9rbq

Semliki Forest virus trimer 1 in complex with ApoER2 LA5

Method: ELECTRON MICROSCOPY D_max: 191.7 Å Quality: REASONABLE

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

LDL receptor related protein 8,Ig gamma-2A chain C region, A allele

Mus musculus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 13 其他Polymer 9 PDB declaration: 13-meric（13） Consistent with protein copy count	Chain A； UniProt 202–254	Not recorded	Protein E3 × 3 （P0DJZ6） Structural polyprotein × 3 （A0A0F6PP03） Envelope glycoprotein E2 × 3 （P0DJZ6） Capsid protein × 3 （P0DJZ6） ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.70 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	E9PKG2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–55； UniProt 202–254

LDL receptor related protein 8,Ig gamma-2A chain C region, A allele

Mus musculus

UniProt P01863

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 13 其他Polymer 9 PDB declaration: 13-meric（13） Consistent with protein copy count	Chain A； UniProt 99–330	Not recorded	Protein E3 × 3 （P0DJZ6） Structural polyprotein × 3 （A0A0F6PP03） Envelope glycoprotein E2 × 3 （P0DJZ6） Capsid protein × 3 （P0DJZ6） ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.70 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9RBQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1GGI CRYSTAL STRUCTURE OF AN HIV-1 NEUTRALIZING ANTIBODY 50.1 IN COMPLEX WITH ITS V3 LOOP PEPTIDE ANTIGEN Deposited 1993-04-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 1–107（107 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1GGI CRYSTAL STRUCTURE OF AN HIV-1 NEUTRALIZING ANTIBODY 50.1 IN COMPLEX WITH ITS V3 LOOP PEPTIDE ANTIGEN Deposited 1993-04-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 1–107（107 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1IGT STRUCTURE OF IMMUNOGLOBULIN Deposited 1996-10-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–326（326 aa） Chain D 1–326（326 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；291 K；7 MICROLITERS OF 4.3 MG/ML MAB231, 3 MICROLITERS 50 MILLIMOLAR TRIS PH 8.0, AND 7 MICROLITERS 4% PEG 3350 EQUILIBRATED AGAINST 25 ML RESERVOIRS OF 4% PEG 3350, AT 18 DEGREE CELSIUS (SANDWICH PLATE)., temperature 291K	Resolution 2.80 Å R-free 0.297
1YEC STRUCTURE OF A CATALYTIC ANTIBODY IGG2A FAB FRAGMENT (D2.3) Deposited 1997-04-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa）	Not recorded	ZN ZINC ION × 7 PNB 4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 1.90 Å R-free 0.252
1YEC STRUCTURE OF A CATALYTIC ANTIBODY IGG2A FAB FRAGMENT (D2.3) Deposited 1997-04-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa）	Not recorded	ZN ZINC ION × 7 PNB 4-NITRO-BENZYLPHOSPHONOBUTANOYL-GLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 1.90 Å R-free 0.252
1YEF STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) COMPLEXED WITH SUBSTRATE ANALOGUE Deposited 1997-05-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa）	Not recorded	ZN ZINC ION × 8 PNC PARA-NITROBENZYL GLUTARYL GLYCINIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP METHOD. PRECIPITANT: 30% (W/V) PEG 600, 100MM CACODYLATE PH7.5, 40MM ZN ACETATE., vapor diffusion - hanging drop	Resolution 2.00 Å R-free 0.248
1YEG STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) COMPLEXED WITH REACTION PRODUCT Deposited 1997-05-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa）	Not recorded	ZN ZINC ION × 7 BPN PARANITROBENZYL ALCOHOL × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP METHOD. PRECIPITANT: 30% (W/V) PEG 600, 100MM CACODYLATE PH7.5, 40MM ZN ACETATE., vapor diffusion - hanging drop	Resolution 2.00 Å R-free 0.240
1YEG STRUCTURE OF IGG2A FAB FRAGMENT (D2.3) COMPLEXED WITH REACTION PRODUCT Deposited 1997-05-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa）	Not recorded	ZN ZINC ION × 7 BPN PARANITROBENZYL ALCOHOL × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP METHOD. PRECIPITANT: 30% (W/V) PEG 600, 100MM CACODYLATE PH7.5, 40MM ZN ACETATE., vapor diffusion - hanging drop	Resolution 2.00 Å R-free 0.240
1YEH STRUCTURE OF IGG2A FAB FRAGMENT Deposited 1997-05-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa）	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP METHOD. PRECIPITANT: 35% (W/V) PEG 600, 100MM CACODYLATE PH7.5, 40MM ZN ACETATE., vapor diffusion - hanging drop	Resolution 2.55 Å R-free 0.231
1YEH STRUCTURE OF IGG2A FAB FRAGMENT Deposited 1997-05-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa）	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；HANGING DROP METHOD. PRECIPITANT: 35% (W/V) PEG 600, 100MM CACODYLATE PH7.5, 40MM ZN ACETATE., vapor diffusion - hanging drop	Resolution 2.55 Å R-free 0.231
3OZ9 Crystal Structure of anti-gp41 Fab NC-1 Deposited 2010-09-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–100（100 aa）	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；1.13M sodium citrate, 0.1M sodium borate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.60 Å R-free 0.233
3ZO0 Mouse IgG2a in complex with mouse TRIM21 PRYSPRY Deposited 2013-02-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 120–327（208 aa） Fragment：FC, RESIDUES 120-327	Not recorded	MAN alpha-D-mannopyranose × 2 FUC alpha-L-fucopyranose × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.99 Å R-free 0.253
5VAA Crystal structure of mouse IgG2a Fc T370K mutant Deposited 2017-03-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 107–330（224 aa） Fragment：UNP residues 107-330 Chain B 107–330（224 aa） Fragment：UNP residues 107-330	Mutation：T370K Mutation：T370K	GOL GLYCEROL × 3 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；40% (w/v) PEG 200, 0.1 M MES, pH 6.5	Resolution 1.55 Å R-free 0.195
8AQW BA.4/5 SARS-CoV-2 Spike bound to mouse ACE2 (local) Deposited 2022-08-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 98–330（233 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

