9eau

RRV DKTA VLP in complex with VLDLR-LBD-Fc

Method: ELECTRON MICROSCOPY D_max: 210.4 Å Quality: GOOD

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

Spike glycoprotein E1

Ross river virus (STRAIN T48)

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 14 PDB declaration: 14-meric（14） Consistent with protein copy count	Chain A； UniProt 817–1254 Chain E； UniProt 817–1254 Chain I； UniProt 817–1254 Chain M； UniProt 817–1254	Mutation：K327D, D345K, E348T, D349A	Spike glycoprotein E2 × 4 （Q076B2） Capsid protein × 4 （P08491） Very low-density lipoprotein receptor × 2 （P98155） CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.06 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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	C9DZM3_9VIRU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–438； UniProt 817–1254 Author chain E； PDBConstruct 1–438； UniProt 817–1254 Author chain I； PDBConstruct 1–438； UniProt 817–1254 Author chain M； PDBConstruct 1–438； UniProt 817–1254

Spike glycoprotein E2

Ross river virus (STRAIN T48)

UniProt Q076B2

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 14 PDB declaration: 14-meric（14） Consistent with protein copy count	Chain B； UniProt 335–753 Chain F； UniProt 335–753 Chain J； UniProt 335–753 Chain N； UniProt 335–753	Not recorded	Spike glycoprotein E1 × 4 （C9DZM3） Capsid protein × 4 （P08491） Very low-density lipoprotein receptor × 2 （P98155） CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.06 Å

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q076B2_9VIRU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–419； UniProt 335–753 Author chain F； PDBConstruct 1–419； UniProt 335–753 Author chain J； PDBConstruct 1–419； UniProt 335–753 Author chain N； PDBConstruct 1–419； UniProt 335–753

Capsid protein

Ross river virus (STRAIN T48)

UniProt P08491

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 14 PDB declaration: 14-meric（14） Consistent with protein copy count	Chain C； UniProt 113–270 Chain G； UniProt 113–270 Chain K； UniProt 113–270 Chain O； UniProt 113–270	Not recorded	Spike glycoprotein E1 × 4 （C9DZM3） Spike glycoprotein E2 × 4 （Q076B2） Very low-density lipoprotein receptor × 2 （P98155） CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.06 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9EAU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6VYV Human mAbs broadly protect against infection of arthritiogenic alphaviruses by recognizing conserved elements of the MXR8 receptor binding domain Deposited 2020-02-27	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 817–1209（393 aa） Fragment：UNP residues 817-1209 Chain B 817–1209（393 aa） Fragment：UNP residues 817-1209 Chain C 817–1209（393 aa） Fragment：UNP residues 817-1209 Chain D 817–1209（393 aa） Fragment：UNP residues 817-1209 Chain E 335–675（341 aa） Fragment：UNP residues 335-675 Chain F 335–675（341 aa） Fragment：UNP residues 335-675 Chain G 335–675（341 aa） Fragment：UNP residues 335-675 Chain H 335–675（341 aa） Fragment：UNP residues 335-675	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.33 Å
6VYV Human mAbs broadly protect against infection of arthritiogenic alphaviruses by recognizing conserved elements of the MXR8 receptor binding domain Deposited 2020-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 817–1209（393 aa） Fragment：UNP residues 817-1209 Chain B 817–1209（393 aa） Fragment：UNP residues 817-1209 Chain C 817–1209（393 aa） Fragment：UNP residues 817-1209 Chain D 817–1209（393 aa） Fragment：UNP residues 817-1209 Chain E 335–675（341 aa） Fragment：UNP residues 335-675 Chain F 335–675（341 aa） Fragment：UNP residues 335-675 Chain G 335–675（341 aa） Fragment：UNP residues 335-675 Chain H 335–675（341 aa） Fragment：UNP residues 335-675	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.33 Å
6VYV Human mAbs broadly protect against infection of arthritiogenic alphaviruses by recognizing conserved elements of the MXR8 receptor binding domain Deposited 2020-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 80 PDB declaration: 80-meric	Chain A 817–1209（393 aa） Fragment：UNP residues 817-1209 Chain B 817–1209（393 aa） Fragment：UNP residues 817-1209 Chain C 817–1209（393 aa） Fragment：UNP residues 817-1209 Chain D 817–1209（393 aa） Fragment：UNP residues 817-1209 Chain E 335–675（341 aa） Fragment：UNP residues 335-675 Chain F 335–675（341 aa） Fragment：UNP residues 335-675 Chain G 335–675（341 aa） Fragment：UNP residues 335-675 Chain H 335–675（341 aa） Fragment：UNP residues 335-675	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.33 Å
6VYV Human mAbs broadly protect against infection of arthritiogenic alphaviruses by recognizing conserved elements of the MXR8 receptor binding domain Deposited 2020-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 96 PDB declaration: 96-meric	Chain A 817–1209（393 aa） Fragment：UNP residues 817-1209 Chain B 817–1209（393 aa） Fragment：UNP residues 817-1209 Chain C 817–1209（393 aa） Fragment：UNP residues 817-1209 Chain D 817–1209（393 aa） Fragment：UNP residues 817-1209 Chain E 335–675（341 aa） Fragment：UNP residues 335-675 Chain F 335–675（341 aa） Fragment：UNP residues 335-675 Chain G 335–675（341 aa） Fragment：UNP residues 335-675 Chain H 335–675（341 aa） Fragment：UNP residues 335-675	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.33 Å
6VYV Human mAbs broadly protect against infection of arthritiogenic alphaviruses by recognizing conserved elements of the MXR8 receptor binding domain Deposited 2020-02-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain A 817–1209（393 aa） Fragment：UNP residues 817-1209 Chain B 817–1209（393 aa） Fragment：UNP residues 817-1209 Chain C 817–1209（393 aa） Fragment：UNP residues 817-1209 Chain D 817–1209（393 aa） Fragment：UNP residues 817-1209 Chain E 335–675（341 aa） Fragment：UNP residues 335-675 Chain F 335–675（341 aa） Fragment：UNP residues 335-675 Chain G 335–675（341 aa） Fragment：UNP residues 335-675 Chain H 335–675（341 aa） Fragment：UNP residues 335-675	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.33 Å

