SAXSdb — 8dpl

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

Glycoprotein GP1

Ebola virus - Mayinga, Zaire, 1976

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 15 其他Polymer 3	2.1.1D5 heavy chain variable domain × 3 2.1.1D5 light chain variable domain × 3 6D6 single-chain variable fragment × 3 Glycoprotein GP2 × 3 （A0A0E3H7K2） ;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VGP_EBOZM
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–280； UniProt 33–312 Author chain I； PDBConstruct 1–280； UniProt 33–312 Author chain M； PDBConstruct 1–280； UniProt 33–312

Glycoprotein GP2

Ebola virus - Mayinga, Zaire, 1976

UniProt A0A0E3H7K2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 15 其他Polymer 3	2.1.1D5 heavy chain variable domain × 3 2.1.1D5 light chain variable domain × 3 6D6 single-chain variable fragment × 3 Glycoprotein GP1 × 3 （Q05320） ;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0E3H7K2_9MONO
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–136； UniProt 502–637 Author chain J； PDBConstruct 1–136； UniProt 502–637 Author chain N； PDBConstruct 1–136； UniProt 502–637

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	8dpl
Deposition date deposition_date	2022-07-15
Structure title title	Structure of EBOV GP lacking the mucin-like domain with 2.1.1D5 scFv and 6D6 scFv bound
Keywords keywords	VIRAL PROTEIN, glycoprotein, immune system, antibody, Ebola virus, 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.

8dpl__assembly_1__model_1

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

Download this curve (.dat)

8dpl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8dpl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.30 Å
Rg (electron density)	41.73 Å
Total Rg	42.28 Å
Atom count	16872
Residues	2163
Excluded volume	298380 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8dpl__assembly_1__model_1`	pentadecameric （15）	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 (7)

Entity 1 Entity 1 polymer

Description description	2.1.1D5 heavy chain variable domain
Molecular weight formula_weight	13057.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,A,K
Atom count atom_count	16872

EVQLVESGGGLVKPGGSLRLSCAASGFTFSNAWMNWVRQAPGKGLEWVGRIKSKTDGGAADYAAPVKGRFTISRDDSKNTLYLQMNSLKTEDTAVYFCTTVYRYNYDSVWGQGTLVTVSS

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Drosophila melanogaster

Entity 2 Entity 2 polymer

Description description	2.1.1D5 light chain variable domain
Molecular weight formula_weight	11738.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,B,L

QSVLTQPPSVSGAPGQRVTISCTGSSSNIGAGYDVYWYQQLPGTAPKLLIYGNSNRPSGVPDRFSGSKSGTSASLAITGLQAEDEADYYCQSFDSSLRDSWVFGGGTKLTVL

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Drosophila melanogaster

Entity 3 Entity 3 polymer

Description description	6D6 single-chain variable fragment
Molecular weight formula_weight	25853.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,C,O

QVQLQQSGTELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGQGLEWIGEINPRNGRTDFSEKFKSKATLTVDTSSSTAFIQLSSLTSEDSAVYYCARWGYYGSSDYWGQGTALTVSSGTGGSGGGGSGGGGSGGGASDIVVTQSHKFMSTSVGDRVSITCKASQDVSVAVAWYQQKTGQSPKLLIYSASYRITGVPDRFTGSGSGTDFTFTISSVQAEDMAVYYCQQHYSTPPWTFGGGTKL

Source Source

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

Entity 4 Entity 4 polymer

Description description	Glycoprotein GP1
Molecular weight formula_weight	31297.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I,D,M

IPLGVIHNSTLQVSDVDKLVCRDKLSSTNQLRSVGLNLEGNGVATDVPSATKRWGFRSGVPPKVVNYEAGEWAENCYNLEIKKPDGSECLPAAPDGIRGFPRCRYVHKVSGTGPCAGDFAFHKEGAFFLYDRLASTVIYRGTTFAEGVVAFLILPQAKKDFFSSHPLREPVNATEDPSSGYYSTTIRYQATGFGTNETEYLFEVDNLTYVQLESRFTPQFLLQLNETIYTSGKRSNTTGKLIWKVNPEIDTTIGEWAFWETKKNLTRKIRSEELSFTVVS

Source Source

Source organism organism	Ebola virus - Mayinga, Zaire, 1976
NCBI taxonomy ID ncbi_taxonomy_id	128952
Host organism host_organism	Drosophila melanogaster

Entity 5 Entity 5 polymer

Description description	Glycoprotein GP2
Molecular weight formula_weight	15335.4 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,E,N

EAIVNAQPKCNPNLHYWTTQDEGAAIGLAWIPYFGPAAEGIYTEGLMHNQDGLICGLRQLANETTQALQLFLRATTELRTFSILNRKAIDFLLQRWGGTCHILGPDCCIEPHDWTKNITDKIDQIIHDFVDKTLPD

Source Source

Source organism organism	Ebola virus - Mayinga, Zaire, 1976
NCBI taxonomy ID ncbi_taxonomy_id	128952
Host organism host_organism	Drosophila melanogaster

Entity 6 Entity 6 branched

Description description	;alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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	1073.0 kDa
Source method src_method	man
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	3

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	8dplA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8dplB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8dplC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8dplC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8dplF01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8dplG01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8dplH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8dplH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8dplK01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8dplL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8dplO01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8dplO02
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	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	2.53 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	610008

Structure of EBOV GP lacking the mucin-like domain with 2.1.1D5 scFv and 6D6 scFv bound

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

Glycoprotein GP1

State in the Current Structure

Other States of the Same Protein in the Database

Glycoprotein GP2

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

8dpl__assembly_1__model_1

8dpl__assembly_1__model_1 | I(q)

8dpl__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 (7)

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 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 branched

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

Structure of EBOV GP lacking the mucin-like domain with 2.1.1D5 scFv and 6D6 scFv bound

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

Glycoprotein GP1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Glycoprotein GP2

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

8dpl__assembly_1__model_1

8dpl__assembly_1__model_1 | I(q)

8dpl__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 (7)

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 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 branched

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)