SAXSdb — 9ay1

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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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 600 其他Polymer 240 PDB declaration: 600-meric（600） Consistent with protein copy count	Chain A； UniProt 802–1201 Chain B； UniProt 802–1201 Chain C； UniProt 802–1201 Chain D； UniProt 802–1201	Not recorded	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 BMA beta-D-mannopyranose × 60 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 240	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.60 Å
2	Other combination Heteromer Protein × 10 其他Polymer 4 PDB declaration: decameric（10） Consistent with protein copy count	Chain A； UniProt 802–1201 Chain B； UniProt 802–1201 Chain C； UniProt 802–1201 Chain D； UniProt 802–1201	Not recorded	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 BMA beta-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.60 Å
3	Other combination Heteromer Protein × 50 其他Polymer 20 PDB declaration: 50-meric（50） Consistent with protein copy count	Chain A； UniProt 802–1201 Chain B； UniProt 802–1201 Chain C； UniProt 802–1201 Chain D； UniProt 802–1201	Not recorded	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 BMA beta-D-mannopyranose × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.60 Å
4	Other combination Heteromer Protein × 60 其他Polymer 24 PDB declaration: 60-meric（60） Consistent with protein copy count	Chain A； UniProt 802–1201 Chain B； UniProt 802–1201 Chain C； UniProt 802–1201 Chain D； UniProt 802–1201	Not recorded	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 BMA beta-D-mannopyranose × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.60 Å
5	Other combination Heteromer Protein × 10 其他Polymer 4 PDB declaration: decameric（10） Consistent with protein copy count	Chain A； UniProt 802–1201 Chain B； UniProt 802–1201 Chain C； UniProt 802–1201 Chain D； UniProt 802–1201	Not recorded	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 BMA beta-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.60 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9AY1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7N69 Pre-fusion state 2 of EEEV with localized reconstruction Deposited 2021-06-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 802–1242（441 aa） Chain B 325–744（420 aa） Chain C 802–1242（441 aa） Chain D 325–744（420 aa） Chain E 802–1242（441 aa） Chain F 325–744（420 aa） Chain G 802–1242（441 aa） Chain H 325–744（420 aa） Chain I 802–1242（441 aa） Chain J 325–744（420 aa） Chain K 802–1242（441 aa） Chain L 325–744（420 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 5.5；pH 5.5 cryo-EM vitrification conditions Cryogen ETHANE；blot for 3.3 seconds before plunging	Resolution 14.10 Å
7N6A Pre-fusion state 1 of EEEV with localized reconstruction Deposited 2021-06-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 802–1242（441 aa） Chain B 325–744（420 aa） Chain C 802–1242（441 aa） Chain D 325–744（420 aa） Chain E 802–1242（441 aa） Chain F 325–744（420 aa） Chain G 802–1242（441 aa） Chain H 325–744（420 aa） Chain I 802–1242（441 aa） Chain J 325–744（420 aa） Chain K 802–1242（441 aa） Chain L 325–744（420 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 5.5；pH 5.5 cryo-EM vitrification conditions Cryogen ETHANE；blot for 3.3 seconds before plunging	Resolution 14.30 Å
7V0N Cryo-EM structure of SINV/EEEV in complex with Fab fragment of a moderately/weakly neutralizing human antibody IgG-21 Deposited 2022-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 802–1201（400 aa） Chain B 802–1201（400 aa） Chain C 802–1201（400 aa） Chain D 802–1201（400 aa） Chain a 325–666（342 aa） Chain b 325–666（342 aa） Chain c 325–666（342 aa） Chain d 325–666（342 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.90 Å
