SAXSdb — 3j6u

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

envelope protein

Dengue virus 3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 480	Fab 5J7 heavy chain × 60 Fab 5J7 light chain × 60	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	Fab 5J7 heavy chain × 1 Fab 5J7 light chain × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 40	Fab 5J7 heavy chain × 5 Fab 5J7 light chain × 5	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 48	Fab 5J7 heavy chain × 6 Fab 5J7 light chain × 6	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 8	Fab 5J7 heavy chain × 1 Fab 5J7 light chain × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6DLV0_9FLAV
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–493； UniProt 281–773 Author chain C； PDBConstruct 1–493； UniProt 281–773 Author chain E； PDBConstruct 1–493； UniProt 281–773 Author chain B； PDBConstruct 1–75； UniProt 206–280 Author chain D； PDBConstruct 1–75； UniProt 206–280 Author chain F； PDBConstruct 1–75； UniProt 206–280

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	3j6u
Deposition date deposition_date	2014-03-26
Structure title title	Cryo-EM structure of Dengue virus serotype 3 in complex with human antibody 5J7 Fab
Keywords keywords	Dengue virus, human antibody, neutralization, VIRUS-IMMUNE SYSTEM complex; VIRUS/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.

3j6u__assembly_1__model_1

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

Download this curve (.dat)

3j6u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3j6u__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)	210.80 Å
Total Rg	210.80 Å
Atom count	0
Residues	0
Excluded volume	15552000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3j6u__assembly_1__model_1`	480-MERIC （480）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3j6u__assembly_2__model_1`	octameric （8）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`3j6u__assembly_3__model_1`	40-meric （40）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`3j6u__assembly_4__model_1`	48-meric （48）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`3j6u__assembly_5__model_1`	octameric （8）	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	envelope protein
Molecular weight formula_weight	53682.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E
Atom count atom_count	1932

MRCVGVGNRDFVEGLSGATWVDVVLEHGGCVTTMAKNKPTLDIELQKTEATQLATLRKLCIEGKITNITTDSRCPTQGEAVLPEEQDQNYVCKHTYVDRGWGNGCGLFGKGSLVTCAKFQCLEPIEGKVVQYENLKYTVIITVHTGDQHQVGNETQGVTAEITPQASTTEAILPEYGTLGLECSPRTGLDFNEMILLTMKNKAWMVHRQWFFDLPLPWASGATTETPTWNRKELLVTFKNAHAKKQEVVVLGSQEGAMHTALTGATEIQNSGGTSIFAGHLKCRLKMDKLELKGMSYAMCTNTFVLKKEVSETQHGTILIKVEYKGEDAPCKIPFSTEDGQGKAHNGRLITANPVVTKKEEPVNIEAEPPFGESNIVIGIGDNALKINWYKKGSSIGKMFEATARGARRMAILGDTAWDFGSVGGVLNSLGKMVHQIFGSAYTALFSGVSWVMKIGIGVLLTWIGLNSKNTSMSFSCIAIGIITLYLGAVVQA

Source Source

Source organism organism	Dengue virus 3
NCBI taxonomy ID ncbi_taxonomy_id	11069
Host organism host_organism	Aedes albopictus

Entity 2 Entity 2 polymer

Description description	membrane protein
Molecular weight formula_weight	8347.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

SVALAPHVGMGLDTRTQTWMSAEGAWRQVEKVETWALRHPGFTILALFLAHYIGTSLTQKVVIFILLMLVTPSMT

Source Source

Source organism organism	Dengue virus 3
NCBI taxonomy ID ncbi_taxonomy_id	11069
Host organism host_organism	Aedes albopictus

Entity 3 Entity 3 polymer

Description description	Fab 5J7 heavy chain
Molecular weight formula_weight	14751.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

WVPGSWAQVQLVQSGAELRKPGSSVKVSCRASGGTFSSYTFNWVRQAPGQGLEWMGGFIPVFNTTNYAQTFQGRVTIAADKSTSTAYMELRSLRSEDTAIYYCARDKELLFSRAFDIWGQGTMVTVSSAGTKGPS

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606

Entity 4 Entity 4 polymer

Description description	Fab 5J7 light chain
Molecular weight formula_weight	12976.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

WVPGVHSDIQMTQSPSSLSASVGDRVTITCRASQSISRYLNWYQREPGKAPKLLIYGASSLQRGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSQYIPYTFGQGTKVDIKRTVA

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606

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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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	9.00 Å
Resolution测定Method resolution_method	Cross-common lines
颗粒数 num_particles	970

Cryo-EM structure of Dengue virus serotype 3 in complex with human antibody 5J7 Fab

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

envelope 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

3j6u__assembly_1__model_1

3j6u__assembly_1__model_1 | I(q)

3j6u__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 (4)

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

7. Citations (1)

Cryo-EM structure of Dengue virus serotype 3 in complex with human antibody 5J7 Fab

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

envelope 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

3j6u__assembly_1__model_1

3j6u__assembly_1__model_1 | I(q)

3j6u__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 (4)

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

7. Citations (1)