SAXSdb — 6wxf

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

Outer capsid protein VP4

Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3])

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Intermediate capsid protein VP6 × 18 （B2BN53） Outer capsid glycoprotein VP7 × 18 （P12476） 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 CALCIUM ION × 54	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G0YZG6_ROTRH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 1； PDBConstruct 1–776； UniProt 1–776 Author chain 2； PDBConstruct 1–776； UniProt 1–776 Author chain 3； PDBConstruct 1–776； UniProt 1–776

Intermediate capsid protein VP6

OrganismNot specified

UniProt B2BN53

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Outer capsid protein VP4 × 3 （G0YZG6） Outer capsid glycoprotein VP7 × 18 （P12476） 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 CALCIUM ION × 54	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VP6_ROTRH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–397； UniProt 1–397 Author chain B； PDBConstruct 1–397； UniProt 1–397 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 Author chain P； PDBConstruct 1–397； UniProt 1–397 Author chain Q； PDBConstruct 1–397； UniProt 1–397 Author chain R； PDBConstruct 1–397； UniProt 1–397

Outer capsid glycoprotein VP7

Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3])

UniProt P12476

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 39	Outer capsid protein VP4 × 3 （G0YZG6） Intermediate capsid protein VP6 × 18 （B2BN53） 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 CALCIUM ION × 54	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VP7_ROTRH
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain a； PDBConstruct 1–326； UniProt 1–326 Author chain b； PDBConstruct 1–326； UniProt 1–326 Author chain c； PDBConstruct 1–326； UniProt 1–326 Author chain d； PDBConstruct 1–326； UniProt 1–326 Author chain e； PDBConstruct 1–326； UniProt 1–326 Author chain f； PDBConstruct 1–326； UniProt 1–326 Author chain g； PDBConstruct 1–326； UniProt 1–326 Author chain h； PDBConstruct 1–326； UniProt 1–326 Author chain i； PDBConstruct 1–326； UniProt 1–326 Author chain j； PDBConstruct 1–326； UniProt 1–326 Author chain k； PDBConstruct 1–326； UniProt 1–326 Author chain l； PDBConstruct 1–326； UniProt 1–326 Author chain m； PDBConstruct 1–326； UniProt 1–326 Author chain n； PDBConstruct 1–326； UniProt 1–326 Author chain o； PDBConstruct 1–326； UniProt 1–326 Author chain p； PDBConstruct 1–326； UniProt 1–326 Author chain q； PDBConstruct 1–326； UniProt 1–326 Author chain r； PDBConstruct 1–326； UniProt 1–326

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	6wxf
Deposition date deposition_date	2020-05-10
Structure title title	Cryo-EM reconstruction of VP5/VP8 assembly from rhesus rotavirus particles - Intermediate conformation
Keywords keywords	non-enveloped virus, viral particle, entry, membrane-penetration, rotavirus, VP4, VP5, VP8, intermediate, 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.

6wxf__assembly_1__model_1

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

Download this curve (.dat)

6wxf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6wxf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	74.58 Å
Rg (electron density)	74.15 Å
Total Rg	74.32 Å
Atom count	212266
Residues	13466
Excluded volume	1908400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6wxf__assembly_1__model_1`	39-meric （39）	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 (5)

Entity 1 Entity 1 polymer

Description description	Outer capsid protein VP4
Molecular weight formula_weight	86703.7 kDa
Mutation mutation	S567C, A590C
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1,2,3
Atom count atom_count	212266