1 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	POLS_RRVT
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–158； UniProt 113–270 Author chain G； PDBConstruct 1–158； UniProt 113–270 Author chain K； PDBConstruct 1–158； UniProt 113–270 Author chain O； PDBConstruct 1–158； UniProt 113–270

Very low-density lipoprotein receptor

Homo sapiens

UniProt P98155

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 14 PDB declaration: 14-meric（14） Consistent with protein copy count	Chain Y； UniProt 111–149 Chain Z； UniProt 111–149	Not recorded	Spike glycoprotein E1 × 4 （C9DZM3） Spike glycoprotein E2 × 4 （Q076B2） Capsid protein × 4 （P08491） CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 3.06 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9EAU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1V9U Human Rhinovirus 2 bound to a fragment of its cellular receptor protein Deposited 2004-02-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 300 PDB declaration: complete icosahedral assembly	Chain 5 111–151（41 aa）	Not recorded	DAO LAURIC ACID × 60 CA CALCIUM ION × 60	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Ammonim sulfate, sodium/potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.60 Å R-free 0.295
1V9U Human Rhinovirus 2 bound to a fragment of its cellular receptor protein Deposited 2004-02-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain 5 111–151（41 aa）	Not recorded	DAO LAURIC ACID × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Ammonim sulfate, sodium/potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.60 Å R-free 0.295
1V9U Human Rhinovirus 2 bound to a fragment of its cellular receptor protein Deposited 2004-02-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric	Chain 5 111–151（41 aa）	Not recorded	DAO LAURIC ACID × 5 CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Ammonim sulfate, sodium/potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.60 Å R-free 0.295
1V9U Human Rhinovirus 2 bound to a fragment of its cellular receptor protein Deposited 2004-02-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain 5 111–151（41 aa）	Not recorded	DAO LAURIC ACID × 6 CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Ammonim sulfate, sodium/potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.60 Å R-free 0.295
1V9U Human Rhinovirus 2 bound to a fragment of its cellular receptor protein Deposited 2004-02-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain 5 111–151（41 aa）	Not recorded	DAO LAURIC ACID × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Ammonim sulfate, sodium/potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.60 Å R-free 0.295
1V9U Human Rhinovirus 2 bound to a fragment of its cellular receptor protein Deposited 2004-02-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 150 PDB declaration: 150-meric	Chain 5 111–151（41 aa）	Not recorded	DAO LAURIC ACID × 30 CA CALCIUM ION × 30	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Ammonim sulfate, sodium/potassium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.60 Å R-free 0.295
3DPR Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3 Deposited 2008-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 300 PDB declaration: 300-MERIC	Chain E 113–151（39 aa）	Not recorded	DAO LAURIC ACID × 60 CA CALCIUM ION × 60	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；Ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.50 Å R-free 0.441
3DPR Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3 Deposited 2008-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 113–151（39 aa）	Not recorded	DAO LAURIC ACID × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；Ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.50 Å R-free 0.441
3DPR Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3 Deposited 2008-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 25 PDB declaration: 25-meric	Chain E 113–151（39 aa）	Not recorded	DAO LAURIC ACID × 5 CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；Ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.50 Å R-free 0.441
3DPR Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3 Deposited 2008-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 30 PDB declaration: 30-meric	Chain E 113–151（39 aa）	Not recorded	DAO LAURIC ACID × 6 CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；Ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.50 Å R-free 0.441
3DPR Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3 Deposited 2008-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 113–151（39 aa）	Not recorded	DAO LAURIC ACID × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；Ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.50 Å R-free 0.441
3DPR Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3 Deposited 2008-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 300 PDB declaration: 300-meric	Chain E 113–151（39 aa）	Not recorded	DAO LAURIC ACID × 60 CA CALCIUM ION × 60	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；Ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.50 Å R-free 0.441
6BYV Solution NMR structure of cysteine-rich calcium bound domains of very low density lipoprotein receptor Deposited 2017-12-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 70–190（121 aa）	Not recorded	CA CALCIUM ION × 3	SOLUTION NMR NMR measurement conditions pH 6.2；306.5 K；Ionic strength (raw mmCIF value) 100；Pressure 760 NMR measurement conditions pH 6.2；306.5 K；Ionic strength (raw mmCIF value) 100；Pressure 760 NMR sample composition 350 uM [U-99% 15N] VLDLR, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 250 uM [U-99% 13C; U-99% 15N] VLDLR, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 250 uM [U-99% 13C; U-99% 15N] VLDLR, 100% D2O \| 100% D2O	Resolution not provided
8IHP Structure of Semliki Forest virus VLP in complex with the receptor VLDLR-LA3 Deposited 2023-02-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain M 111–149（39 aa） Chain N 111–149（39 aa） Chain O 111–149（39 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 CA CALCIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8UA4 Structure of eastern equine encephalitis virus VLP in complex with VLDLR LA1 Deposited 2023-09-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain R 33–68（36 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 12 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.58 Å