7V0O Cryo-EM structure of SINV/EEEV in complex with Fab fragment of a moderately/weakly neutralizing human antibody IgG-94 Deposited 2022-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 802–1201（400 aa） Chain B 802–1201（400 aa） Chain C 802–1201（400 aa） Chain D 802–1201（400 aa） Chain a 325–666（342 aa） Chain b 325–666（342 aa） Chain c 325–666（342 aa） Chain d 325–666（342 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.60 Å
7V0P Cryo-EM structure of SINV/EEEV in complex with Fab fragment of a potently neutralizing human antibody IgG-106 Deposited 2022-05-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 802–1201（400 aa） Chain B 802–1201（400 aa） Chain C 802–1201（400 aa） Chain D 802–1201（400 aa） Chain a 325–666（342 aa） Chain b 325–666（342 aa） Chain c 325–666（342 aa） Chain d 325–666（342 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.20 Å
8VSV Cryo-EM structure of SINV/EEEV in complex with a potently neutralizing intact human antibody EEEV-373 Deposited 2024-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 16-meric	Chain A 802–1201（400 aa） Chain B 802–1201（400 aa） Chain C 802–1201（400 aa） Chain D 802–1201（400 aa） Chain E 802–1201（400 aa） Chain F 802–1201（400 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8XI4 Structure of Eastern Equine Encephalitis VLP in complex with the receptor VLDLR LA1-2 Deposited 2023-12-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric	Chain A 802–1242（441 aa） Chain B 325–744（420 aa） Chain C 1–261（261 aa） Chain D 802–1242（441 aa） Chain E 325–744（420 aa） Chain F 1–261（261 aa） Chain G 802–1242（441 aa） Chain H 325–744（420 aa） Chain I 1–261（261 aa） Chain J 802–1242（441 aa） Chain K 325–744（420 aa） Chain L 1–261（261 aa）	Mutation：K67N Mutation：K67N Mutation：K67N Mutation：K67N	CA CALCIUM ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8XI5 Structure of Eastern Equine Encephalitis VLP in complex with the receptor VLDLR LA3-5 Deposited 2023-12-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: 20-meric	Chain A 802–1242（441 aa） Chain B 325–744（420 aa） Chain C 1–261（261 aa） Chain D 802–1242（441 aa） Chain E 325–744（420 aa） Chain F 1–261（261 aa） Chain G 802–1242（441 aa） Chain H 325–744（420 aa） Chain I 1–261（261 aa） Chain J 802–1242（441 aa） Chain K 325–744（420 aa） Chain L 1–261（261 aa）	Mutation：K67N Mutation：K67N Mutation：K67N Mutation：K67N	CA CALCIUM ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8YS2 Overall structure of Eastern Equine Encephalitis virus VLP in complex with the receptor VLDLR LA1-2 Deposited 2024-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 960 PDB declaration: 960-meric	Chain A 802–1242（441 aa） Chain B 325–744（420 aa） Chain C 1–261（261 aa） Chain D 802–1242（441 aa） Chain E 325–744（420 aa） Chain F 1–261（261 aa） Chain G 802–1242（441 aa） Chain H 325–744（420 aa） Chain I 1–261（261 aa） Chain J 802–1242（441 aa） Chain K 325–744（420 aa） Chain L 1–261（261 aa）	Mutation：K67N Mutation：K67N Mutation：K67N Mutation：K67N	CA CALCIUM ION × 480	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.20 Å
8YS4 Overall structure of Eastern Equine Encephalitis virus VLP in complex with the receptor VLDLR LA3-5 Deposited 2024-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 1200 PDB declaration: 1200-meric	Chain A 802–1242（441 aa） Chain B 325–744（420 aa） Chain C 1–261（261 aa） Chain D 802–1242（441 aa） Chain E 325–744（420 aa） Chain F 1–261（261 aa） Chain G 802–1242（441 aa） Chain H 325–744（420 aa） Chain I 1–261（261 aa） Chain J 802–1242（441 aa） Chain K 325–744（420 aa） Chain L 1–261（261 aa）	Mutation：K67N Mutation：K67N Mutation：K67N Mutation：K67N	CA CALCIUM ION × 480	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å

