4ylo

E. coli Transcription Initiation Complex - 16-bp spacer and 4-nt RNA

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase subunit alpha

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit beta × 1 （A7ZUK1） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A7ZUK2） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） RNA polymerase sigma factor RpoD × 1 （P00579） NT strand DNA (49-MER) × 1 T strand DNA (49-MER) × 1 ;RNA (5'-D((GTP))-R(PAPGPU)-3') ; × 1 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers
2	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit beta × 1 （A7ZUK1） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A7ZUK2） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） RNA polymerase sigma factor RpoD × 1 （P00579） NT strand DNA (49-MER) × 1 T strand DNA (49-MER) × 1 ;RNA (5'-D((GTP))-R(PAPGPU)-3') ; × 1 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers
3	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit beta × 1 （A7ZUK1） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A7ZUK2） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） RNA polymerase sigma factor RpoD × 1 （P00579） NT strand DNA (49-MER) × 1 T strand DNA (49-MER) × 1 ;RNA (5'-D((GTP))-R(PAPGPU)-3') ; × 1 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOA_ECO24
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–242； UniProt 1–235 Author chain B； PDBConstruct 8–242； UniProt 1–235 Author chain G； PDBConstruct 8–242； UniProt 1–235 Author chain H； PDBConstruct 8–242； UniProt 1–235 Author chain M； PDBConstruct 8–242； UniProt 1–235 Author chain N； PDBConstruct 8–242； UniProt 1–235

DNA-directed RNA polymerase subunit beta

Escherichia coli

UniProt A7ZUK1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （A7ZSI4） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A7ZUK2） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） RNA polymerase sigma factor RpoD × 1 （P00579） NT strand DNA (49-MER) × 1 T strand DNA (49-MER) × 1 ;RNA (5'-D((GTP))-R(PAPGPU)-3') ; × 1 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers
2	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （A7ZSI4） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A7ZUK2） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） RNA polymerase sigma factor RpoD × 1 （P00579） NT strand DNA (49-MER) × 1 T strand DNA (49-MER) × 1 ;RNA (5'-D((GTP))-R(PAPGPU)-3') ; × 1 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers
3	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （A7ZSI4） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A7ZUK2） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） RNA polymerase sigma factor RpoD × 1 （P00579） NT strand DNA (49-MER) × 1 T strand DNA (49-MER) × 1 ;RNA (5'-D((GTP))-R(PAPGPU)-3') ; × 1 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOB_ECO24
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–1342； UniProt 1–1342 Author chain I； PDBConstruct 1–1342； UniProt 1–1342 Author chain O； PDBConstruct 1–1342； UniProt 1–1342

;DNA-directed RNA polymerase subunit beta' ;

Escherichia coli

UniProt A7ZUK2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （A7ZSI4） DNA-directed RNA polymerase subunit beta × 1 （A7ZUK1） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） RNA polymerase sigma factor RpoD × 1 （P00579） NT strand DNA (49-MER) × 1 T strand DNA (49-MER) × 1 ;RNA (5'-D((GTP))-R(PAPGPU)-3') ; × 1 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers
2	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （A7ZSI4） DNA-directed RNA polymerase subunit beta × 1 （A7ZUK1） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） RNA polymerase sigma factor RpoD × 1 （P00579） NT strand DNA (49-MER) × 1 T strand DNA (49-MER) × 1 ;RNA (5'-D((GTP))-R(PAPGPU)-3') ; × 1 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers
3	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （A7ZSI4） DNA-directed RNA polymerase subunit beta × 1 （A7ZUK1） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） RNA polymerase sigma factor RpoD × 1 （P00579） NT strand DNA (49-MER) × 1 T strand DNA (49-MER) × 1 ;RNA (5'-D((GTP))-R(PAPGPU)-3') ; × 1 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOC_ECO24
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–1407； UniProt 1–1407 Author chain J； PDBConstruct 1–1407； UniProt 1–1407 Author chain P； PDBConstruct 1–1407； UniProt 1–1407

DNA-directed RNA polymerase subunit omega

Escherichia coli

UniProt A7ZTK1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （A7ZSI4） DNA-directed RNA polymerase subunit beta × 1 （A7ZUK1） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A7ZUK2） RNA polymerase sigma factor RpoD × 1 （P00579） NT strand DNA (49-MER) × 1 T strand DNA (49-MER) × 1 ;RNA (5'-D((GTP))-R(PAPGPU)-3') ; × 1 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers
2	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （A7ZSI4） DNA-directed RNA polymerase subunit beta × 1 （A7ZUK1） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A7ZUK2） RNA polymerase sigma factor RpoD × 1 （P00579） NT strand DNA (49-MER) × 1 T strand DNA (49-MER) × 1 ;RNA (5'-D((GTP))-R(PAPGPU)-3') ; × 1 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers
3	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （A7ZSI4） DNA-directed RNA polymerase subunit beta × 1 （A7ZUK1） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A7ZUK2） RNA polymerase sigma factor RpoD × 1 （P00579） NT strand DNA (49-MER) × 1 T strand DNA (49-MER) × 1 ;RNA (5'-D((GTP))-R(PAPGPU)-3') ; × 1 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOZ_ECO24
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain E； PDBConstruct 1–90； UniProt 2–91 Author chain K； PDBConstruct 1–90； UniProt 2–91 Author chain Q； PDBConstruct 1–90； UniProt 2–91