10 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GCAA_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 70–301； UniProt 99–330

Protein E3

Semliki Forest virus

UniProt P0DJZ6

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 13 其他Polymer 9 PDB declaration: 13-meric（13） Consistent with protein copy count	Chain D； UniProt 268–333 Chain E； UniProt 268–333 Chain F； UniProt 268–333 Chain J； UniProt 334–755 Chain K； UniProt 334–755 Chain L； UniProt 334–755 Chain M； UniProt 1–267 Chain N； UniProt 1–267 Chain O； UniProt 1–267	Not recorded	LDL receptor related protein 8,Ig gamma-2A chain C region, A allele × 1 （E9PKG2,P01863） Structural polyprotein × 3 （A0A0F6PP03） ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.70 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9RBQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9KQR Cryo-EM Structure of Mature Semliki Forest Virus Deposited 2024-11-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric	Chain b 334–755（422 aa） Chain c 1–267（267 aa） Chain e 334–755（422 aa） Chain f 1–267（267 aa） Chain h 334–755（422 aa） Chain i 1–267（267 aa） Chain k 334–755（422 aa） Chain l 1–267（267 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.73 Å
9RBR Semliki Forest virus trimer 2 in complex with ApoER2 LA5 Deposited 2025-05-27	Different oligomeric state Different ligand/ion	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain D 268–333（66 aa） Chain E 268–333（66 aa） Chain F 268–333（66 aa） Chain J 334–755（422 aa） Chain K 334–755（422 aa） Chain L 334–755（422 aa） Chain M 1–267（267 aa） Chain N 1–267（267 aa） Chain O 1–267（267 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	POLSF_SFV
Isoform	—
PDB entities	2, 4, 5
Chains and sequence ranges	Author chain D； PDBConstruct 1–66； UniProt 268–333 Author chain E； PDBConstruct 1–66； UniProt 268–333 Author chain F； PDBConstruct 1–66； UniProt 268–333 Author chain J； PDBConstruct 1–422； UniProt 334–755 Author chain K； PDBConstruct 1–422； UniProt 334–755 Author chain L； PDBConstruct 1–422； UniProt 334–755 Author chain M； PDBConstruct 1–267； UniProt 1–267 Author chain N； PDBConstruct 1–267； UniProt 1–267 Author chain O； PDBConstruct 1–267； UniProt 1–267

Structural polyprotein

Semliki Forest virus

UniProt A0A0F6PP03

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Insufficient information Heteromer Protein × 13 其他Polymer 9 PDB declaration: 13-meric（13） Consistent with protein copy count	Chain G； UniProt 816–1253 Chain H； UniProt 816–1253 Chain I； UniProt 816–1253	Not recorded	LDL receptor related protein 8,Ig gamma-2A chain C region, A allele × 1 （E9PKG2,P01863） Protein E3 × 3 （P0DJZ6） Envelope glycoprotein E2 × 3 （P0DJZ6） Capsid protein × 3 （P0DJZ6） ;beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 ;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 3 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.4 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.70 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9RBQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 A 816–1253（438 aa） Chain E 816–1253（438 aa） Chain I 816–1253（438 aa） Chain M 816–1253（438 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
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 C 816–1253（438 aa） Chain G 816–1253（438 aa） Chain K 816–1253（438 aa） Chain O 816–1253（438 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 12-meric	Chain C 816–1253（438 aa） Chain G 816–1253（438 aa） Chain K 816–1253（438 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 11 PDB declaration: 11-meric	Chain C 816–1253（438 aa） Chain G 816–1253（438 aa） Chain K 816–1253（438 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
9RBR Semliki Forest virus trimer 2 in complex with ApoER2 LA5 Deposited 2025-05-27	Different oligomeric state Different ligand/ion	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain G 816–1253（438 aa） Chain H 816–1253（438 aa） Chain I 816–1253（438 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å