10 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 600 其他Polymer 240 PDB declaration: 600-meric（600） Consistent with protein copy count	Chain a； UniProt 1–338 Chain b； UniProt 1–338 Chain c； UniProt 1–338 Chain d； UniProt 1–338	Not recorded	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 BMA beta-D-mannopyranose × 60 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 240	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.60 Å
2	Other combination Heteromer Protein × 10 其他Polymer 4 PDB declaration: decameric（10） Consistent with protein copy count	Chain a； UniProt 1–338 Chain b； UniProt 1–338 Chain c； UniProt 1–338 Chain d； UniProt 1–338	Not recorded	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 BMA beta-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.60 Å
3	Other combination Heteromer Protein × 50 其他Polymer 20 PDB declaration: 50-meric（50） Consistent with protein copy count	Chain a； UniProt 1–338 Chain b； UniProt 1–338 Chain c； UniProt 1–338 Chain d； UniProt 1–338	Not recorded	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 BMA beta-D-mannopyranose × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 20	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.60 Å
4	Other combination Heteromer Protein × 60 其他Polymer 24 PDB declaration: 60-meric（60） Consistent with protein copy count	Chain a； UniProt 1–338 Chain b； UniProt 1–338 Chain c； UniProt 1–338 Chain d； UniProt 1–338	Not recorded	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 BMA beta-D-mannopyranose × 6 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 24	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.60 Å
5	Other combination Heteromer Protein × 10 其他Polymer 4 PDB declaration: decameric（10） Consistent with protein copy count	Chain a； UniProt 1–338 Chain b； UniProt 1–338 Chain c； UniProt 1–338 Chain d； UniProt 1–338	Not recorded	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 BMA beta-D-mannopyranose × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 4.60 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 9AY1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8VSV Cryo-EM structure of SINV/EEEV in complex with a potently neutralizing intact human antibody EEEV-373 Deposited 2024-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 16-meric	Chain a 1–338（338 aa） Chain b 1–338（338 aa） Chain c 1–338（338 aa） Chain d 1–338（338 aa） Chain e 1–338（338 aa） Chain f 1–338（338 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9YAW Localized reconstruction of the asymmetric unit of SINV/EEEV in complex with Fab EEEV-33 at arm 4 at pH 5.6. Deposited 2025-09-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: 14-meric	Chain a 2–419（418 aa） Chain b 1–419（419 aa） Chain c 1–419（419 aa） Chain d 2–419（418 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 5.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
9YB3 Localized reconstruction of the asymmetric unit of SINV/EEEV. Deposited 2025-09-16	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 12-meric	Chain a 2–419（418 aa） Chain b 1–419（419 aa） Chain c 1–419（419 aa） Chain d 2–419（418 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9YB4 Localized reconstruction of the asymmetric unit of the low pH treated back neutralized SINV/EEEV. Deposited 2025-09-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 12-meric	Chain a 2–419（418 aa） Chain b 1–419（419 aa） Chain c 1–419（419 aa） Chain d 2–419（418 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	58.83 Å
Radius of gyration Rg (electron density) rg_electron	57.49 Å
Forward intensity I(0) i0	2009790000.00
Molecular weight molecular_weight	353650.0 kDa
Excluded volume excluded_volume	433190 Å³
Envelope volume envelope_volume	702770 Å³
Hydration-shell volume shell_volume	102830 Å³
Envelope diameter envelope_diameter	211.2 Å
Shell Rg shell_rg	57.73 Å
Envelope Rg envelope_rg	57.84 Å
Shape Rg shape_rg	57.56 Å
Total Rg total_rg	57.26 Å
Total atoms total_atoms	24892
Residues n_residues	3394
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	199.4 Å
Rg (real space) rg_real	58.82 Å
Rg uncertainty (real space) rg_real_error	1.79 Å
I(0) (real space) i0_real	2.0100e+09
I(0) uncertainty (real space) i0_real_error	4.2230e+07
Rg (reciprocal space) rg_reciprocal	58.81 Å
I(0) (reciprocal space) i0_reciprocal	2010000000.0000
Solution quality estimate total_estimate	0.8738
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	73.9 Å
Skewness Skewness skewness	0.316
Kurtosis Kurtosis kurtosis	-0.262
Angular range angular_range	— – 0.1350 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	87110000.0000
Real-space data points n_real_points	28
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.741

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 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

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 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

来源 Source

来源生物 organism	Eastern equine encephalitis virus
NCBI Class编号 ncbi_taxonomy_id	11021
宿主生物 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

来源 Source

来源生物 organism	Eastern equine encephalitis virus
NCBI Class编号 ncbi_taxonomy_id	11021
宿主生物 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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8. Citations (1)

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Resolution resolution	4.60 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	15932

fit	/app/data/saxs_computation/ay/9ay1/9ay1.fit
pddf	/app/data/pr_computation/ay/9ay1/9ay1.pr.out
profile	/app/data/saxs_computation/ay/9ay1/9ay1.dat

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 branched

Entity 6 Entity 6 branched

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)