SAXSdb — 9bbn

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

E3 glycoprotein

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	E1 glycoprotein × 4 （Q88628） E2 glycoprotein × 4 （Q88628） Heavy chain of C9 × 4 Light chain of C9 × 4 Capsid protein × 4 （Q88628）	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D2KBQ2_CHIKV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain U； PDBConstruct 1–60； UniProt 266–325 Author chain V； PDBConstruct 1–60； UniProt 266–325 Author chain W； PDBConstruct 1–60； UniProt 266–325 Author chain X； PDBConstruct 1–60； UniProt 266–325

E1 glycoprotein

OrganismNot specified

UniProt Q88628

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	E3 glycoprotein × 4 （D2KBQ2） Heavy chain of C9 × 4 Light chain of C9 × 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	2, 3, 6
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 Author chain E； PDBConstruct 1–419； UniProt 330–748 Author chain F； PDBConstruct 1–419； UniProt 330–748 Author chain G； PDBConstruct 1–419； UniProt 330–748 Author chain H； PDBConstruct 1–419； UniProt 330–748 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	9bbn
Deposition date deposition_date	2024-04-06
Structure title title	Cryo-EM structure of Chikungunya virus asymmetric unit with Fab C9
Keywords keywords	CHIKV asymmetric unit with Fab C9, VIRAL PROTEIN-IMMUNE SYSTEM complex; VIRAL PROTEIN/IMMUNE SYSTEM
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.

9bbn__assembly_1__model_1

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

Download this curve (.dat)

9bbn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9bbn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	70.64 Å
Rg (electron density)	70.64 Å
Total Rg	70.74 Å
Atom count	92155
Residues	6060
Excluded volume	824480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9bbn__assembly_1__model_1`	24-meric （24）	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	E3 glycoprotein
Molecular weight formula_weight	6955.1 kDa
EC 编号 ec_number	3.4.21.90
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U,W,X,V
Atom count atom_count	92155

PVMCLLANTTFPCSQPPCTPCCYEKEPEETLRMLEDNVMRPGYYQLLQASLTCSPHRQRR

Entity 2 Entity 2 polymer

Description description	E1 glycoprotein
Molecular weight formula_weight	47497.9 kDa
EC 编号 ec_number	3.4.21.90
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

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

YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYVKCCGTAECKDKSLPDYSCKVFTGVYPFMWGGAYCFCDTENTQLSEAHVEKSESCKTEFASAYRAHTASASAKLRVLYQGNNVTVSAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVYKGDVYNMDYPPFGAGRPGQFGDIQSRTPESEDVYANTQLVLQRPSAGTVHVPYSQAPSGFKYWLKERGASLQHTAPFGCQIATNPVRAMNCAVGNMPISIDIPDAAFTRVVDAPSLTDMSCEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFSTALASAEFRVQVCSTQVHCAAECHPPKDHIVNYPASHTTLGVQDISVTAMSWVQKITGGVGLVVAVAALILIVVLCVSFSRH

Entity 3 Entity 3 polymer

Description description	E2 glycoprotein
Molecular weight formula_weight	47077.7 kDa
EC 编号 ec_number	3.4.21.90
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

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

NFNVYKAIRPYLAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDDSHDWTKLRYMDNHMPADAERARLFVRTSAPCTITGTMGHFILARCPKGETLTVGFTDGRKISHSCTHPFHHDPPVIGREKFHSRPQHGRELPCSTYAQSTAATAEEIEVHMPPDTPDRTLMSQQSGNVKITVNSQTVRYKCNCGDSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSPLVPRNAELGDRKGKVHIPFPLANVTCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNMGEEPNYQEEWVTHKKEIRLTVPTEGLEVTWGNNEPYKYWPQLSTNGTAHGHPHEIILYYYELYPTMTVVVVSVASFVLLSMVGVAVGMCMCARRRCITPYELTPGATVPFLLSLICCIRTAKA

Entity 4 Entity 4 polymer

Description description	Heavy chain of C9
Molecular weight formula_weight	24747.7 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,O,Q,S

EVQLVQSGAEVKKPGSSVKVSCKAFGGTFSSYAITWVRQAPGQGLEWMGGIIPILGTTDYAQKFQGRVTITADKSTSTAYMELSSLRSEDTAVYYCARDPPTHGGDFNYYYYGVAVWGQGTTVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	Light chain of C9
Molecular weight formula_weight	23061.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N,P,R,T

EIVLTQSPGTLSLSPGERATLSCRASQSNNYLAWYQQKPGQAPRLLIYGASIRATGIPDRFSGSGSGTDFTLTISRLAPEDFAVYYCQQYGSSPLTFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Homo sapiens

Entity 6 Entity 6 polymer

Description description	Capsid protein
Molecular weight formula_weight	16428.6 kDa
EC 编号 ec_number	3.4.21.90
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

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

NDCIFEVKHEGKVTGYACLVGDKVMKPAHVKGTIDNADLAKLAFKRSSKYDLECAQIPVHMKSDASKFTHEKPEGYYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLGGANEGARTALSVVTWNKDIVTKITPEGAEEW

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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	3.300 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	3.30 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	1151475

Cryo-EM structure of Chikungunya virus asymmetric unit with Fab C9

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

E3 glycoprotein

State in the Current Structure

Other States of the Same Protein in the Database

E1 glycoprotein

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

9bbn__assembly_1__model_1

9bbn__assembly_1__model_1 | I(q)

9bbn__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

7. Citations (1)

Cryo-EM structure of Chikungunya virus asymmetric unit with Fab C9

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

E3 glycoprotein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

E1 glycoprotein

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

9bbn__assembly_1__model_1

9bbn__assembly_1__model_1 | I(q)

9bbn__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

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 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

7. Citations (1)