MASLIYRQLLTNSYTVDLSDEIQEIGSTKTQNVTINLGPFAQTGYAPVNWGPGETNDSTTVEPVLDGPYQPTTFNPPVDYWMLLAPTAAGVVVEGTNNTDRWLATILVEPNVTSETRSYTLFGTQEQITIANASQTQWKFIDVVKTTQNGSYSQYGPLQSTPKLYAVMKHNGKIYTYNGETPNVTTKYYSTTNYDSVNMTAFCDFYIIPREEESTCTEYINNGLPPIQNTRNIVPLALSARNIISHRAQANEDIVVSKTSLWKEMQYNRDITIRFKFASSIVKSGGLGYKWSEISFKPANYQYTYTRDGEEVTAHTTCSVNGMNDFNFNGGSLPTDFVISRYEVIKENSYVYVDYWDDSQAFRNMVYVRSLAANLNSVICTGGDYSFALPVGQWPVMTGGAVSLHSAGVTLSTQFTDFVSLNSLRFRFRLTVEEPSFSITRTRVSRLYGLPAANPNNGKEYYEVAGRFSLISLVPSNDDYQTPITNSVTVRQDLERQLGELREEFNALSQEIAMSQLIDLALLPLDMFSMFSGIKSTIDAAKSMATSVMKKFKKSGLANSVSTLTDCLSDAASSISRGASIRSVGSSASCWTDVSTQITDVSSSVSSISTQTSTISRRLRLKEMATQTEGMNFDDISAAVLKTKIDRSTQISPNTLPDIVTEASEKFIPNRAYRVINNDEVFEAGTDGRFFAYRVETFDEIPFDVQKFADLVTDSPVISAIIDFKTLKNLNDNYGISRQQAFNLLRSDPRVLREFINQDNPIIRNRIEQLIMQCRL

Source Source

Source organism organism	Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3])
Common name common_name	RV-A
NCBI taxonomy ID ncbi_taxonomy_id	444185
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Intermediate capsid protein VP6
Molecular weight formula_weight	44934.8 kDa
Source method src_method	nat
Copy count entity_count	18

Polymer Polymer

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

MDVLYSLSKTLKDARDKIVEGTLYSNVSDLIQQFNQMIITMNGNEFQTGGIGNLPIRNWNFDFGLLGTTLLNLDANYVETARNTIDYFVDFVDNVCMDEMVRESQRNGIAPQSDSLRKLSGIKFKRINFDNSSEYIENWNLQNRRQRTGFTFHKPNIFPYSASFTLNRSQPAHDNLMGTMWLNAGSEIQVAGFDYSCAINAPANIQQFEHIVQLRRVLTTATITLLPDAERFSFPRVINSADGATTWYFNPVILRPNNVEVEFLLNGQIINTYQARFGTIIARNFDTIRLSFQLMRPPNMTPAVAALFPNAQPFEHHATVGLTLRIESAVCESVLADASKTMLANVTSVRQEYAIPVGPVFPPGMNWTDLITNYSPSREDNLQRVFTVASIRSMLVK

Entity 3 Entity 3 polymer

Description description	Outer capsid glycoprotein VP7
Molecular weight formula_weight	37136.5 kDa
Source method src_method	man
Copy count entity_count	18

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a,b,c,d,e,f,g,h,i,j,k,l,m,n,o,p,q,r

MYGIEYTTVLTFLISLILLNYILKSLTRMMDFIIYRFLFIVVILSPLLKAQNYGINLPITGSMDTAYANSTQEETFLTSTLCLYYPTEAATEINDNSWKDTLSQLFLTKGWPTGSVYFKEYTDIASFSVDPQLYCDYNVVLMKYDATLQLDMSELADLILNEWLCNPMDITLYYYQQTDEANKWISMGSSCTIKVCPLNTQTLGIGCLTTDTATFEEVATAEKLVITDVVDGVNHKLDVTTATCTIRNCKKLGPRENVAVIQVGGSDVLDITADPTTAPQTERMMRINWKKWWQVFYTVVDYVNQIIQAMSKRSRSLNSAAFYYRI

Source Source

Source organism organism	Rotavirus A (strain RVA/Monkey/United States/RRV/1975/G3P5B[3])
Common name common_name	RV-A
NCBI taxonomy ID ncbi_taxonomy_id	444185
Host organism host_organism	Spodoptera frugiperda

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	18

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	54

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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	4.30 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	82008

Cryo-EM reconstruction of VP5/VP8 assembly from rhesus rotavirus particles - Intermediate conformation

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

Outer capsid protein VP4

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

Outer capsid glycoprotein VP7

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

6wxf__assembly_1__model_1

6wxf__assembly_1__model_1 | I(q)

6wxf__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)

Cryo-EM reconstruction of VP5*/VP8* assembly from rhesus rotavirus particles - Intermediate conformation

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

Outer capsid protein VP4

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

Outer capsid glycoprotein VP7

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

6wxf__assembly_1__model_1

6wxf__assembly_1__model_1 | I(q)

6wxf__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

7. Citations (1)

Cryo-EM reconstruction of VP5/VP8 assembly from rhesus rotavirus particles - Intermediate conformation