9rjs

Structure of the Bacteriophage PhiKZ non-virion RNA Polymerase bound to an analogue of its promoter

Method: ELECTRON MICROSCOPY

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

DNA-directed RNA polymerase,PHIKZ056.1

Phikzvirus phiKZ

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5 DNA 2	PHIKZ068 × 1 （Q8SD94） PHIKZ071 × 1 PHIKZ074 × 1 （Q8SD88） PHIKZ123 × 1 （Q8SD39） DNA - ATGAGTAATTTTAGTGAATGTATTTGCTATATTGCTATGTAGACAGTTCCCAAAAGCCTAAAGTTACAATATAGG × 1 DNA - CCTATATTGTAACTTTAGGCTTTTGGGAACTCCTCTCATATTCCCATAGCAAATACATTCACTAAAATTACTCAT × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	I7DB47_9CAUD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–441； UniProt 1–421

DNA-directed RNA polymerase,PHIKZ056.1

Phikzvirus phiKZ

UniProt L7T138

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5 DNA 2	PHIKZ068 × 1 （Q8SD94） PHIKZ071 × 1 PHIKZ074 × 1 （Q8SD88） PHIKZ123 × 1 （Q8SD39） DNA - ATGAGTAATTTTAGTGAATGTATTTGCTATATTGCTATGTAGACAGTTCCCAAAAGCCTAAAGTTACAATATAGG × 1 DNA - CCTATATTGTAACTTTAGGCTTTTGGGAACTCCTCTCATATTCCCATAGCAAATACATTCACTAAAATTACTCAT × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	L7T138_BPDPK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 448–508； UniProt 1–61

PHIKZ068

Phikzvirus phiKZ

UniProt Q8SD94

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5 DNA 2	DNA-directed RNA polymerase,PHIKZ056.1 × 1 （I7DB47,L7T138） PHIKZ071 × 1 PHIKZ074 × 1 （Q8SD88） PHIKZ123 × 1 （Q8SD39） DNA - ATGAGTAATTTTAGTGAATGTATTTGCTATATTGCTATGTAGACAGTTCCCAAAAGCCTAAAGTTACAATATAGG × 1 DNA - CCTATATTGTAACTTTAGGCTTTTGGGAACTCCTCTCATATTCCCATAGCAAATACATTCACTAAAATTACTCAT × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8SD94_BPDPK
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–521； UniProt 1–521

PHIKZ074

Phikzvirus phiKZ

UniProt Q8SD88

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5 DNA 2	DNA-directed RNA polymerase,PHIKZ056.1 × 1 （I7DB47,L7T138） PHIKZ068 × 1 （Q8SD94） PHIKZ071 × 1 PHIKZ123 × 1 （Q8SD39） DNA - ATGAGTAATTTTAGTGAATGTATTTGCTATATTGCTATGTAGACAGTTCCCAAAAGCCTAAAGTTACAATATAGG × 1 DNA - CCTATATTGTAACTTTAGGCTTTTGGGAACTCCTCTCATATTCCCATAGCAAATACATTCACTAAAATTACTCAT × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8SD88_BPDPK
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–677； UniProt 1–677

PHIKZ123

Phikzvirus phiKZ

UniProt Q8SD39

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 5 DNA 2	DNA-directed RNA polymerase,PHIKZ056.1 × 1 （I7DB47,L7T138） PHIKZ068 × 1 （Q8SD94） PHIKZ071 × 1 PHIKZ074 × 1 （Q8SD88） DNA - ATGAGTAATTTTAGTGAATGTATTTGCTATATTGCTATGTAGACAGTTCCCAAAAGCCTAAAGTTACAATATAGG × 1 DNA - CCTATATTGTAACTTTAGGCTTTTGGGAACTCCTCTCATATTCCCATAGCAAATACATTCACTAAAATTACTCAT × 1 ZINC ION × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8SD39_BPDPK
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–543； UniProt 1–543

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	9rjs
Deposition date deposition_date	2025-06-12
Structure title title	Structure of the Bacteriophage PhiKZ non-virion RNA Polymerase bound to an analogue of its promoter
Keywords keywords	PhiKZ, nvRNAP, RNA, DNA, transcription, RNA BINDING PROTEIN; RNA BINDING PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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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.

