9ay1

Cryo-EM structure of SINV/EEEV in complex with a potently neutralizing human antibody IgG EEEV-373

Method: ELECTRON MICROSCOPY

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

Spike glycoprotein E1

Eastern equine encephalitis virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 600 其他Polymer 240	IgG EEEV-373 Heavy chain × 60 IgG EEEV-373 Light chain × 60 E2 glycoprotein × 240 （A9XR09） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 180 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 60 beta-D-mannopyranose × 60 2-acetamido-2-deoxy-beta-D-glucopyranose × 240	Consistent with protein count
2	Other combination	Heteromer	Protein 10 其他Polymer 4	IgG EEEV-373 Heavy chain × 1 IgG EEEV-373 Light chain × 1 E2 glycoprotein × 4 （A9XR09） 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 × 1 beta-D-mannopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	Consistent with protein count
3	Other combination	Heteromer	Protein 50 其他Polymer 20	IgG EEEV-373 Heavy chain × 5 IgG EEEV-373 Light chain × 5 E2 glycoprotein × 20 （A9XR09） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 15 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 5 beta-D-mannopyranose × 5 2-acetamido-2-deoxy-beta-D-glucopyranose × 20	Consistent with protein count
4	Other combination	Heteromer	Protein 60 其他Polymer 24	IgG EEEV-373 Heavy chain × 6 IgG EEEV-373 Light chain × 6 E2 glycoprotein × 24 （A9XR09） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 18 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 beta-D-mannopyranose × 6 2-acetamido-2-deoxy-beta-D-glucopyranose × 24	Consistent with protein count
5	Other combination	Heteromer	Protein 10 其他Polymer 4	IgG EEEV-373 Heavy chain × 1 IgG EEEV-373 Light chain × 1 E2 glycoprotein × 4 （A9XR09） 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 × 1 beta-D-mannopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLS_EEEVF
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–400； UniProt 802–1201 Author chain B； PDBConstruct 1–400； UniProt 802–1201 Author chain C； PDBConstruct 1–400； UniProt 802–1201 Author chain D； PDBConstruct 1–400； UniProt 802–1201

E2 glycoprotein

Eastern equine encephalitis virus

UniProt A9XR09

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 600 其他Polymer 240	IgG EEEV-373 Heavy chain × 60 IgG EEEV-373 Light chain × 60 Spike glycoprotein E1 × 240 （Q4QXJ7） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 180 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 60 beta-D-mannopyranose × 60 2-acetamido-2-deoxy-beta-D-glucopyranose × 240	Consistent with protein count
2	Other combination	Heteromer	Protein 10 其他Polymer 4	IgG EEEV-373 Heavy chain × 1 IgG EEEV-373 Light chain × 1 Spike glycoprotein E1 × 4 （Q4QXJ7） 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 × 1 beta-D-mannopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	Consistent with protein count
3	Other combination	Heteromer	Protein 50 其他Polymer 20	IgG EEEV-373 Heavy chain × 5 IgG EEEV-373 Light chain × 5 Spike glycoprotein E1 × 20 （Q4QXJ7） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 15 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 5 beta-D-mannopyranose × 5 2-acetamido-2-deoxy-beta-D-glucopyranose × 20	Consistent with protein count
4	Other combination	Heteromer	Protein 60 其他Polymer 24	IgG EEEV-373 Heavy chain × 6 IgG EEEV-373 Light chain × 6 Spike glycoprotein E1 × 24 （Q4QXJ7） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 18 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 beta-D-mannopyranose × 6 2-acetamido-2-deoxy-beta-D-glucopyranose × 24	Consistent with protein count
5	Other combination	Heteromer	Protein 10 其他Polymer 4	IgG EEEV-373 Heavy chain × 1 IgG EEEV-373 Light chain × 1 Spike glycoprotein E1 × 4 （Q4QXJ7） 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 × 1 beta-D-mannopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A9XR09_EEEV
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain a； PDBConstruct 1–338； UniProt 1–338 Author chain b； PDBConstruct 1–338； UniProt 1–338 Author chain c； PDBConstruct 1–338； UniProt 1–338 Author chain d； PDBConstruct 1–338； UniProt 1–338

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	9ay1
Deposition date deposition_date	2024-03-07
Structure title title	Cryo-EM structure of SINV/EEEV in complex with a potently neutralizing human antibody IgG EEEV-373
Keywords keywords	cryo-EM, single particle, virus neutralization, intra-virion crosslink, VIRUS-IMMUNE SYSTEM complex, VIRUS; VIRUS
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.

