SAXSdb — 9j6d

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

chikungunya E3

Chikungunya virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 16 其他Polymer 8	chikungunya virus E1 × 4 （A4L7I5） chikungunya E2 × 4 （Q88628） CHIKV capsid protein × 4 （A0A6B9KBE1） ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 4 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A7S7YHM2_CHIKV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain U； PDBConstruct 1–55； UniProt 266–320 Author chain V； PDBConstruct 1–55； UniProt 266–320 Author chain W； PDBConstruct 1–55； UniProt 266–320 Author chain X； PDBConstruct 1–55； UniProt 266–320

chikungunya virus E1

Chikungunya virus

UniProt A4L7I5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 16 其他Polymer 8	chikungunya E3 × 4 （A0A7S7YHM2） chikungunya E2 × 4 （Q88628） CHIKV capsid protein × 4 （A0A6B9KBE1） ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 4 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A4L7I5_CHIKV
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–439； UniProt 810–1248 Author chain B； PDBConstruct 1–439； UniProt 810–1248 Author chain C； PDBConstruct 1–439； UniProt 810–1248 Author chain D； PDBConstruct 1–439； UniProt 810–1248

chikungunya E2

Chikungunya virus

UniProt Q88628

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 16 其他Polymer 8	chikungunya E3 × 4 （A0A7S7YHM2） chikungunya virus E1 × 4 （A4L7I5） CHIKV capsid protein × 4 （A0A6B9KBE1） ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 4 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q88628_CHIKV
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 1–414； UniProt 330–743 Author chain F； PDBConstruct 1–414； UniProt 330–743 Author chain G； PDBConstruct 1–414； UniProt 330–743 Author chain H； PDBConstruct 1–414； UniProt 330–743

CHIKV capsid protein

Chikungunya virus

UniProt A0A6B9KBE1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 16 其他Polymer 8	chikungunya E3 × 4 （A0A7S7YHM2） chikungunya virus E1 × 4 （A4L7I5） chikungunya E2 × 4 （Q88628） ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 4 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6B9KBE1_CHIKV
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain I； PDBConstruct 1–151； UniProt 111–261 Author chain J； PDBConstruct 1–151； UniProt 111–261 Author chain K； PDBConstruct 1–151； UniProt 111–261 Author chain L； PDBConstruct 1–151； UniProt 111–261

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	9j6d
Deposition date deposition_date	2024-08-15
Last revision last_revision	2025-12-03
Structure title title	Structure of Chikungunya virus infectious particles, 2f block.
Keywords keywords	chikungunya, VIRUS; VIRUS
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.

9j6d__assembly_1__model_1

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

Download this curve (.dat)

9j6d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9j6d__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	65.87 Å
Rg (electron density)	65.34 Å
Total Rg	65.51 Å
Atom count	32993
Residues	4233
Excluded volume	585920 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9j6d__assembly_1__model_1`	16-meric （16）	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 (6)

Entity 1 Entity 1 polymer

Description description	chikungunya E3
Molecular weight formula_weight	6217.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U,V,W,X
Atom count atom_count	32993

PVMCLLANTTFPCSQPPCTPCCYEKEPEETLRMLEDNVMRPGYYQLLQASLTCSP

Source Source

Source organism organism	Chikungunya virus
NCBI taxonomy ID ncbi_taxonomy_id	37124
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	chikungunya virus E1
Molecular weight formula_weight	47497.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYVKCCGTAECKDKSLPDYSCKVFTGVYPFMWGGAYCFCDTENTQLSEAHVEKSESCKTEFASAYRAHTASASAKLRVLYQGNNVTVSAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVYKGDVYNMDYPPFGAGRPGQFGDIQSRTPESEDVYANTQLVLQRPSAGTVHVPYSQAPSGFKYWLKERGASLQHTAPFGCQIATNPVRAMNCAVGNMPISIDIPDAAFTRVVDAPSLTDMSCEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFSTALASAEFRVQVCSTQVHCAAECHPPKDHIVNYPASHTTLGVQDISVTAMSWVQKITGGVGLVVAVAALILIVVLCVSFSRH

Source Source

Source organism organism	Chikungunya virus
NCBI taxonomy ID ncbi_taxonomy_id	37124
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	chikungunya E2
Molecular weight formula_weight	46548.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

NFNVYKAIRPYLAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDDSHDWTKLRYMDNHMPADAERARLFVRTSAPCTITGTMGHFILARCPKGETLTVGFTDGRKISHSCTHPFHHDPPVIGREKFHSRPQHGRELPCSTYAQSTAATAEEIEVHMPPDTPDRTLMSQQSGNVKITVNSQTVRYKCNCGDSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSPLVPRNAELGDRKGKVHIPFPLANVTCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNMGEEPNYQEEWVTHKKEIRLTVPTEGLEVTWGNNEPYKYWPQLSTNGTAHGHPHEIILYYYELYPTMTVVVVSVASFVLLSMVGVAVGMCMCARRRCITPYELTPGATVPFLLSLICCI

Source Source

Source organism organism	Chikungunya virus
NCBI taxonomy ID ncbi_taxonomy_id	37124
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	CHIKV capsid protein
Molecular weight formula_weight	16428.6 kDa
EC 编号 ec_number	3.4.21.90
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,J,K,L

NDCIFEVKHEGKVTGYACLVGDKVMKPAHVKGTIDNADLAKLAFKRSSKYDLECAQIPVHMKSDASKFTHEKPEGYYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLGGANEGARTALSVVTWNKDIVTKITPEGAEEW

Source Source

Source organism organism	Chikungunya virus
NCBI taxonomy ID ncbi_taxonomy_id	37124
Host organism host_organism	Homo sapiens

Entity 5 Entity 5 branched

Description description	;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	732.7 kDa
Source method src_method	man
Copy count entity_count	4

Entity 6 Entity 6 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	4

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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	—

Resolution resolution	3.11 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	1618503

Structure of Chikungunya virus infectious particles, 2f block.

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

chikungunya E3

State in the Current Structure

Other States of the Same Protein in the Database

chikungunya virus E1

State in the Current Structure

Other States of the Same Protein in the Database

chikungunya E2

State in the Current Structure

Other States of the Same Protein in the Database

CHIKV capsid protein

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

9j6d__assembly_1__model_1

9j6d__assembly_1__model_1 | I(q)

9j6d__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 (6)

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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

7. Citations (1)

Structure of Chikungunya virus infectious particles, 2f block.

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

chikungunya E3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

chikungunya virus E1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

chikungunya E2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

CHIKV capsid 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9j6d__assembly_1__model_1

9j6d__assembly_1__model_1 | I(q)

9j6d__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 (6)

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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

7. Citations (1)