9rjs__assembly_1__model_1

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

Download this curve (.dat)

9rjs__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9rjs__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	45.36 Å
Rg (electron density)	44.54 Å
Total Rg	44.87 Å
Atom count	21114
Residues	2551
Excluded volume	373070 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9rjs__assembly_1__model_1`	heptameric （7）	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 (8)

Entity 1 Entity 1 polymer

Description description	DNA-directed RNA polymerase,PHIKZ056.1
Molecular weight formula_weight	57976.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	21114

MGSSHHHHHHSSGLVPRGSHMGLYAKVVDHNEVHDQFTGKRIYANDYNTSNSDEKEEFDRHFYSHFQDSEAIESSVSCDCRAIEDAHKLGVICDICNTPVVNTSSRPIEPSMWVRTPKHVRSLINPRLIIMLTGYLVTKEFDFLAYLTDTSYRYDVESIGSKETRRKVDRLLHRGFERGLNHFIDNFNEIFQFLLDANIISNNKSEFAQFVAQNKDKLFPKYLPVPSKLCFVAESTTSGTYLDKPIEAAIDATLTFASIDASSVPLSPIKAQNRTMRGLRLYGQFYEIYAKSRIAQKPGLARRHMFGARLNATARAVITSISDPHDYDELHIPWGVGCQLLKYHLTNKLKAKFNMTTREAFSFVYENVLQYNQIIADLFKELIAEAAPYKGMGCTFHRNPTLQRGSTQQFFITKVKDDINDNSISMSVLCLKAPNADFDGDQLNLTLMPDVYLTKATERIAPHTWVLSIDEPHEISGNLELQGPVVETIINWAHEKYLPPLEEWLKAK

Source Source

Source organism organism	Phikzvirus phiKZ
NCBI taxonomy ID ncbi_taxonomy_id	169683
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	PHIKZ068
Molecular weight formula_weight	59442.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MEIIVTGVQGTGFTEVATEHNGKRLTWTTTAYSKIRVQDQQRVFQEINDYWSGLSAEAQQHIWNCYVEIRKIMDMAMHPMRIAMSLSYYIKEMYKAMPMNSFRRWLLTIGKLYIPVDIEEVITDDSRYNRPDQTYLKHDYINLASVSLALRPLVPIWGEFIDQGTSQEMHKECEVISLISDCEVNHWPVDEISIDGTPVETAYDKLSAYVKFCVEDEAPTLANLYRGMSSAEVPDILQAKVMVRRLTILPLNDATSHSIVSNMFRYVKSNLNPAERSTADRVNDKRPDKGGIDDDDKTSFIESHKTKQRVTPGDIVAYNLDALDVVKLVHKIDDTVPVELIQECLDCVAVTATKDIYPHQILLAQWVMHKAFPARAFSHINKNAVNHLLAAAQSLMWHWGFQQVAVFMQVELYYSGEHAMSIQPRNSTRIQIKYKDVMDELYPHQRQQRAINGVPVAPVNIAGIAVQSAHASIRSSNWIYHGPDRLFKEAEQVTQNKVLVVPATIKSVITELVIHLGKLNQ

Source Source

Source organism organism	Phikzvirus phiKZ
NCBI taxonomy ID ncbi_taxonomy_id	169683
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	PHIKZ071
Molecular weight formula_weight	78780.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSQLGRREIDLTLLGHTGLDPWYGTTSSARGAMFVTHIGQAPEVNGNESRYFLTGAELEYAKYTHDVRFPEDCRVLHVLRKYPTGIGKDSIRSNPVTTIIYENYFDKYKTIGVLHVPEYMSHHQDFGYELVKNREVWETIAPNEMFSKDTVIAQSGAVKKDGTLGMGVNANVVFLSAAGTIEDGFVANKNFLKRMMPTSYSTAVANAGRKAFFLNMYGDDKIYKPFPDIGDVIRPDGVIFAIRDHDDDLAPAEMTPRALRTLDRTFDRAVIGTPGAKVIDIDIWRDERVNPSPTPTGMDAQLVKYHTHLSSYYRELLKIYRGLLARRKDDLHITEEFERLIVTAQMFLPQPDNVRKLSRFYRLDPLDEWRVEVTYKAQKMPAGAFKMTDFHGGKGVICKVMEDEDMPIDENGNRADLIIFGGSTMRRSNYGRIYEHGFGAAARDLAQRLRVEAGLDRHAKPTQQQLNSVMGNTQWVDYAFKELLGFYEIIAPTMHSKMMEHPNPAEHVKTVLMDGFPYIYAPVDDPVDLMAAVNKLINSDKYRPHYGKVSYRDQAGKWVTTKDNVLMGPLYMMLLEKIGEDWSAAASVKTQPFGLPSKLNNADRASTPGRETAIRSFGESETRSYNCTVGPGPTAEILDQTNNPLAHAAVIESWLTAEKPSSVPVAVDREKIPFGGSRPVAMFDHLLECSGIALEYAPDH

