9c1k

Rhesus rotavirus (empty structure at 2.68 Angstrom resolution)

Method: ELECTRON MICROSCOPY

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

Outer capsid glycoprotein VP7

Simian rotavirus A strain RRV

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 40	Inner capsid protein VP2 × 2 （B3F2X3） Intermediate capsid protein VP6 × 19 （B2BN53） 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 CALCIUM ION × 76 ZINC ION × 26 CHLORIDE ION × 7	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	1
Chains and sequence ranges	Author chain 0； PDBConstruct 1–326； UniProt 1–326 Author chain 1； 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 Author chain S； PDBConstruct 1–326； UniProt 1–326 Author chain T； PDBConstruct 1–326； UniProt 1–326 Author chain U； PDBConstruct 1–326； UniProt 1–326 Author chain V； PDBConstruct 1–326； UniProt 1–326 Author chain W； PDBConstruct 1–326； UniProt 1–326 Author chain X； PDBConstruct 1–326； UniProt 1–326 Author chain Y； PDBConstruct 1–326； UniProt 1–326 Author chain Z； PDBConstruct 1–326； UniProt 1–326 Author chain t； PDBConstruct 1–326； UniProt 1–326 Author chain u； PDBConstruct 1–326； UniProt 1–326 Author chain v； PDBConstruct 1–326； UniProt 1–326 Author chain w； PDBConstruct 1–326； UniProt 1–326 Author chain x； PDBConstruct 1–326； UniProt 1–326 Author chain y； PDBConstruct 1–326； UniProt 1–326

Inner capsid protein VP2

Simian rotavirus A strain RRV

UniProt B3F2X3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 40	Outer capsid glycoprotein VP7 × 19 （P12476） Intermediate capsid protein VP6 × 19 （B2BN53） 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 CALCIUM ION × 76 ZINC ION × 26 CHLORIDE ION × 7	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	B3F2X3_ROTRH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–887； UniProt 1–887 Author chain B； PDBConstruct 1–887； UniProt 1–887

Intermediate capsid protein VP6

Simian rotavirus A strain RRV

UniProt B2BN53

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 40	Outer capsid glycoprotein VP7 × 19 （P12476） Inner capsid protein VP2 × 2 （B3F2X3） 2-acetamido-2-deoxy-beta-D-glucopyranose × 19 CALCIUM ION × 76 ZINC ION × 26 CHLORIDE ION × 7	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	3
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 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

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	9c1k
Deposition date deposition_date	2024-05-29
Structure title title	Rhesus rotavirus (empty structure at 2.68 Angstrom resolution)
Keywords keywords	Rotavirus, non-enveloped virus, viral particle, 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.

9c1k__assembly_1__model_1

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

Download this curve (.dat)

9c1k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9c1k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	81.70 Å
Rg (electron density)	81.21 Å
Total Rg	81.38 Å
Atom count	226399
Residues	14277
Excluded volume	2037400 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9c1k__assembly_1__model_1`	40-meric （40）	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 (7)

Entity 1 Entity 1 polymer

Description description	Outer capsid glycoprotein VP7
Molecular weight formula_weight	37136.5 kDa
Source method src_method	man
Copy count entity_count	19

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	0,1,P,Q,R,S,T,U,V,W,X,Y,Z,t,u,v,w,x,y
Atom count atom_count	226399

MYGIEYTTVLTFLISLILLNYILKSLTRMMDFIIYRFLFIVVILSPLLKAQNYGINLPITGSMDTAYANSTQEETFLTSTLCLYYPTEAATEINDNSWKDTLSQLFLTKGWPTGSVYFKEYTDIASFSVDPQLYCDYNVVLMKYDATLQLDMSELADLILNEWLCNPMDITLYYYQQTDEANKWISMGSSCTIKVCPLNTQTLGIGCLTTDTATFEEVATAEKLVITDVVDGVNHKLDVTTATCTIRNCKKLGPRENVAVIQVGGSDVLDITADPTTAPQTERMMRINWKKWWQVFYTVVDYVNQIIQAMSKRSRSLNSAAFYYRI

Source Source

Source organism organism	Simian rotavirus A strain RRV
NCBI taxonomy ID ncbi_taxonomy_id	444185
Host organism host_organism	Simian rotavirus A strain RRV

