SAXSdb — 4f5x

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

VP2 protein

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 960	Intermediate capsid protein VP6 × 780 （A7J3A1） RNA-directed RNA polymerase × 60 （O37061） ZINC ION × 300	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 16	Intermediate capsid protein VP6 × 13 （A7J3A1） RNA-directed RNA polymerase × 1 （O37061） ZINC ION × 5	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 80	Intermediate capsid protein VP6 × 65 （A7J3A1） RNA-directed RNA polymerase × 5 （O37061） ZINC ION × 25	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 96	Intermediate capsid protein VP6 × 78 （A7J3A1） RNA-directed RNA polymerase × 6 （O37061） ZINC ION × 30	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 16	Intermediate capsid protein VP6 × 13 （A7J3A1） RNA-directed RNA polymerase × 1 （O37061） ZINC ION × 5	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 960	Intermediate capsid protein VP6 × 780 （A7J3A1） RNA-directed RNA polymerase × 60 （O37061） ZINC ION × 300	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H9N1A6_9REOV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–880； UniProt 1–880 Author chain B； PDBConstruct 1–880； UniProt 1–880

Intermediate capsid protein VP6

OrganismNot specified

UniProt A7J3A1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 960	VP2 protein × 120 （H9N1A6） RNA-directed RNA polymerase × 60 （O37061） ZINC ION × 300	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 16	VP2 protein × 2 （H9N1A6） RNA-directed RNA polymerase × 1 （O37061） ZINC ION × 5	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 80	VP2 protein × 10 （H9N1A6） RNA-directed RNA polymerase × 5 （O37061） ZINC ION × 25	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 96	VP2 protein × 12 （H9N1A6） RNA-directed RNA polymerase × 6 （O37061） ZINC ION × 30	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 16	VP2 protein × 2 （H9N1A6） RNA-directed RNA polymerase × 1 （O37061） ZINC ION × 5	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 960	VP2 protein × 120 （H9N1A6） RNA-directed RNA polymerase × 60 （O37061） ZINC ION × 300	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VP6_ROTBN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–397； UniProt 1–397 Author chain D； PDBConstruct 1–397； UniProt 1–397 Author chain E； PDBConstruct 1–397； UniProt 1–397 Author chain F； PDBConstruct 1–397； UniProt 1–397 Author chain G； PDBConstruct 1–397； UniProt 1–397 Author chain H； PDBConstruct 1–397； UniProt 1–397 Author chain I； PDBConstruct 1–397； UniProt 1–397 Author chain J； PDBConstruct 1–397； UniProt 1–397 Author chain K； PDBConstruct 1–397； UniProt 1–397 Author chain L； PDBConstruct 1–397； UniProt 1–397 Author chain M； PDBConstruct 1–397； UniProt 1–397 Author chain N； PDBConstruct 1–397； UniProt 1–397 Author chain O； PDBConstruct 1–397； UniProt 1–397

RNA-directed RNA polymerase

OrganismNot specified

UniProt O37061

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 960	VP2 protein × 120 （H9N1A6） Intermediate capsid protein VP6 × 780 （A7J3A1） ZINC ION × 300	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 16	VP2 protein × 2 （H9N1A6） Intermediate capsid protein VP6 × 13 （A7J3A1） ZINC ION × 5	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 80	VP2 protein × 10 （H9N1A6） Intermediate capsid protein VP6 × 65 （A7J3A1） ZINC ION × 25	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 96	VP2 protein × 12 （H9N1A6） Intermediate capsid protein VP6 × 78 （A7J3A1） ZINC ION × 30	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 16	VP2 protein × 2 （H9N1A6） Intermediate capsid protein VP6 × 13 （A7J3A1） ZINC ION × 5	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 960	VP2 protein × 120 （H9N1A6） Intermediate capsid protein VP6 × 780 （A7J3A1） ZINC ION × 300	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RDRP_ROTSP
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain W； PDBConstruct 1–1089； UniProt 1–1089

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	4f5x
Deposition date deposition_date	2012-05-13
Structure title title	Location of the dsRNA-dependent polymerase, VP1, in rotavirus particles
Keywords keywords	beta-jellyroll, polymerase, transcriptase, VIRUS; VIRUS
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.