8UA8 Structure of Semliki Forest virus VLP in complex with VLDLR LA2 Deposited 2023-09-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: heptadecameric	Chain R 72–108（37 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
8UFB Eastern equine encephalitis virus (PE-6) VLP in complex with full-length VLDLR (asymmetric unit) Deposited 2023-10-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric	Chain R 28–769（742 aa） Chain S 28–769（742 aa） Chain T 28–769（742 aa） Chain U 28–769（742 aa） Chain V 28–769（742 aa） Chain W 28–769（742 aa） Chain X 28–769（742 aa） Chain Y 28–769（742 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CA CALCIUM ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.89 Å
8UFC Eastern equine encephalitis virus (PE-6) VLP in complex with VLDLR LA(1-2) (asymmetric unit) Deposited 2023-10-04	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 V 31–108（78 aa） Fragment：UNP residues 31-108 Chain W 31–108（78 aa） Fragment：UNP residues 31-108 Chain X 31–108（78 aa） Fragment：UNP residues 31-108 Chain Y 31–108（78 aa） Fragment：UNP residues 31-108	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 CA CALCIUM ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
8X0K Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(2-fold) Deposited 2023-11-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: 16-meric	Chain D 113–149（37 aa） Chain H 113–149（37 aa） Chain L 113–149（37 aa） Chain P 113–149（37 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8X0L Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(3-fold) Deposited 2023-11-04	Different construct Different mutation/modification 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 D 113–149（37 aa） Chain H 113–149（37 aa） Chain L 113–149（37 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8X0M Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(5-fold) Deposited 2023-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: 11-meric	Chain D 113–149（37 aa） Chain H 113–149（37 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 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 M 31–113（83 aa） Chain N 31–113（83 aa） Chain O 31–113（83 aa） Chain P 31–113（83 aa）	Not recorded	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 M 191–231（41 aa） Chain N 191–231（41 aa） Chain O 191–231（41 aa） Chain P 191–231（41 aa） Chain Q 111–151（41 aa） Chain R 111–151（41 aa） Chain S 111–151（41 aa） Chain T 111–151（41 aa）	Not recorded	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 M 31–110（80 aa） Chain N 31–110（80 aa） Chain O 31–110（80 aa） Chain P 31–110（80 aa）	Not recorded	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 M 191–231（41 aa） Chain N 191–231（41 aa） Chain O 191–231（41 aa） Chain P 191–231（41 aa） Chain Q 111–151（41 aa） Chain R 111–151（41 aa） Chain S 111–151（41 aa） Chain T 111–151（41 aa）	Not recorded	CA CALCIUM ION × 480	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
8YVZ Semliki Forest virus viron Deposited 2024-03-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: eicosameric	Chain E 110–151（42 aa） Chain R 110–151（42 aa） Chain S 110–151（42 aa） Chain T 110–151（42 aa）	Not recorded	CA CALCIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.45 Å
8YW0 Semliki Forest virus viron Deposited 2024-03-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: nonadecameric	Chain E 191–230（40 aa） Chain R 191–230（40 aa） Chain T 191–230（40 aa）	Not recorded	CA CALCIUM ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.55 Å
8YW1 Semliki Forest virus viron in complex with VLDLR Deposited 2024-03-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 33 PDB declaration: 33-meric	Chain C 111–231（121 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.44 Å
8YW2 Semliki Forest virus viron in complex with VLDLR Deposited 2024-03-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 65 PDB declaration: 65-meric	Chain A 70–231（162 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
9DQZ Structure of western equine encephalitis virus McMillan VLP in complex with human VLDLR Deposited 2024-09-24	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 M 33–110（78 aa） Chain N 33–110（78 aa） Chain O 33–110（78 aa） Chain P 33–110（78 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 16 CA CALCIUM ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9E9Y WEEV McMillan VLP in complex with VLDLR LA(1-2) Deposited 2024-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric	Chain V 31–108（78 aa） Fragment：UNP residues 31-108 Chain X 31–108（78 aa） Fragment：UNP residues 31-108 Chain Y 31–108（78 aa） Fragment：UNP residues 31-108 Chain Z 31–108（78 aa） Fragment：UNP residues 31-108	Not recorded	CA CALCIUM ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.96 Å
9E9Z SINV-WEEV Fleming in complex with VLDLR LA(1-2) Deposited 2024-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: 16-meric	Chain V 31–108（78 aa） Fragment：UNP residues 31-108 Chain W 31–108（78 aa） Fragment：UNP residues 31-108 Chain X 31–108（78 aa） Fragment：UNP residues 31-108 Chain Y 31–108（78 aa） Fragment：UNP residues 31-108	Not recorded	CA CALCIUM ION × 8	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.95 Å
9L99 Structure of Western equine encephalitis virus McMillan strain in complex with VLDLR LA1-2 Deposited 2024-12-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain N 31–110（80 aa）	Not recorded	CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9L9A Structure of Western equine encephalitis virus McMillan strain in complex with VLDLR LA2-3 Deposited 2024-12-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain M 70–151（82 aa）	Not recorded	CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
9WSL CryoEM structure of Western equine encephalitis virus California VLP in complex with VLDLR-LBD Deposited 2025-09-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain R 32–110（79 aa） Chain S 32–110（79 aa） Chain T 32–110（79 aa）	Not recorded	CA CALCIUM ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.27 Å