Entity 2 Entity 2 polymer

Description description	Inner capsid protein VP2
Molecular weight formula_weight	103426.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MAYRKRGARRETNLKQDDRMQEKEENKNVNTNSENKNATKPQLSEKVLSQKEEVITDNQEEIKIADEVKKSNKEESKQLLEVLKTKEEHQKEVQYEILQKTIPTFEPKESILKKLEDIKPEQVKKQTKLFRIFEPRQLPVYRANGEKELRNRWYWKLKRDTLPDGDYDVREYFLNLYDQVLTEMPDYLLLKDMAVENKNSRDAGKVVDSETAAICDAIFQDEETEGVVRRFIAEMRQRVQADRNVVNYPSILHPIDHAFNEYFLQHQLVEPLNNDIIFNYIPERIRNDVNYILNMDRNLPSTARYIRPNLLQDRLNLHDNFESLWDTITTSNYILARSVVPDLKELVSTEAQIQKMSQDLQLEALTIQSETQFLTGINSQAANDCFKTLIAAMLSQRTMSLDFVTTNYMSLISGMWLLTVVPNDMFIRESLVACQLAIINTIIYPAFGMQRMHYRNGDPQTPFQIAEQQIQNFQVANWLHFVNNNQFRQVVIDGVLNQVLNDNIRNGHVVNQLMEALMQLSRQQFPTMPVDYKRSIQRGILLLSNRLGQLVDLTRLLAYNYETLMACITMNMQHVQTLTTEKLQLTSVTSLCMLIGNATVIPSPQTLFHYYNVNVNFHSNYNERINDAVAIITAANRLNLYQKKMKSIVEDFLKRLQIFDISRVPDDQMYRLRDRLRLLPVEIRRLDIFNLILMNMEQIERASDKIAQGVIIAYRDMQLERDEMYGYVNIARNLDGFQQINLEELMRTGDYAQITNMLLNNQPVALVGALPFITDSSVISLVAKLDATVFAQIVKLRKVDTLKPILYKINSDSNDFYLVANYDWVPTSTTKVYKQIPQQFDFRASMHMLTSNLTFTVYSDLLAFVSADTVEPINAVAFDNMRIMNEL

Source Source

Source organism organism	Simian rotavirus A strain RRV
NCBI taxonomy ID ncbi_taxonomy_id	444185
Host organism host_organism	Simian rotavirus A strain RRV

Entity 3 Entity 3 polymer

Description description	Intermediate capsid protein VP6
Molecular weight formula_weight	44962.8 kDa
Source method src_method	man
Copy count entity_count	19

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D,E,F,G,H,I,J,K,L,M,N,O,f,g,h,i,j,k

MDVLYSLSKTLKDARDKIVEGTLYSNVSDLIQQFNQMIITMNGNEFQTGGIGNLPIRNWNFDFGLLGTTLLNLDANYVETARNTIDYFVDFVDNVCMDEMVRESQRNGIAPQSDSLRKLSGIKFKRINFDNSSEYIENWNLQNRRQRTGFTFHKPNIFPYSASFTLNRSQPAHDNLMGTMWLNAGSEIQVAGFDYSCAINAPANIQQFEHIVQLRRVLTTATITLLPDAERFSFPRVINSADGATTWYFNPVILRPNNVEVEFLLNGQIINTYQARFGTIIARNFDTIRLSFQLMRPPNMTPAVAALFPNAQPFEHHATVGLTLRIESAVCESVLADASKTMLANVTSVRQEYAIPVGPVFPPGMNWTDLITNYSPSREDNLQRVFTVASIRSMLVK

Source Source

Source organism organism	Simian rotavirus A strain RRV
NCBI taxonomy ID ncbi_taxonomy_id	444185
Host organism host_organism	Simian rotavirus A strain RRV

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	syn
Copy count entity_count	19

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	76

Entity 6 Entity 6 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	26

Entity 7 Entity 7 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	7

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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	2.68 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	1970094

Rhesus rotavirus (empty structure at 2.68 Angstrom resolution)

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

Outer capsid glycoprotein VP7

State in the Current Structure

Other States of the Same Protein in the Database

Inner capsid protein VP2

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9c1k__assembly_1__model_1

9c1k__assembly_1__model_1 | I(q)

9c1k__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 (7)

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

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)

Rhesus rotavirus (empty structure at 2.68 Angstrom resolution)

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

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

Inner capsid protein VP2

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9c1k__assembly_1__model_1

9c1k__assembly_1__model_1 | I(q)

9c1k__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 (7)

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

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)