4f5x__assembly_1__model_1

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

Download this curve (.dat)

4f5x__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4f5x__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	0.00 Å
Rg (electron density)	284.20 Å
Total Rg	283.90 Å
Atom count	3720840
Residues	463620
Excluded volume	66194000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4f5x__assembly_1__model_1`	960-MERIC （960）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4f5x__assembly_2__model_1`	hexadecameric （16）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`4f5x__assembly_3__model_1`	80-meric （80）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`4f5x__assembly_4__model_1`	96-meric （96）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`4f5x__assembly_5__model_1`	hexadecameric （16）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
6	1	`4f5x__assembly_6__model_1`	960-meric （960）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.

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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	VP2 protein
Molecular weight formula_weight	102595.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	62014

MAYRKRGARREANINNNDRMQEKDDEKQDQNNRMQLSDKVLSKKEEVVTDSQEEIKIADEVKKSTKEESKQLLEVLKTKEEHQKEIQYEILQKTIPTFEPKESILKKLEDIKPEQAKKQTKLFRIFEPRQLPIYRANGEKELRNRWYWKLKKDTLPDGDYDVREYFLNLYDQVLTEMPDYLLLKDMAVENKNSRDAGKVVDSETASICDAIFQDEETEGAVRRFIAEMRQRVQADRNVVNYPSILHPIDYAFNEYFLQHQLVEPLNNDIIFNYIPERIRNDVNYILNMDRNLPSTARYIRPNLLQDRLNLHDNFESLWDTITTSNYILARSVVPDLKELVSTEAQIQKMSQDLQLEALTIQSETQFLTGINSQAANDCFKTLIAAMLSQRTMSLDFVTTNYMSLISGMWLLTVVPNDMFIRESLVACQLAIVNTIIYPAFGMQRMHYRNGDPQTPFQIAEQQIQNFQVANWLHFVNNNQFRQVVIDGVLNQVLNDNIRNGHVINQLMEALMQLSRQQFPTMPVDYKRSIQRGILLLSNRLGQLVDLTRLLAYNYETLMACVTMNMQHVQTLTTEKLQLTSVTSLCMLIGNATVIPSPQTLFHYYNVNVNFHSNYNERINDAVAIITAANRLNLYQKKMKAIVEDFLKRLHIFDVARVPDDQMYRLRDRLRLLPVEVRRLDIFNLILMNMDQIERASDKIAQGVIIAYRDMQLERDEMYGYVNIARNLDGFQQINLEELMRTGDYAQITNMLLNNQPVALVGALPFVTDSSVISLIAKLDATVFAQIVKLRKVDTLKPILYKINSDSNDFYLVANYDWVPTSTTKVYKQVPQQFDFRNSMHMLTSNLTFTVYSDLLAFVSADTVEPINAVAFDNMRIMNEL

Entity 2 Entity 2 polymer

Description description	Intermediate capsid protein VP6
Molecular weight formula_weight	44922.6 kDa
Source method src_method	nat
Copy count entity_count	13

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,E,F,G,H,I,J,K,L,M,N,O

MDVLYSLSKTLKDARDKIVEGTLYSNVSDLIQQFNQMIITMNGNEFQTGGIGNLPIRNWNFDFGLLGTTLLNLDANYVETARNTIDYFVDFVDNVCMDEMVRESQRNGIAPQSDSLRKLSGLKFKRINFDNSSEYIENWNLQNRRQRTGFTFHKPNIFPYSASFTLNRSQPAHDNLMGTMWLNAGSEIQVAGFDYSCAINAPANTQQFEHIVQLRRVLTTATITLLPDAERFSFPRVINSADGATTWYFNPVILRPNNVEVEFLLNGQIINTYQARFGTIIARNFDTIRLSFQLMRPPNMTPAVAALFPNAQPFEHHATVGLTLRIESAVCESVLADASETMLANVTSVRQEYAIPVGPVFPPGMNWTDLITNYSPSREDNLQRVFTVASIRSMLVK