25 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VLDLR_HUMAN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain Y； PDBConstruct 1–39； UniProt 111–149 Author chain Z； PDBConstruct 1–39； UniProt 111–149

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9eau
Deposition date deposition_date	2024-11-11
Structure title title	RRV DKTA VLP in complex with VLDLR-LBD-Fc
Keywords keywords	Alphavirus Receptor, VIRAL PROTEIN; VIRAL PROTEIN
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	66.19 Å
Radius of gyration Rg (electron density) rg_electron	65.44 Å
Forward intensity I(0) i0	2968520000.00
Molecular weight molecular_weight	452810.0 kDa
Excluded volume excluded_volume	563740 Å³
Envelope volume envelope_volume	985370 Å³
Hydration-shell volume shell_volume	126440 Å³
Envelope diameter envelope_diameter	210.7 Å
Shell Rg shell_rg	67.78 Å
Envelope Rg envelope_rg	62.10 Å
Shape Rg shape_rg	65.35 Å
Total Rg total_rg	65.77 Å
Total atoms total_atoms	31779
Residues n_residues	4138
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	210.4 Å
Rg (real space) rg_real	65.83 Å
Rg uncertainty (real space) rg_real_error	1.65 Å
I(0) (real space) i0_real	2.9690e+09
I(0) uncertainty (real space) i0_real_error	5.1300e+07
Rg (reciprocal space) rg_reciprocal	66.44 Å
I(0) (reciprocal space) i0_reciprocal	2972000000.0000
Solution quality estimate total_estimate	0.8326
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	87.7 Å
Skewness Skewness skewness	0.075
Kurtosis Kurtosis kurtosis	-0.606
Angular range angular_range	— – 0.1200 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	130300000.0000
Real-space data points n_real_points	25
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.950; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Spike glycoprotein E1
Molecular weight formula_weight	47432.6 kDa
Mutation mutation	K327D, D345K, E348T, D349A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,E,I,M
Atom count atom_count	31779

