SAXSdb — 3j8d

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

Envelope protein E

Dengue virus 2 Thailand/16681/84

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 420	glycoprotein DIII × 120 antibody E111 Fab fragment × 120	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 7	glycoprotein DIII × 2 antibody E111 Fab fragment × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 35	glycoprotein DIII × 10 antibody E111 Fab fragment × 10	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 42	glycoprotein DIII × 12 antibody E111 Fab fragment × 12	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 7	glycoprotein DIII × 2 antibody E111 Fab fragment × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLG_DEN2P
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–394； UniProt 281–674 Author chain H； PDBConstruct 1–394； UniProt 281–674 Author chain I； PDBConstruct 1–394； UniProt 281–674

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	3j8d
Deposition date deposition_date	2014-10-13
Structure title title	Cryoelectron microscopy of dengue-Fab E104 complex at pH 5.5
Keywords keywords	Dengue virus, DENV2 Fab E104, Low pH, fusion trimer, 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.

3j8d__assembly_1__model_1

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

Download this curve (.dat)

3j8d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3j8d__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)	283.90 Å
Total Rg	283.90 Å
Atom count	0
Residues	0
Excluded volume	16050000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3j8d__assembly_1__model_1`	420-MERIC （420）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3j8d__assembly_2__model_1`	heptameric （7）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`3j8d__assembly_3__model_1`	35-meric （35）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`3j8d__assembly_4__model_1`	42-meric （42）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`3j8d__assembly_5__model_1`	heptameric （7）	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 (3)

Entity 1 Entity 1 polymer

Description description	glycoprotein DIII
Molecular weight formula_weight	10616.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,F
Atom count atom_count	1990

YVMCTGSFKLEKEVAETQHGTVLVQVKYEGTDAPCKIPFSSQDEKGVTQNGRLITANPIVTDKEKPVNIEAEPPFGESYIVVGAGEKALKLSWFKKG

Source Source

Source organism organism	Dengue virus 2 Thailand/16681/84
Common name common_name	DENV-2
NCBI taxonomy ID ncbi_taxonomy_id	31634
Host organism host_organism	unidentified

Entity 2 Entity 2 polymer

Description description	antibody E111 Fab fragment
Molecular weight formula_weight	46637.7 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

NIVLTQSPASLAVSLGQRATISCRASESVDSFIYWYQQKPGQPPKLLIYLASNLESGVPARFSGSGSETDFTLTIDSVETDDAATYYCQQNNEDPYTFGGGTKLEIKQVQLLQPGAELVKPGASMKLSCKASGYTFTNWWMHWVRLRPGRGLEWIGRIDPNSDVNKYNEKFENRASLTVDKHSSTAYMQLTSEDSAIYYCARWFFPWYFDVWGTGTTVTVSRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRSAKTTAPSVYPLAPVCGGTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQSGLYTLSSSVTVTSNTWPSQTITCNVAHPASSTKVDKKIES

Entity 3 Entity 3 polymer

Description description	Envelope protein E
Molecular weight formula_weight	43819.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

MRCIGISNRDFVEGVSGGSWVDIVLEHGSCVTTMAKNKPTLDFELIKTEAKQPATLRKYCIEAKLTNTTTESRCPTQGEPTLNEEQDKRFVCKHSMVDRGWGNGCGLFGKGGIVTCAMFTCKKNMEGKIVQPENLEYTVVITPHSGEEHAVGNDTGKHGKEVKITPQSSITEAELTGYGTVTMECSPRTGLDFNEMVLLQMKDKAWLVHRQWFLDLPLPWLPGADTQGSNWIQKETLVTFKNPHAKKQDVVVLGSQEGAMHTALTGATEIQMSSGNLLFTGHLKCRLRMDKLQLKGMSYSMCTGKFKVVKEIAETQHGTIVIRVQYEGDGSPCKIPFEIMDLEKRHVLGRLITVNPIVTEKDSPVNIEAEPPFGDSYIIIGVEPGQLKLNWFKK

Source Source

Source organism organism	Dengue virus 2 Thailand/16681/84
Common name common_name	DENV-2
NCBI taxonomy ID ncbi_taxonomy_id	31634
Host organism host_organism	unidentified

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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	26.00 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	528

Cryoelectron microscopy of dengue-Fab E104 complex at pH 5.5

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

Envelope protein E

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

3j8d__assembly_1__model_1

3j8d__assembly_1__model_1 | I(q)

3j8d__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 (3)

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

7. Citations (1)

Cryoelectron microscopy of dengue-Fab E104 complex at pH 5.5

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

Envelope protein E

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

3j8d__assembly_1__model_1

3j8d__assembly_1__model_1 | I(q)

3j8d__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 (3)

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

7. Citations (1)