9yax

Localized reconstruction of the asymmetric unit of the low pH treated back neutralized SINV/EEEV in complex with Fab fragment of the antibody EEEV-179

Method: ELECTRON MICROSCOPY

▼

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

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 17 其他Polymer 4	EEEV-179 Heavy chain × 1 EEEV-179 Light chain × 1 Capsid protein × 5 （Q88793） E2 × 5 （E9KXL2） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 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	W8RHT7_EEEV
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–437； UniProt 802–1238 Author chain B； PDBConstruct 1–437； UniProt 802–1238 Author chain C； PDBConstruct 1–437； UniProt 802–1238 Author chain D； PDBConstruct 1–437； UniProt 802–1238 Author chain E； PDBConstruct 1–437； UniProt 802–1238

Capsid protein

Eastern equine encephalitis virus

UniProt Q88793

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 17 其他Polymer 4	EEEV-179 Heavy chain × 1 EEEV-179 Light chain × 1 E1 × 5 （W8RHT7） E2 × 5 （E9KXL2） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 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	Q88793_EEEV
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain P； PDBConstruct 1–160； UniProt 102–261 Author chain Q； PDBConstruct 1–160； UniProt 102–261 Author chain R； PDBConstruct 1–160； UniProt 102–261 Author chain S； PDBConstruct 1–160； UniProt 102–261 Author chain T； PDBConstruct 1–160； UniProt 102–261

E2

Eastern equine encephalitis virus

UniProt E9KXL2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 17 其他Polymer 4	EEEV-179 Heavy chain × 1 EEEV-179 Light chain × 1 E1 × 5 （W8RHT7） Capsid protein × 5 （Q88793） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 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	E9KXL2_EEEV
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain a； PDBConstruct 1–420； UniProt 325–744 Author chain b； PDBConstruct 1–420； UniProt 325–744 Author chain c； PDBConstruct 1–420； UniProt 325–744 Author chain d； PDBConstruct 1–420； UniProt 325–744 Author chain e； PDBConstruct 1–420； UniProt 325–744

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9yax
Deposition date deposition_date	2025-09-16
Structure title title	Localized reconstruction of the asymmetric unit of the low pH treated back neutralized SINV/EEEV in complex with Fab fragment of the antibody EEEV-179
Keywords keywords	;Eastern Equine Encephalitis Virus, Cryo-EM, Single Particle Averaging, localized reconstruction, asymmetric unit, low pH back neutralization., VIRUS ;; VIRUS
Experimental Method method	ELECTRON MICROSCOPY

▼

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.

9yax__assembly_1__model_1

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

Download this curve (.dat)

9yax__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9yax__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	71.70 Å
Rg (electron density)	71.22 Å
Total Rg	71.45 Å
Atom count	41372
Residues	5533
Excluded volume	727910 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9yax__assembly_1__model_1`	17-meric （17）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	EEEV-179 Heavy chain
Molecular weight formula_weight	24245.3 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	41372

QVQLLQSGAEVKKPGSSVKVSCKASGGTFSNIGISWVRQAPRQGLEWMGGIIPLFATTNYAQNFQGRLTITADKSTTTAYMELNSLRSDDTGVYFCARQLGWAYCNSSTCSKGWFNPWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK

Source Source

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

Entity 2 Entity 2 polymer

Description description	EEEV-179 Light chain
Molecular weight formula_weight	24277.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	2

DIVMTQTPLSLPVTPGEPASISCRSSQSLLDSDDGNTYLDWYLQKPGQSPHLLIYTVSYRASGVPDRFSGSGSGTDFTLKISTVEAEDVGVYYCMQRTEFPYTFGQGTKLEIRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLRSPVTKSFNRGEC

Source Source

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

Entity 3 Entity 3 polymer

Description description	E1
Molecular weight formula_weight	47357.5 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

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

YEHTAVMPNKVGIPYKALVERPGYAPVHLQIQLVNTRIIPSTNLEYITCKYKTKVPSPVVKCCGATQCTSKPHPDYQCQVFTGVYPFMWGGAYCFCDTENTQMSEAYVERSEECSIDHAKAYKVHTGTVQAMVNITYGSVSWRSADVYVNGETPAKIGDAKLIIGPLSSAWSPFDNKVVVYGHEVYNYDFPEYGTGKAGSFGDLQSRTSTSNDLYANTNLKLQRPQAGIVHTPFTQAPSGFERWKRDKGAPLNDVAPFGCSIALEPLRAENCAVGSIPISIDIPDAAFTRISETPTVSDLECKITECTYASDFGGIATVAYKSSKAGNCPIHSPSGVAVIKENDVTLAESGSFTFHFSTANIHPAFKLQVCTSAVTCKGDCKPPKDHIVDYPAQHTESFTSAISATAWSWLKVLVGGTSAFIVLGLIATAVVALVLF

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	Capsid protein
Molecular weight formula_weight	17650.0 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q,R,S,T

QRMCMKLESDKTFPIMLNGQVNGYACVVGGRVFKPLHVEGRIDNEQLAAIKLKKASIYDLEYGDVPQCMKSDTLQYTSDKPPGFYNWHHGAVQYENNRFTVPRGVGGKGDSGRPILDNKGRVVAIVLGGVNEGSRTALSVVTWNQKGVTVKDTPEGSEPW

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 polymer

Description description	E2
Molecular weight formula_weight	47047.0 kDa
EC 编号 ec_number	3.4.21.90
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

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

DLDTHFTQYKLARPYIADCPNCGHSRCDSPIAIEEVRGDAHAGVIRIQTSAMFGLKTDGVDLAYMSFMNGKTQKSIKIDNLHVRTSAPCSLVSHHGYYILAQCPPGDTVTVGFHDGPNRHTCTVAHKVEFRPVGREKYRHPPEHGVELPCNRYTHKRADQGHYVEMHQPGLVADHSLLSIHSAKVKITVPSGAQVKYYCKCPDVREGITSSDHTTTCTDVKQCRAYLIDNKKWVYNSGRLPRGEGDTFKGKLHVPFVPVKAKCIATLAPEPLVEHKHRTLILHLHPDHPTLLTTRSLGSDANPTRQWIERPTTVNFTVTGEGLEYTWGNHPPKRVWAQESGEGNPHGWPHEVVVYYYNRYPLTTIIGLCTCVAIIMVSCVTSVWLLCRTRNLCITPYKLAPNAQVPILLALLCCIKPTRA

Source Source

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

Entity 6 Entity 6 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	4

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

▶

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	4.200 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	4.20 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	878089

Localized reconstruction of the asymmetric unit of the low pH treated back neutralized SINV/EEEV in complex with Fab fragment of the antibody EEEV-179

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

E1

State in the Current Structure

Other States of the Same Protein in the Database

Capsid protein

State in the Current Structure

Other States of the Same Protein in the Database

E2

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

9yax__assembly_1__model_1

9yax__assembly_1__model_1 | I(q)

9yax__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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

7. Citations (1)

Localized reconstruction of the asymmetric unit of the low pH treated back neutralized SINV/EEEV in complex with Fab fragment of the antibody EEEV-179

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

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

Capsid protein

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

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

9yax__assembly_1__model_1

9yax__assembly_1__model_1 | I(q)

9yax__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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

7. Citations (1)