948280000.00
molecular_weight	377930.0 kDa
excluded_volume	358840 Å³
envelope_volume	692670 Å³
shell_volume	112790 Å³
envelope_diameter	196.8 Å
shell_rg	56.09 Å
envelope_rg	49.41 Å
shape_rg	49.32 Å
total_rg	49.49 Å
total_atoms	28515
n_residues	3447
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	186.5 Å
rg_real	49.49 Å
rg_real_error	1.88 Å
i0_real	4.9480e+09
i0_real_error	1.0520e+08
rg_reciprocal	49.53 Å
i0_reciprocal	4949000000.0000
total_estimate	0.8182
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	58.3 Å
skewness	0.434
kurtosis	0.080
angular_range	— – 0.1600 Å⁻¹
current_alpha	0.0000
highest_alpha	535200000.0000
n_real_points	33
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.552; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.981

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4. Crystallography & Experiment

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5. Entities & Polymer Info (11)

Entity 1 polymer

description	DNA-directed RNA polymerase subunit alpha
formula_weight	35056.2 kDa
ec_number	2.7.7.6
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	28523

MLDSKLKAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIMNPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIKDRINAIPVDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQAAAVAAPEEAKEPEAPPEQEEELDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEKKGFTLKE

Entity 2 polymer

description	DNA-directed RNA polymerase subunit beta
formula_weight	125436.5 kDa
ec_number	2.7.7.6
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRENVGIQAAFRETFPIEEEDKGKGGLVLDFLEYRLGEPPFPQDECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHIPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPKRGPWIDLEVEPNGVVSMKVNKRKFPLVLLLRVLGYDQETLARELGAYGELVQGLMDESVFAMRPEEALIRLFTLLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSGRTLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDHLGNRRIRTVGELMTDQFRVGLARLARGVRERMLMGSEDSLTPAKLVNSRPLEAAIREFFSRSQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDELGFIRTPYRRVVGGVVTDEVVYMTATEEDRYTIAQANTPLEGNRIAAERVVARRKGEPVIVSPEEVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEEDGEVAKVDGNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQRPRVVVGQRVRKGDLLADGPASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPEEQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAHTLQEMLTLKSDDIEGRNAAYEAIIKGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDNPVDIFEGLASKR

Entity 3 polymer

description	;DNA-directed RNA polymerase subunit beta' ;
formula_weight	170997.4 kDa
ec_number	2.7.7.6
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	D

MKKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQLLTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGVALYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEILAELPEPYLFRAEEEGVVELKELEEGAFLVLRREDEPVATYFLPVGMTPLVVHGEIVEKGQPLAEAKGLLRMPRQVRAAQVEAEEEGETVYLTLFLEWTEPKDYRVQPHMNVVVPEGARVEAGDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYPFEDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYDIDARMGAEAIQQLLKELDLEALEKELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALLAVAHGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVESEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKEAVEAKERPAARRGVKREQPGKQA

Entity 4 polymer

description	DNA-directed RNA polymerase subunit omega
formula_weight	11533.3 kDa
ec_number	2.7.7.6
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	E

MAEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNAVTWAMKELLTGRLVFGENLVPEDRLQKEMERLYPVEREE

Entity 5 polymer

description	RNA polymerase sigma factor SigA
formula_weight	50900.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	F

MGSSHHHHHHSSGLVPRGSHMMKKSKRKNAQAQEAQETEVLVQEEAEELPEFPEGEPDPDLEDPDLTLEDDLLDLPEEGEGLDLEEEEEDLPIPKISTSDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLKYHESRTRKLRDFLD

Source

organism	Thermus thermophilus HB8
ncbi_taxonomy_id	300852
host_organism	Escherichia coli BL21(DE3)

Entity 6 polymer

description	template DNA strand
formula_weight	14831.5 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	G

GCATCCGTGAGTCGAGGGTAATAAGCACAATTTAACACTTTTGTCAAG

Entity 7 polymer

description	non-template DNA strand
formula_weight	14863.5 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	H

CTTGACAAAAGTGTTAAATTGTGCTATACTGGGAGCCGTCACGGATGC

Entity 8 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	3

Entity 9 non-polymer

description	CHAPSO
formula_weight	631.9 kDa
src_method	syn
entity_count	1

Entity 10 non-polymer

description	;P1-(5'-Adenosyl) P4-(5'-guanosyl) tetraphosphate ;
formula_weight	852.4 kDa
src_method	syn
entity_count	1

Entity 11 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

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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	3.160 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	3.16 Å
resolution_method	—
num_particles	288053

fit	/app/data/saxs_computation/up/9upw/9upw.fit
pddf	/app/data/pr_computation/up/9upw/9upw.pr.out
profile	/app/data/saxs_computation/up/9upw/9upw.dat

CryoEM structure of the T.thermophilus transcription initiation complex in the presence of Gp4A, -1 dC in the template DNA strand

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 (11)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)