SAXSdb — 3s88

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

Envelope glycoprotein

Sudan ebolavirus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 4 其他Polymer 2	16F6 - Heavy chain × 1 16F6 - Light chain × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2	Consistent with protein count
2	Other combination	Heteromer	Protein 48 其他Polymer 24	16F6 - Heavy chain × 12 16F6 - Light chain × 12 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 24	Consistent with protein count
3	Other combination	Heteromer	Protein 12 其他Polymer 6	16F6 - Heavy chain × 3 16F6 - Light chain × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6	Consistent with protein count
4	Other combination	Heteromer	Protein 12 其他Polymer 6	16F6 - Heavy chain × 3 16F6 - Light chain × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6	Consistent with protein count
5	Other combination	Heteromer	Protein 12 其他Polymer 6	16F6 - Heavy chain × 3 16F6 - Light chain × 3 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VGP_EBOSU
Isoform	—
PDB entities	2, 3
Chains and sequence ranges	Author chain I； PDBConstruct 17–298； UniProt 32–313 Author chain J； PDBConstruct 1–167； UniProt 473–639

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	3s88
Deposition date deposition_date	2011-05-27
Structure title title	Crystal structure of Sudan Ebolavirus Glycoprotein (strain Gulu) bound to 16F6
Keywords keywords	Glycosylation, Viral membrane, IMMUNE SYSTEM-VIRAL PROTEIN complex; IMMUNE SYSTEM/VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

3s88__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3s88__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3s88__assembly_2__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)	99.02 Å
Total Rg	98.76 Å
Atom count	72480
Residues	9444
Excluded volume	1277800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3s88__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3s88__assembly_2__model_1`	48-meric （48）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3s88__assembly_3__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3s88__assembly_4__model_1`	dodecameric （12）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3s88__assembly_5__model_1`	dodecameric （12）	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 (5)

Entity 1 Entity 1 polymer

Description description	16F6 - Heavy chain
Molecular weight formula_weight	23600.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H
Atom count atom_count	6040

EVQLVESGGGLVTPGGSLKLSCAASGFAFNYYDMFWVRQNTEKRLEWVAYINSGGGNTYYPDTVKGRFTISRDNAKKTLFLQMSSLRSEDTAMYYCARQLYGNSFFDYWGQGTSLTVSAAKTTPPSVYPLAPGSAAAAASMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPAD

Source Source

Source organism organism	Mus musculus
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Mus musculus

Entity 2 Entity 2 polymer

Description description	Envelope glycoprotein
Molecular weight formula_weight	33447.3 kDa
Mutation mutation	I631V, Q638V
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

YPYDVPDYAIEGRGARSMPLGVVTNSTLEVTEIDQLVCKDHLASTDQLKSVGLNLEGSGVSTDIPSATKRWGFRSGVPPKVVSYEAGEWAENCYNLEIKKPDGSECLPPPPDGVRGFPRCRYVHKAQGTGPCPGDYAFHKDGAFFLYDRLASTVIYRGVNFAEGVIAFLILAKPKETFLQSPPIREAVNYTENTSSYYATSYLEYEIENFGAQHSTTLFKIDNNTFVRLDRPHTPQFLFQLNDTIHLHQQLSNTTGRLIWTLDANINADIGEWAFWENKKNLSEQLRGEELSFEALSL

Source Source

Source organism organism	Sudan ebolavirus
Common name common_name	SEBOV
NCBI taxonomy ID ncbi_taxonomy_id	186540
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Envelope glycoprotein
Molecular weight formula_weight	18709.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

PQESTSNGLITSTVTGILGSLGLRKRSRRQTNTKATGKCNPNLHYWTAQEQHNAAGIAWIPYFGPGAEGIYTEGLMHNQNALVCGLRQLANETTQALQLFLRATTELRTYTILNRKAIDFLLRRWGGTCRILGPDCCIEPHDWTKNITDKINQIIHDFVDNPLPNVD

Source Source

Source organism organism	Sudan ebolavirus
Common name common_name	SEBOV
NCBI taxonomy ID ncbi_taxonomy_id	186540
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	16F6 - Light chain
Molecular weight formula_weight	23457.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIVMTQSHKFMSTSVGDRVTITCKASQDVTTAVAWYQQKPGHSPKLLIYWASTRHTGVPDRFTGSGSGTAFTLTLNSVQAEDLALYYCQQHYSTPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN

Source Source

Source organism organism	Mus musculus
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Mus musculus

Entity 5 Entity 5 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3s88H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3s88H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3s88L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3s88L02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	193.591 Å
Unit-cell length b length_b	193.591 Å
Unit-cell length c length_c	193.591 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	24

Space group space_group	I 2 3
Space-group number int_tables_number	197
Crystal system crystal_system	—

Resolution resolution	3.351 Å
Low-resolution limit resolution_low	45.630 Å
R factor r_factor	0.2217
R_work r_work	0.2217
R_free r_free	0.2776

Crystal structure of Sudan Ebolavirus Glycoprotein (strain Gulu) bound to 16F6

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

Envelope 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

3s88__assembly_2__model_1

3s88__assembly_2__model_1 | I(q)

3s88__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

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

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of Sudan Ebolavirus Glycoprotein (strain Gulu) bound to 16F6

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

Envelope 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

3s88__assembly_2__model_1

3s88__assembly_2__model_1 | I(q)

3s88__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

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

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)