RNA polymerase sigma factor RpoD

Escherichia coli

UniProt P00579

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （A7ZSI4） DNA-directed RNA polymerase subunit beta × 1 （A7ZUK1） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A7ZUK2） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） NT strand DNA (49-MER) × 1 T strand DNA (49-MER) × 1 ;RNA (5'-D((GTP))-R(PAPGPU)-3') ; × 1 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers
2	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （A7ZSI4） DNA-directed RNA polymerase subunit beta × 1 （A7ZUK1） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A7ZUK2） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） NT strand DNA (49-MER) × 1 T strand DNA (49-MER) × 1 ;RNA (5'-D((GTP))-R(PAPGPU)-3') ; × 1 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers
3	Other combination	Heteromer	Protein 6 DNA 2 RNA 1	DNA-directed RNA polymerase subunit alpha × 2 （A7ZSI4） DNA-directed RNA polymerase subunit beta × 1 （A7ZUK1） ;DNA-directed RNA polymerase subunit beta' ; × 1 （A7ZUK2） DNA-directed RNA polymerase subunit omega × 1 （A7ZTK1） NT strand DNA (49-MER) × 1 T strand DNA (49-MER) × 1 ;RNA (5'-D((GTP))-R(PAPGPU)-3') ; × 1 MAGNESIUM ION × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPOD_ECOLI
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain F； PDBConstruct 16–628； UniProt 1–613 Author chain L； PDBConstruct 16–628； UniProt 1–613 Author chain R； PDBConstruct 16–628； UniProt 1–613

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4ylo
Deposition date deposition_date	2015-03-05
Structure title title	E. coli Transcription Initiation Complex - 16-bp spacer and 4-nt RNA
Keywords keywords	RNA Polymerase, Initiation Complex, DNA Bubble, TRANSCRIPTION-DNA-RNA complex; TRANSCRIPTION/DNA/RNA
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4ylo__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4ylo__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ylo__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	51.94 Å
Rg (electron density)	51.61 Å
Total Rg	51.82 Å
Atom count	31536
Residues	3849
Excluded volume	554570 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ylo__assembly_1__model_1`	nonameric （9）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4ylo__assembly_2__model_1`	nonameric （9）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4ylo__assembly_3__model_1`	nonameric （9）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	DNA-directed RNA polymerase subunit alpha
Molecular weight formula_weight	26899.6 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,G,H,M,N
Atom count atom_count	94608

AHHHHHHMQGSVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLR

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	DNA-directed RNA polymerase subunit beta
Molecular weight formula_weight	150820.9 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,I,O

MVYSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQDPEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDVQECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEVYMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLDLLAKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYGAAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLLKEIRSLGINIELEDE

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	;DNA-directed RNA polymerase subunit beta' ;
Molecular weight formula_weight	155366.8 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,J,P

MKDLLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAGEAPAAPQVTAEDASASLAELLNAGLGGSDNE

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 polymer

Description description	DNA-directed RNA polymerase subunit omega
Molecular weight formula_weight	10118.4 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,K,Q

ARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAELQAVTAIAEGRR

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	RNA polymerase sigma factor RpoD
Molecular weight formula_weight	72206.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,L,R

MRGSHHHHHHTDQFTMEQNPQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQMINDMGIQVMEEAPDADDLMLAENTADEDAAEAAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAEEDLAPTATHVGSELSQEDLDDDEDEDEEDGDDDSADDDNSIDPELAREKFAELRAQYVVTRDTIKAKGRSHATAQEEILKLSEVFKQFRLVPKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 6 Entity 6 polymer

Description description	NT strand DNA (49-MER)
Molecular weight formula_weight	15024.6 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	1,4,7

ACTTGACATCCACCTCACGTATGCTATAATGTGTGCAGTCTGACGCGGC

Entity 7 Entity 7 polymer

Description description	T strand DNA (49-MER)
Molecular weight formula_weight	15233.8 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	2,5,8

GCCGCGTCAGACTCGTAGGATTATAGCATACGTGAGGTGGATGTCAAGT

Entity 8 Entity 8 polymer

Description description	;RNA (5'-D((GTP))-R(PAPGPU)-3') ;
Molecular weight formula_weight	1440.8 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	3,6,9

GAGU

Entity 9 Entity 9 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 10 Entity 10 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	6

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Unit-cell length a length_a	240.888 Å
Unit-cell length b length_b	208.174 Å
Unit-cell length c length_c	256.323 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	119.31 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	6.000 Å
Low-resolution limit resolution_low	39.950 Å
R factor r_factor	0.2315
R_work r_work	0.2269
R_free r_free	0.3143

E. coli Transcription Initiation Complex - 16-bp spacer and 4-nt RNA

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-directed RNA polymerase subunit beta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

;DNA-directed RNA polymerase subunit beta' ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-directed RNA polymerase subunit omega

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

RNA polymerase sigma factor RpoD

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4ylo__assembly_1__model_1

4ylo__assembly_1__model_1 | I(q)

4ylo__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

7. Citations (1)