Source Source

Source organism organism	Phikzvirus phiKZ
NCBI taxonomy ID ncbi_taxonomy_id	169683
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	PHIKZ074
Molecular weight formula_weight	77513.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MNLNRYKARDLLNLSYDDLWSLPSEWHLIEFDDGKTVVSVDRITKLSVLCWYPLKHYKDCPIPSDHHIDFNRILTDNPKDYLNVEGGRVTSKAMVKHLNKAIWNIYDWSGETVDPEVLSKLAIEGKNWLYNQTTVKLSEYLATLSMFDIAEVYNHPKVREANHNIEPTTYGIEKISYGKVKEVFNDPTQFIGNSIIEGLRSGTQKTEQLLQAFAWRGFPTDINSDIFKYPVTTGYIDGIWNLYENMIESRSGTKALLYNKELLRVTEYFNRKSQLIAQYVQRLHPGDCKTTILAEYPVTKLTLKAFKGKYYQKEDGKLDWIRGNETHLIGTKQKFRSVFGCNHPDSQGICMTCYGRLGINIPKGTNIGQVAAVSMGDKITSAVLSTKHTDASSAVEQYKLGKIESNYLRTGEIPETLYLKKELTQKDYRLVIARSEAENLADILMIDDLTAYPATSATELTSLALVYDDEVNGECGDVLTVSLYNRRASLSIEMLKHIKMVRWELDQRDNIVISLRGFDFNLPFLTLPNKHVNMYEVMKRFQSFLHSGSDSAEAGKLSTEKVGYTSKTYLKNYKSPIEALPVFATMANEKISLNISHCEILIYAMMIRSAQYRDYRLPKPGINGQFEKYNRLMQCRSLGGAMAFEKQHEPLNNPGSFLNKMRNDHPYDLLVKGGKLR

Source Source

Source organism organism	Phikzvirus phiKZ
NCBI taxonomy ID ncbi_taxonomy_id	169683
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	PHIKZ123
Molecular weight formula_weight	62959.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MPDPFLIEKIRENTPCMNPTLANGITVEHTMTRDPNTGVNMTRRYIDSLFDISSVLFPDGFKYEGNRACTPLKHFEEITREYNAKRIANIAPTDMYMIDLMFSYKGEMLYPRPMLLPAFKRGNMVTINGAKYIGSPVLTDVGFSVLNDSIFIPFRRTKLTFKQTDHHYMCNGQRKIMYVIWSQIHNEMAKRTKRDLGNRPHIESCLAHYFFCQFGVTQTFKQWANVDVKCGLLSDFPEEEYPREKWNIYSSATLKGKHPTGEMVLVIPRHQESIFATRLIAGFWYVVDAFPMRFTRPEYVDSTNLWRVILGHMVFGDFEHQGKVEENIDSHLHSFCNSLDEMTIEELKTVGVNVSTIWELLYEIMTSLAHHLYATDIDETSMYGKRLTVLHYLMSEFNYAVSMFGYMFQSRRDREWTVQELNEGLKRSFKLQTAIKRLTVDHGELDTMSNPNSSMLIKGTSILVTQDRAKTAKAHNKSLINDSSRIIHASIAEVGQYKNQPKNNPDGRGRLNMYTKVGPTGLVERREEVREIIDNAQLMFRAK

Source Source

Source organism organism	Phikzvirus phiKZ
NCBI taxonomy ID ncbi_taxonomy_id	169683
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	DNA - ATGAGTAATTTTAGTGAATGTATTTGCTATATTGCTATGTAGACAGTTCCCAAAAGCCTAAAGTTACAATATAGG
Molecular weight formula_weight	23219.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	X

ATGAGTAATTTTAGTGAATGTATTTGCTATATTGCTATGTAGACAGTTCCCAAAAGCCTAAAGTTACAATATAGG

Entity 7 Entity 7 polymer

Description description	DNA - CCTATATTGTAACTTTAGGCTTTTGGGAACTCCTCTCATATTCCCATAGCAAATACATTCACTAAAATTACTCAT
Molecular weight formula_weight	22881.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	Y

CCTATATTGTAACTTTAGGCTTTTGGGAACTCCTCTCATATTCCCATAGCAAATACATTCACTAAAATTACTCAT

Entity 8 Entity 8 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	triclinic

Resolution resolution	2.59 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	329400

Structure of the Bacteriophage PhiKZ non-virion RNA Polymerase bound to an analogue of its promoter

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

DNA-directed RNA polymerase,PHIKZ056.1

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,PHIKZ056.1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PHIKZ068

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PHIKZ074

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PHIKZ123

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

9rjs__assembly_1__model_1

9rjs__assembly_1__model_1 | I(q)

9rjs__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

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 non-polymer

7. Citations (1)