YEHTATIPNVVGFPYKAHIERNGFSPMTLQLEVVETSLEPTLNLEYITCEYKTVVPSPFIKCCGTSECSSKEQPDYQCKVYTGVYPFMWGGAYCFCDSENTQLSEAYVDRSDVCKHDHASAYKAHTASLKATIRISYGTINQTTEAFVNGEHAVNVGGSKFIFGPISTAWSPFDNKIVVYKDDVYNQDFPPYGSGQPGRFGDIQSRTVESKDLYANTALKLSRPSPGVVHVPYTQTPSGFKYWLKEKGSSLNTKAPFGCKIKTNPVRAMDCAVGSIPVSMDIPDSAFTRVVDAPAVTDLSCQVVVCTHSSDFGGVATLSYKTDKPGDCAVHSHSNVATLQEATVKVKTAGKVTVHFSTASASPAFKVSVCDAKTTCTAACEPPKDHIVPYGASHNNQVFPDMSGTAMTWVQRLASGLGGLALIAVVVLVLVTCITMRR

来源 Source

来源生物 organism	Ross river virus (STRAIN T48)
NCBI Class编号 ncbi_taxonomy_id	11032
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Spike glycoprotein E2
Molecular weight formula_weight	46427.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

SVTEHFNVYKATRPYLAYCADCGDGYFCYSPVAIEKIRDEASDGMLKIQVSAQIGLDKAGTHAHTKIRYMAGHDVQESKRDSLRVYTSAACSIHGTMGHFIVAHCPPGDYLKVSFEDADSHVKACKVQYKHDPLPVGREKFVVRPHFGVELPCTSYQLTTAPTDEEIDMHTPPDIPDRTLLSQTAGNVKITAGGRTIRYNCTCGRDNVGTTSTDKTINTCKIDQCHAAVTSHDKWQFTSPFVPRADQTARRGKVHVPFPLTNVTCRVPLARAPDVTYGKKEVTLRLHPDHPTLFSYRSLGAEPHPYEEWVDKFSERIIPVTEEGIEYQWGNNPPVRLWAQLTTEGKPHGWPHEIIQYYYGLYPAATIAAVSGASLMALLTLAATCCMLATARRKCLTPYALTPGAVVPLTLGLLCCAPR

来源 Source

来源生物 organism	Ross river virus (STRAIN T48)
NCBI Class编号 ncbi_taxonomy_id	11032
宿主生物 host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Capsid protein
Molecular weight formula_weight	17367.8 kDa
EC 编号 ec_number	3.4.21.90
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

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

RMCMKIENDCIFEVKLDGKVTGYACLVGDKVMKPAHVKGTIDNPDLAKLTYKKSSKYDLECAQIPVHMKSDASKYTHEKPEGHYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLGGANEGARTALSVVTWTKDMVTRVTPEGTEEW

来源 Source

来源生物 organism	Ross river virus (STRAIN T48)
NCBI Class编号 ncbi_taxonomy_id	11032
宿主生物 host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	Very low-density lipoprotein receptor
Molecular weight formula_weight	4361.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y,Z

RTCRIHEISCGAHSTQCIPVSWRCDGENDCDSGEDEENC

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 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

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8. Citations (1)

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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	3.06 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	1173256

fit	/app/data/saxs_computation/ea/9eau/9eau.fit
pddf	/app/data/pr_computation/ea/9eau/9eau.pr.out
profile	/app/data/saxs_computation/ea/9eau/9eau.dat

RRV DKTA VLP in complex with VLDLR-LBD-Fc

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

Spike glycoprotein E2

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

Very low-density lipoprotein receptor

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

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (5)

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 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)