SAXSdb — 9raf

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1. Structure Basics

entry_id	9raf
deposition_date	2025-05-20
title	Influenza A/H7N9 polymerase in complex with a 70-mer template in stalled elongation with backtracking and stem.
keywords	Influenza polymerase, VIRAL PROTEIN; VIRAL PROTEIN
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	37.48 Å
rg_electron	37.28 Å
i0	905870000.00
molecular_weight	224230.0 kDa
excluded_volume	271350 Å³
envelope_volume	346710 Å³
shell_volume	73524 Å³
envelope_diameter	133.4 Å
shell_rg	45.93 Å
envelope_rg	37.20 Å
shape_rg	37.31 Å
total_rg	37.62 Å
total_atoms	30261
n_residues	1796
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	122.7 Å
rg_real	37.30 Å
rg_real_error	0.82 Å
i0_real	9.0590e+08
i0_real_error	1.5630e+07
rg_reciprocal	37.41 Å
i0_reciprocal	906000000.0000
total_estimate	0.8757
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	46.7 Å
skewness	0.259
kurtosis	-0.246
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	209500000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.934

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Polymerase acidic protein
formula_weight	82829.6 kDa
mutation	E349K; R490I
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	31095

MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFASICTHLEVCFMYSDFHFIDERGESTIIESGDPNVLLKHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQEMASRGLWDSFRQSERGEETIEERFEITGTMRRLADQSLPPNFSSLENFRAYVDGFEPNGCIEGKLSQMSKEVNARIEPFLRTTPRPLRLPDGPPCSQRSKFLLMDALKLSIEDPSHEGEGIPLYDAIKCMKTFFGWKEPNIIKPHEKGINPNYLLTWKQVLAELQDIKNEEKIPRTKNMKKTSQLKWALGENMAPEKVDFEDCKDVNDLKQYDSDEPEPRSLACWIQSEFNKACELTDSSWVELDEIGEDVAPIEHIASMRRNYFTAEVSHCRATEYIMKGVYINTALLNASCAAMDDFQLIPMISKCITKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKYCVLEIGDMLLRTAVGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAESSVKEKDLTKEFFENKSETWPIGESPKGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFSAESRKLLLIVQALRDNLEPGTFDLEGLYEAIEECLINDPWVLLNASWFNSFLTHALR

Source

organism	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
ncbi_taxonomy_id	1318616
host_organism	Trichoplusia ni

Entity 2 polymer

description	Polymerase basic protein 2
formula_weight	89038.6 kDa
mutation	G74R; K627; D701
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMKYPITADKRIMEMIPERNEQRQTLWSKTNDAGSDRVMVSPLAVTWWNRNGPTTSTVHYPKVYKTYFEKVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQDVIMEVVFPNEVGARILTSESQLTITKEKKKELQDCKIAPLMVAYMLERELVRKTRFLPVAGGTSSVYIEVLHLTQGTCWEQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADPLASLLEMCHSTQIGGVRMVDILRQNPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTSGSSVKREEEVLTGNLQTLKIRVHEGYEEFTMVGRRATAILRKATRRLIQLIVSGKDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNFVNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSLRGVRVSKMGVDEYSSTERVVVSIDRFLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEINGPESVLVNTYQWIIRNWENVKIQWSQDPTMLYNKMEFEPFQSLVPKAARGQYSGFVRVLFQQMRDVLGTFDTVQIIKLLPFAAAPPKQSRMQFSSLTVNVRGSGMRIVVRGNSPVFNYNKATKRLTVLGKDAGALMEDPDEGTAGVESAVLRGFLILGKEDKRYGPALSINELSNLAKGEKANVLIGQGDVVLVMKRKRDSSILTDSQTATKRIRMAINGWSHPQFEKGGGSGGGSGGSAWSHPQFEK

Source

organism	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
ncbi_taxonomy_id	1318616
host_organism	Trichoplusia ni

Entity 3 polymer

description	RNA Pol II CTD 6 repeats (site 1A/2A)
formula_weight	4816.3 kDa
src_method	syn
entity_count	1

Polymer

type	polypeptide(L)
strand_id	G

YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS

Entity 4 polymer

description	RNA product
formula_weight	4171.6 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	M

CCGCAGGGAGCUC

Entity 5 polymer

description	RNA-directed RNA polymerase catalytic subunit
formula_weight	86424.0 kDa
mutation	K577G
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MDVNPTLLFLKVPVQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHKYSEKGKWTTNTETGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHPGIFENSCLETMEIVQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVFRSNGLTANESGRLIDFLKDVMDSMDKEEMEITTHFQRKRRVRDNMTKKMVTQRTIGKKKQRLNKRSYLIRALTLNTMTKDAERGKLKRRAIATPGMQIRGFVYFVEALARSICEKLEQSGLPVGGNEKKAKLANVVRKMMTNSQDTELSFTITGDNTKWNENQNPRMFLAMITYITRNQPEWFRNVLSIAPIMFSNKMARLGKGYMFESKSMKLRTQVPAEMLANIDLKYFNKSTREKIEKIRPLLIDGTASLSPGMMMGMFNMLSTVLGVSILNLGQKKYTKTTYWWDGLQSSDDFALIVNAPNHEGIQAGVDRFYRTCKLVGINMSKKKSYINRTGTFEFTSFFYRYGFVANFSMELPSFGVSGINESADMSVGVTVIKNNMINNDLGPATAQMALQLFIKDYRYTYRCHRGDTQIQTRRAFELGKLWEQTRSKAGLLVSDGGPNLYNIRNLHIPEVCLKWELMDEDYQGRLCNPMNPFVSHKEIDSVNNAVVMPAHGPAKSMEYDAVATTHSWIPKRNRSILNTSQRGILEDEQMYQKCCNLFEKFFPSSSYRRPVGISSMVEAMVSRARIDARIDFESGRIKKEEFAEIMKICSTIEELRRQK

Source

organism	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
ncbi_taxonomy_id	1318616
host_organism	Trichoplusia ni

Entity 6 polymer

description	RNA template (70-mer)
formula_weight	22480.3 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	T

AGUAGAAACAAGGAUCAGGAAUGUCCCACAAAGAGCUCCCUGCGGUCUUUGUGGGGCUCCUGCUUUUGCU

Entity 7 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	3

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	652

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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	2.150 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.15 Å
resolution_method	—
num_particles	195294

fit	/app/data/saxs_computation/ra/9raf/9raf.fit
pddf	/app/data/pr_computation/ra/9raf/9raf.pr.out
profile	/app/data/saxs_computation/ra/9raf/9raf.dat

Influenza A/H7N9 polymerase in complex with a 70-mer template in stalled elongation with backtracking and stem.

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 (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Source

Entity 6 polymer

Polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)