Entity 3 Entity 3 polymer

Description description	RNA-directed RNA polymerase
Molecular weight formula_weight	125495.6 kDa
EC 编号 ec_number	2.7.7.48
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	W

MGKYNLILSEYLSFIYNSQSAVQIPIYYSSNSELENRCIEFHSKCLENSKNGLSLRKLFVEYNDVIENATLLSILSYSYDKYNAVERKLVKYAKGKPLEADLTVNELDYENNKMTSELFPTAEEYTDSLMDPAILTSLSSNLNAVMFWLEKHENDVAEKLKVYKRRLDLFTIVASTINKYGVPRHNAKYRYEYDVMKDKPYYLVTWANSSIEMLMSVFSHDDYLIAKELIVLSYSNRSTLAKLVSSPMSILVALVDINGTFITNEELELEFSNKYVRAIVPDQTFDELNQMLDNMRKAGLVDIPKMIQDWLVDRSIEKFPLMAKIYSWSFHVGFRKQKMLDAALDQLKTEYTENVDDEMYREYTMLIRDEVVKMLEEPVKHDDHLLRDSELAGLLSMSSASNGESRQLKFGRKTIFSTKKNMHVMDDMANERYTPGIIPPVNVDKPIPLGRRDVPGRRTRIIFILPYEYFIAQHAVVEKMLIYAKHTREYAEFYSQSNQLLSYGDVTRFLSNNTMVLYTDVSQWDSSQHNTQPFRKGIIMGLDILANMTNDAKVLQTLNLYKQTQINLMDSYVQIPDGNVIKKIQYGAVASGEKQTKAANSIANLALIKTVLSRISNKHSFATKIIRVDGDDNYAVLQFNTEVTKQMIQDVSNDVRETYARMNAKVKALVSTVGIEIAKRYIAGGKIFFRAGINLLNNEKRGQSTQWDQAAILYSNYIVNRLRGFETDREFILTKIMQMTSVAITGSLRLFPSERVLTTNSTFKVFDSEDFIIEYGTTVDEVYIQRAFMSLSSQKSGIADEIAASSTFKNYVTRLSEQLLFSKNNIVSRGIALTEKAKLNSYAPISLEKRRAQISALLTMLQKPVTFKSSKITINDILRDIKPFFTVSDAHLPIQYQKFMPTLPDNVQYIIQCIGSRTYQIEDDGSKSAISRLISKYSVYKPSIEELYKVISLHENEIQLYLISLGIPKIDADTYVGSKIYSRDKYRILESYVYNLLSINYGCYQLFDFNSPDLEKLIRIPFKGKIPAVTFILHLYAKLEVINYAIKNGSWISLFCNYPKSEMIKLWKKMWNITSLRSPYTNANFFQEP

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	5

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Unit-cell length a length_a	740.750 Å
Unit-cell length b length_b	1198.070 Å
Unit-cell length c length_c	1345.410 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	3120

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	5.000 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2931
R_free r_free	0.2958

Location of the dsRNA-dependent polymerase, VP1, in rotavirus particles

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

VP2 protein

State in the Current Structure

Other States of the Same Protein in the Database

Intermediate capsid protein VP6

State in the Current Structure

Other States of the Same Protein in the Database

RNA-directed RNA polymerase

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

4f5x__assembly_1__model_1

4f5x__assembly_1__model_1 | I(q)

4f5x__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

7. Citations (1)

Location of the dsRNA-dependent polymerase, VP1, in rotavirus particles

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

VP2 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

Intermediate capsid protein VP6

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

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

4f5x__assembly_1__model_1

4f5x__assembly_1__model_1 | I(q)

4f5x__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

7. Citations (1)