9ay1__assembly_1__model_1

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

Download this curve (.dat)

9ay1__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9ay1__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)	296.20 Å
Total Rg	295.80 Å
Atom count	1493520
Residues	203640
Excluded volume	25992000 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9ay1__assembly_1__model_1`	600-meric （600）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9ay1__assembly_2__model_1`	decameric （10）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
3	1	`9ay1__assembly_3__model_1`	50-meric （50）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
4	1	`9ay1__assembly_4__model_1`	60-meric （60）	Excluded	—	—
	Exclusion reason： Auxiliary symmetry representation; not a complete or representative biological assembly.
5	1	`9ay1__assembly_5__model_1`	decameric （10）	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 (8)

Entity 1 Entity 1 polymer

Description description	IgG EEEV-373 Heavy chain
Molecular weight formula_weight	24386.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1
Atom count atom_count	24892

QVQLVESGGGVVQPGRSLRLSCAASGFTFSSHVMYWVRQAPGKGLEWVAVITYDGGNKYYADSVRGRLTISRDNSKNTLYLQMNSLRAEDTAVYYCASPRGDSGSYYDIDYFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Source Source

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

Entity 2 Entity 2 polymer

Description description	IgG EEEV-373 Light chain
Molecular weight formula_weight	23296.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	2

DIQMTQSPSAMSASVGDRVTITCRASQGISNYLAWFQQKPGKVPKRLIYAASSLQSGVPSRFSGSGSGTEFTLTISSLQPEDFATYYCLQHNTSPSPFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKLYACEVTHQGLSSPVTKSFNRGEC

Source Source

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

Entity 3 Entity 3 polymer

Description description	Spike glycoprotein E1
Molecular weight formula_weight	43628.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

YEHTAVMPNKVGIPYKALVERPGYAPVHLQIQLVNTRIIPSTNLEYITCKYKTKVPSPVVKCCGATQCTSKPHPDYQCQVFTGVYPFMWGGAYCFCDTENTQMSEAYVERSEECSIDHAKAYKVHTGTVQAMVNITYGSVSWRSADVYVNGETPAKIGDAKLIIGPLSSAWSPFDNKVVVYGHEVYNYDFPEYGTGKAGSFGDLQSRTSTSNDLYANTNLKLQRPQAGIVHTPFTQAPSGFERWKRDKGAPLNDVAPFGCSIALEPLRAENCAVGSIPISIDIPDAAFTRISETPTVSDLECKITECTYASDFGGIATVAYKSSKAGNCPIHSPSGVAVIKENDVTLAESGSFTFHFSTANIHPAFKLQVCTSAVTCKGDCKPPKDHIVDYPAQHTESFT

Source Source

Source organism organism	Eastern equine encephalitis virus
NCBI taxonomy ID ncbi_taxonomy_id	11021
Host organism host_organism	Mesocricetus auratus

Entity 4 Entity 4 polymer

Description description	E2 glycoprotein
Molecular weight formula_weight	37921.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

DLDTHFTQYKLARPYIADCPNCGHSRCDSPIAIEEVRGDAHAGVIRIQTSAMFGLKTDGVDLAYMSFMNGKTQKSIKIDNLHVRTSAPCSLVSHHGYYILAQCPPGDTVTVGFHDGPNRHTCTVAHKVEFRPVGREKYRHPPEHGVELPCNRYTHKRADQGHYVEMHQPGLVADHSLLSIHSAKVKITVPSGAQVKYYCKCPDVREGITSSDHTTTCTDVKQCRAYLIDNKKWVYNSGRLPRGEGDTFKGKLHVPFVPVKAKCIATLAPEPLVEHKHRTLILHLHPDHPTLLTTRSLGSDANPTRQWIERPTTVNFTVTGEGLEYTWGNHPPKRVWAQ

Source Source

Source organism organism	Eastern equine encephalitis virus
NCBI taxonomy ID ncbi_taxonomy_id	11021
Host organism host_organism	Mesocricetus auratus

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	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	beta-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 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	4

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Resolution resolution	4.60 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	15932

Cryo-EM structure of SINV/EEEV in complex with a potently neutralizing human antibody IgG EEEV-373

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

Spike glycoprotein E1

State in the Current Structure

Other States of the Same Protein in the Database

E2 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

9ay1__assembly_1__model_1

9ay1__assembly_1__model_1 | I(q)

9ay1__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

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

Entity 8 Entity 8 non-polymer

7. Citations (1)

Cryo-EM structure of SINV/EEEV in complex with a potently neutralizing human antibody IgG EEEV-373

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

Spike glycoprotein E1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

E2 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

9ay1__assembly_1__model_1

9ay1__assembly_1__model_1 | I(q)

9ay1__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (8)

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

Entity 8 Entity 8 non-polymer

7. Citations (1)