SAXSdb — 5d98

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

Polymerase acidic protein

Influenza C virus (strain C/Johannesburg/1/1966)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	RNA-directed RNA polymerase catalytic subunit × 1 （Q9IMP4） Polymerase basic protein 2 × 1 （Q9IMP3） MAGNESIUM ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	RNA-directed RNA polymerase catalytic subunit × 1 （Q9IMP4） Polymerase basic protein 2 × 1 （Q9IMP3） MAGNESIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PA_INCJH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–709； UniProt 1–709 Author chain D； PDBConstruct 1–709； UniProt 1–709

RNA-directed RNA polymerase catalytic subunit

Influenza C virus (strain C/Johannesburg/1/1966)

UniProt Q9IMP4

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Polymerase acidic protein × 1 （Q9IMP5） Polymerase basic protein 2 × 1 （Q9IMP3） MAGNESIUM ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Polymerase acidic protein × 1 （Q9IMP5） Polymerase basic protein 2 × 1 （Q9IMP3） MAGNESIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RDRP_INCJH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–754； UniProt 1–754 Author chain E； PDBConstruct 1–754； UniProt 1–754

Polymerase basic protein 2

Influenza C virus (strain C/Johannesburg/1/1966)

UniProt Q9IMP3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Polymerase acidic protein × 1 （Q9IMP5） RNA-directed RNA polymerase catalytic subunit × 1 （Q9IMP4） MAGNESIUM ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Polymerase acidic protein × 1 （Q9IMP5） RNA-directed RNA polymerase catalytic subunit × 1 （Q9IMP4） MAGNESIUM ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PB2_INCJH
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–774； UniProt 1–774 Author chain F； PDBConstruct 1–774； UniProt 1–774

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	5d98
Deposition date deposition_date	2015-08-18
Structure title title	Influenza C Virus RNA-dependent RNA Polymerase - Space group P43212
Keywords keywords	RNA-dependent RNA polymerase, Influenza, Influenza C virus, Negative-strand virus, transferase-RNA complex; TRANSFERASE/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.

5d98__assembly_1__model_1

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

Download this curve (.dat)

5d98__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5d98__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.91 Å
Rg (electron density)	40.44 Å
Total Rg	40.79 Å
Atom count	17360
Residues	2166
Excluded volume	311400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5d98__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5d98__assembly_2__model_1`	trimeric （3）	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 (4)

Entity 1 Entity 1 polymer

Description description	Polymerase acidic protein
Molecular weight formula_weight	82025.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	34720

MSKTFAEIAEAFLEPEAVRIAKEAVEEYGDHERKIIQIGIHFQVCCMFCDEYLSTNGSDRFVLIEGRKRGTAVSLQNELCKSYDLEPLPFLCDIFDREEKQFVEIGITRKADDSYFQSKFGKLGNSCKIFVFSYDGRLDKNCEGPMEEQKLRIFSFLATAADFLRKENMFNEIFLPDNEETIIEMKKGKTFLELRDESVPLPFQTYEQMKDYCEKFKGNPRELASKVSQMQSNIKLPIKHYEQNKFRQIRLPKGPMAPYTHKFLMEEAWMFTKISDPERSRAGEILIDFFKKGNLSAIRPKDKPLQGKYPIHYKNLWNQIKAAIADRTMVINENDHSEFLGGIGRASKKIPEISLTQDVITTEGLKQSENKLPEPRSFPRWFNAEWMWAIKDSDLTGWVPMAEYPPADNELEDYAEHLNKTMEGVLQGTNCAREMGKCILTVGALMTECRLFPGKIKVVPIYARSKERKSMQEGLPVPSEMDCLFGICVKSKSHLNKDDGMYTIITFEFSIREPNLEKHQKYTVFEAGHTTVRMKKGESVIGREVPLYLYCRTTALSKIKNDWLSKARRCFITTMDTVETICLRESAKAEENLVEKTLNEKQMWIGKKNGELIAQPLREALRVQLVQQFYFCIYNDSQLEGFCNEQKKILMALEGDKKNKSSFGFNPEGLLEKIEECLINNPMCLFMAQRLNELVIEASKRGAKFFKTD

Source Source

Source organism organism	Influenza C virus (strain C/Johannesburg/1/1966)
NCBI taxonomy ID ncbi_taxonomy_id	100673
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	RNA-directed RNA polymerase catalytic subunit
Molecular weight formula_weight	86145.9 kDa
EC 编号 ec_number	2.7.7.48
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

