SAXSdb — 8pnp

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

Polymerase acidic protein

Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 4 RNA 1	RNA-directed RNA polymerase catalytic subunit × 1 （S5ME50） Polymerase basic protein 2 × 1 （X5F427） 51-mer vRNA loop (v51_mut_S) × 1 RNA Pol II CTD 6 repeats (site 1A/2A) × 1 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	M9TI86_9INFA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 14–729； UniProt 1–716

RNA-directed RNA polymerase catalytic subunit

Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))

UniProt S5ME50

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 4 RNA 1	Polymerase acidic protein × 1 （M9TI86） Polymerase basic protein 2 × 1 （X5F427） 51-mer vRNA loop (v51_mut_S) × 1 RNA Pol II CTD 6 repeats (site 1A/2A) × 1 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	S5ME50_9INFA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–757； UniProt 1–757

Polymerase basic protein 2

Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))

UniProt X5F427

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Heteromer	Protein 4 RNA 1	Polymerase acidic protein × 1 （M9TI86） RNA-directed RNA polymerase catalytic subunit × 1 （S5ME50） 51-mer vRNA loop (v51_mut_S) × 1 RNA Pol II CTD 6 repeats (site 1A/2A) × 1 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	X5F427_9INFA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–759； UniProt 1–759

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	8pnp
Deposition date deposition_date	2023-06-30
Structure title title	Influenza A/H7N9 polymerase in pre-initiation state with continuous Pol II pS5 CTD peptide mimic bound in site 1A/2A
Keywords keywords	Viral polymerase, VIRAL PROTEIN; VIRAL 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.

8pnp__assembly_1__model_1

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

Download this curve (.dat)

8pnp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8pnp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.84 Å
Rg (electron density)	37.60 Å
Total Rg	37.91 Å
Atom count	14417
Residues	1742
Excluded volume	254530 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8pnp__assembly_1__model_1`	pentameric （5）	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 (6)

Entity 1 Entity 1 polymer

Description description	Polymerase acidic protein
Molecular weight formula_weight	84354.2 kDa
Mutation mutation	E349K; R490I
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	14460

MHHHHHHHHGSGSMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFASICTHLEVCFMYSDFHFIDERGESTIIESGDPNVLLKHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERGEETIEERFEITGTMRRLADQSLPPNFSSLENFRAYVDGFEPNGCIEGKLSQMSKEVNARIEPFLRTTPRPLRLPDGPPCSQRSKFLLMDALKLSIEDPSHEGEGIPLYDAIKCMKTFFGWKEPNIIKPHEKGINPNYLLTWKQVLAELQDIKNEEKIPRTKNMKKTSQLKWALGENMAPEKVDFEDCKDVNDLKQYDSDEPEPRSLACWIQSEFNKACELTDSSWVELDEIGEDVAPIEHIASMRRNYFTAEVSHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKCITKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEIGDMLLRTAVGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAESSVKEKDLTKEFFENKSETWPIGESPKGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFSAESRKLLLIVQALRDNLEPGTFDLEGLYEAIEECLINDPWVLLNASWFNSFLTHALR

Source Source

Source organism organism	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
NCBI taxonomy ID ncbi_taxonomy_id	1318616
Host organism host_organism	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	RNA-directed RNA polymerase catalytic subunit
Molecular weight formula_weight	86424.0 kDa
Mutation mutation	K577G
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MDVNPTLLFLKVPVQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHKYSEKGKWTTNTETGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHPGIFENSCLETMEIVQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVFRSNGLTANESGRLIDFLKDVMDSMDKEEMEITTHFQRKRRVRDNMTKKMVTQRTIGKKKQRLNKRSYLIRALTLNTMTKDAERGKLKRRAIATPGMQIRGFVYFVEALARSICEKLEQSGLPVGGNEKKAKLANVVRKMMTNSQDTELSFTITGDNTKWNENQNPRMFLAMITYITRNQPEWFRNVLSIAPIMFSNKMARLGKGYMFESKSMKLRTQVPAEMLANIDLKYFNKSTREKIEKIRPLLIDGTASLSPGMMMGMFNMLSTVLGVSILNLGQKKYTKTTYWWDGLQSSDDFALIVNAPNHEGIQAGVDRFYRTCKLVGINMSKKKSYINRTGTFEFTSFFYRYGFVANFSMELPSFGVSGINESADMSVGVTVIKNNMINNDLGPATAQMALQLFIKDYRYTYRCHRGDTQIQTRRAFELGKLWEQTRSKAGLLVSDGGPNLYNIRNLHIPEVCLKWELMDEDYQGRLCNPMNPFVSHKEIDSVNNAVVMPAHGPAKSMEYDAVATTHSWIPKRNRSILNTSQRGILEDEQMYQKCCNLFEKFFPSSSYRRPVGISSMVEAMVSRARIDARIDFESGRIKKEEFAEIMKICSTIEELRRQK

Source Source

Source organism organism	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
NCBI taxonomy ID ncbi_taxonomy_id	1318616
Host organism host_organism	Trichoplusia ni

Entity 3 Entity 3 polymer

Description description	Polymerase basic protein 2
Molecular weight formula_weight	89037.6 kDa
Mutation mutation	G74R
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMKYPITADKRIMEMIPERNEQRQTLWSKTNDAGSDRVMVSPLAVTWWNRNGPTTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQDVIMEVVFPNEVGARILTSESQLTITKEKKKELQDCKIAPLMVAYMLERELVRKTRFLPVAGGTSSVYIEVLHLTQGTCWEQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADPLASLLEMCHSTQIGGVRMVDILRQNPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTSGSSVKREEEVLTGNLQTLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGKDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSLRGVRVSKMGVDEYSSTERVVVSIDRFLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTYQWIIRNWENVKIQWSQDPTMLYNKMEFEPFQSLVPKAARGQYSGFVRVLFQQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGMRIVVRGNSPVFNYNKATKRLTVLGKDAGALMEDPDEGTAGVESAVLRGFLILGKENKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRDSSILTDSQTATKRIRMAINGWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Source Source

Source organism organism	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
NCBI taxonomy ID ncbi_taxonomy_id	1318616
Host organism host_organism	Trichoplusia ni

Entity 4 Entity 4 polymer

Description description	51-mer vRNA loop (v51_mut_S)
Molecular weight formula_weight	16093.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	V

AGUAGAAACAAGGGUGUAUUUUCCCCUCUUUUUGUUUCCCCUGCUUUUGCU

Entity 5 Entity 5 polymer

Description description	RNA Pol II CTD 6 repeats (site 1A/2A)
Molecular weight formula_weight	4736.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	43

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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	—

Resolution resolution	2.49 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	260565

Influenza A/H7N9 polymerase in pre-initiation state with continuous Pol II pS5 CTD peptide mimic bound in site 1A/2A

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

Polymerase acidic protein

State in the Current Structure

Other States of the Same Protein in the Database

RNA-directed RNA polymerase catalytic subunit

State in the Current Structure

Other States of the Same Protein in the Database

Polymerase basic protein 2

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8pnp__assembly_1__model_1

8pnp__assembly_1__model_1 | I(q)

8pnp__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 (6)

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

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 water

7. Citations (1)

Influenza A/H7N9 polymerase in pre-initiation state with continuous Pol II pS5 CTD peptide mimic bound in site 1A/2A

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

Polymerase acidic protein

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-directed RNA polymerase catalytic subunit

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Polymerase basic protein 2

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

8pnp__assembly_1__model_1

8pnp__assembly_1__model_1 | I(q)

8pnp__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 (6)

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

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 water

7. Citations (1)