SAXSdb — 8dmh

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

Glycoprotein G1

Lymphocytic choriomeningitis virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 12 其他Polymer 18	18.5C-M28 Fab Light Chain × 3 18.5C-M28 Fab Heavy Chain × 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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 15 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	GLYC_LYCVA
Isoform	—
PDB entities	1, 4
Chains and sequence ranges	Author chain A； PDBConstruct 18–225； UniProt 58–265 Author chain B； PDBConstruct 18–225； UniProt 58–265 Author chain C； PDBConstruct 18–225； UniProt 58–265 Author chain a； PDBConstruct 1–165； UniProt 266–430 Author chain b； PDBConstruct 1–165； UniProt 266–430 Author chain c； PDBConstruct 1–165； UniProt 266–430

Glycoprotein G2,Cobalamin adenosyltransferase-like domain-containing protein trimerization tag

Lymphocytic choriomeningitis virus

UniProt Q9HIA7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 12 其他Polymer 18	Glycoprotein G1 × 3 （P09991） 18.5C-M28 Fab Light Chain × 3 18.5C-M28 Fab Heavy Chain × 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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 15 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	Q9HIA7_THEAC
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain a； PDBConstruct 170–318； UniProt 23–171 Author chain b； PDBConstruct 170–318； UniProt 23–171 Author chain c； PDBConstruct 170–318； UniProt 23–171

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	8dmh
Deposition date deposition_date	2022-07-08
Structure title title	Lymphocytic choriomeningitis virus glycoprotein in complex with neutralizing antibody M28
Keywords keywords	Viral glycoprotein, arenavirus, LCMV, GP, antibody, neutralization, VIRAL PROTEIN, 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.

8dmh__assembly_1__model_1

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

Download this curve (.dat)

8dmh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8dmh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.59 Å
Rg (electron density)	37.97 Å
Total Rg	38.37 Å
Atom count	14259
Residues	1725
Excluded volume	252840 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8dmh__assembly_1__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 (7)

Entity 1 Entity 1 polymer

Description description	Glycoprotein G1
Molecular weight formula_weight	25521.2 kDa
Mutation mutation	G207C, L264R, A265R
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	14259

MKLCILLAVVAFVGLSLGMYGLKGPDIYKGVYQFKSVEFDMSHLNLTMPNACSANNSHHYISMGTSGLELTFTNDSIISHNFCNLTSAFNKKTFDHTLMSIVSSLHLSIRGNSNYKAVSCDFNNGITIQYNLTFSDAQSAQSQCRTFRGRVLDMFRTAFGGKYMRSCWGWTGSDGKTTWCSQTSYQYLIIQNRTWENHCTYAGPFGMSRILLSQEKTKFLTRRRR

Source Source

Source organism organism	Lymphocytic choriomeningitis virus
NCBI taxonomy ID ncbi_taxonomy_id	11623
Host organism host_organism	Drosophila melanogaster

Entity 2 Entity 2 polymer

Description description	18.5C-M28 Fab Light Chain
Molecular weight formula_weight	23306.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

DIVLTQSPGTLSLSPGERATLSCRASQSVISYYVAWYQHKGGQAPRLLIYGASSRATGVPDRFSGSGSGTDFTLTISSLEPEDFALYYCQYYGSSPLWAFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

Entity 3 Entity 3 polymer

Description description	18.5C-M28 Fab Heavy Chain
Molecular weight formula_weight	23610.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

DEVQLVQSGGGLVRPGGSLRLSCAAAGFTFKRYSMNWVRQAPGRGLEWVSSITSRGGSKTYYADVVKGRFTVSRDNAKQSLYLQMNSLRAEDTAIYFCARSLHSTSQPSYMDVWGRKITVIVSSASTKGPSVFPLAPSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

Entity 4 Entity 4 polymer

Description description	Glycoprotein G2,Cobalamin adenosyltransferase-like domain-containing protein trimerization tag
Molecular weight formula_weight	42166.8 kDa
Mutation mutation	E334P,G366C,S398A
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	a,b,c

GTFTWTLSDSSGVENPGGYCLTKWMILAAELKCFGNTAVAKCNVNHDEEFCDMLRLIDYNKAALSKFKPDVESALHLFKTTVNSLISDQLLMRNHLRDLMCVPYCNYSKFWYLEHAKTGETSVPKCWLVTNGAYLNETHFSDQIEQEADNMITEMLRKDYIKRQGLEGGSPVVEVQGTIDELNSFIGYALVLSRWDDIRNDLFRIQNDLFVLGEDVSTGGKGRTVTREMIDYLEARVKEMKAEIGKIELFVVPGGSVESASLHMARAVSRRLERRIVAASKLTEINKNVLIYANRLSSILFMHALISNKRLNIPEKIWALEVDDDDKAGWSHPQFEKGGGSGGGSGGGSWSHPQFEKGSGGLNDIFEAQKIEWHE

Source Source

Source organism organism	Lymphocytic choriomeningitis virus
NCBI taxonomy ID ncbi_taxonomy_id	11623
Host organism host_organism	Drosophila melanogaster

Entity 5 Entity 5 branched

Description description	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	586.5 kDa
Source method src_method	man
Copy count entity_count	3

Entity 6 Entity 6 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	15

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	6

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	8dmhE01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8dmhF01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8dmhG01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8dmhH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8dmhI01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	8dmhJ01
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	3.19 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	34783

Lymphocytic choriomeningitis virus glycoprotein in complex with neutralizing antibody M28

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

Glycoprotein G1

State in the Current Structure

Other States of the Same Protein in the Database

Glycoprotein G2,Cobalamin adenosyltransferase-like domain-containing protein trimerization tag

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

8dmh__assembly_1__model_1

8dmh__assembly_1__model_1 | I(q)

8dmh__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 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

Lymphocytic choriomeningitis virus glycoprotein in complex with neutralizing antibody M28

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

Glycoprotein G1

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 G2,Cobalamin adenosyltransferase-like domain-containing protein trimerization tag

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

8dmh__assembly_1__model_1

8dmh__assembly_1__model_1 | I(q)

8dmh__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 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 non-polymer

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)