MEINPYLMFLNNDVTSLISTTYPYTGPPPMSHGSSTKYTLETIKRTYDYSRTSVEKTSKVFNIPRRKFCNCLEDKDELVKPTGNVDISSLLGLAEMMEKRMGEGFFKHCVMEAETEILKMHFSRLTEGRQTYDWTSERNMPAATALQLTVDAIKETEGPFKGTTMLEYCNKMIEMLDWKEIKFKKVKTVVRREKDKRSGKEIKTKVPVMGIDSIKHDEFLIRALTINTMAKDGERGKLQRRAIATPGMIVRPFSKIVETVAQKICEKLKESGLPVGGNEKKAKLKTTVTSLNARMNSDQFAVNITGDNSKWNECQQPEAYLALLAYITKDSSDLMKDLCSVAPVLFCNKFVKLGQGIRLSNKRKTKEVIIKAEKMGKYKNLMREEYKNLFEPLEKYIQKDVCFLPGGMLMGMFNMLSTVLGVSTLCYMDEELKAKGCFWTGLQSSDDFVLFAVASNWSNIHWTIRRFNAVCKLIGINMSLEKSYGSLPELFEFTSMFFDGEFVSNLAMELPAFTTAGVNEGVDFTAAMSIIKTNMINNSLSPSTALMALRICLQEFRATYRVHPWDSRVKGGRMKIINEFIKTIENKDGLLIADGGKLMNNISTLHIPEEVLKFEKMDEQYRNRVFNPKNPFTNFDKTIDIFRAHGPIRVEENEAVVSTHSFRTRANRTLLNTDMRAMMAEEKRYQMVCDMFKSVFESADINPPIGAMSIGEAIEEKLLERAKMKRDIGAIEDSEYEEIKDIIRDAKKARLESR

Source Source

Source organism organism	Influenza C virus (strain C/Johannesburg/1/1966)
NCBI taxonomy ID ncbi_taxonomy_id	100673
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	Polymerase basic protein 2
Molecular weight formula_weight	88972.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSLLLTIAKEYKRLCQDAKAAQMMTVGTVSNYTTFKKWTTSRKEKNPSLRMRWAMSSKFPIIANKRMLEEAQIPKEHNNVALWEDTEDVSKRDHVLASASCINYWNFCGPCVNNSEVIKEVYKSRFGRLERRKEIMWKELRFTLVDRQRRRVDTQPVEQRLRTGEIKDLQMWTLFEDEAPLASKFILDNYGLVKEMRSKFANKPLNKEVVAHMLEKQFNPESRFLPVFGAIRPERMELIHALGGETWIQEANTAGISNVDQRKNDIRAVCRKVCLAANASIMNAKSKLVEYIKSTSMRIGETERKLEELILETDDVSPEVTLCKSALGGQLGKTLSFGPMLLKKISGSGVKVKDTVYIQGVRAVQFEYWSEQEEFYGEYKSATALFSRKERSLEWITIGGGINEDRKRLLAMCMIFCRDGDYFKDAPATITMADLSTKLGREIPYQYVMMNWIQKSEDNLEALLYSRGIVETNPGKMGSSMGIDGSKRAIKSLRAVTIQSGKIDMPESKEKIHLELSDNLEAFDSSGRIVATILDLPSDKKVTFQDVSFQHPDLAVLRDEKTAITKGYEALIKRLGTGDNDIPSLIAKKDYLSLYNLPEVKLMAPLIRPNRKGVYSRVARKLVSTQVTTGHYSLHELIKVLPFTYFAPKQGMFEGRLFFSNDSFVEPGVNNNVFSWSKADSSKIYCHGIAIRVPLVVGDEHMDTSLALLEGFSVCENDPRAPMVTRQDLIDVGFGQKVRLFVGQGSVRTFKRTASQRAASSDVNKNVKKIKMSNARENLYFQ

Source Source

Source organism organism	Influenza C virus (strain C/Johannesburg/1/1966)
NCBI taxonomy ID ncbi_taxonomy_id	100673
Host organism host_organism	Spodoptera frugiperda

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

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Unit-cell length a length_a	185.660 Å
Unit-cell length b length_b	185.660 Å
Unit-cell length c length_c	598.220 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	3.900 Å
Low-resolution limit resolution_low	50.010 Å
R factor r_factor	0.2878
R_work r_work	0.2858
R_free r_free	0.3257

Influenza C Virus RNA-dependent RNA Polymerase - Space group P43212

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

5d98__assembly_1__model_1

5d98__assembly_1__model_1 | I(q)

5d98__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

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 non-polymer

7. Citations (1)

Influenza C Virus RNA-dependent RNA Polymerase - Space group P43212

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

5d98__assembly_1__model_1

5d98__assembly_1__model_1 | I(q)

5d98__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

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 non-polymer

7. Citations (1)