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

View Construct and Data Evidence

UniProt name	A0A0F6PP03_SFV
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–438； UniProt 816–1253 Author chain H； PDBConstruct 1–438； UniProt 816–1253 Author chain I； PDBConstruct 1–438； UniProt 816–1253

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	9rbq
Deposition date deposition_date	2025-05-27
Structure title title	Semliki Forest virus trimer 1 in complex with ApoER2 LA5
Keywords keywords	Semliki Forest virus, SFV, ApoER2 receptor, localized reconstruction, 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	61.34 Å
Radius of gyration Rg (electron density) rg_electron	60.90 Å
Forward intensity I(0) i0	1964590000.00
Molecular weight molecular_weight	364950.0 kDa
Excluded volume excluded_volume	453440 Å³
Envelope volume envelope_volume	755090 Å³
Hydration-shell volume shell_volume	103890 Å³
Envelope diameter envelope_diameter	190.5 Å
Shell Rg shell_rg	63.34 Å
Envelope Rg envelope_rg	58.79 Å
Shape Rg shape_rg	60.81 Å
Total Rg total_rg	61.25 Å
Total atoms total_atoms	25585
Residues n_residues	3267
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	191.7 Å
Rg (real space) rg_real	61.28 Å
Rg uncertainty (real space) rg_real_error	1.87 Å
I(0) (real space) i0_real	1.9650e+09
I(0) uncertainty (real space) i0_real_error	4.0710e+07
Rg (reciprocal space) rg_reciprocal	61.35 Å
I(0) (reciprocal space) i0_reciprocal	1965000000.0000
Solution quality estimate total_estimate	0.6150
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	66.3 Å
Skewness Skewness skewness	0.212
Kurtosis Kurtosis kurtosis	-0.613
Angular range angular_range	— – 0.1300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	76310000.0000
Real-space data points n_real_points	27
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 0.025; Positv: 1.000; Valcen: 0.996; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	LDL receptor related protein 8,Ig gamma-2A chain C region, A allele
Molecular weight formula_weight	33306.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	25585

GSADPACGPREFRCGGDGGGACIPERWVCDRQFDCEDRSDEAAELCGRPGPGATSAPAAGSLEVLFQGPPRGPTIKPCPPCKCPAPNLLGGPSVFIFPPKIKDVLMISLSPIVTCVVVDVSEDDPDVQISWFVNNVEVHTAQTQTHREDYNSTLRVVSALPIQHQDWMSGKEFKCKVNNKDLPAPIERTISKPKGSVRAPQVYVLPPPEEEMTKKQVTLTCMVTDFMPEDIYVEWTNNGKTELNYKNTEPVLDSDGSYFMYSKLRVEKKNWVERNSYSCSVVHEGLHNHHTTKSFSRTPGK

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Protein E3
Molecular weight formula_weight	7384.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

SAPLITAMCVLANATFPCFQPPCVPCCYENNAEATLRMLEDNVDRPGYYDLLQAALTCRNGTRHRR

来源 Source

来源生物 organism	Semliki Forest virus
NCBI Class编号 ncbi_taxonomy_id	11033
宿主生物 host_organism	Mesocricetus auratus

Entity 3 Entity 3 polymer

Description description	Structural polyprotein
Molecular weight formula_weight	47489.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

YEHSTVMPNVVGFPYKAHIERPGYSPLTLQMQVVETSLEPTLNLEYITCEYKTVVPSPYVKCCGASECSTKEKPDYQCKVYTGVYPFMWGGAYCFCDSENTQLSEAYVDRSDVCRHDHASAYKAHTASLKAKVRVMYGNVNQTVDVYVNGDHAVTIGGTQFIFGPLSSAWTPFDNKIVVYKDEVFNQDFPPYGSGQPGRFGDIQSRTVESNDLYANTALKLARPSPGMVHVPYTQTPSGFKYWLKEKGTALNTKAPFGCQIKTNPVRAMNCAVGNIPVSMNLPDSAFTRIVEAPTIIDLTCTVATCTHSSDFGGVLTLTYKTDKNGDCSVHSHSNVATLQEATAKVKTAGKVTLHFSTASASPSFVVSLCSARATCSASCEPPKDHIVPYAASHSNVVFPDMSGTALSWVQKISGGLGAFAIGAILVLVVVTCIGLRR

来源 Source

来源生物 organism	Semliki Forest virus
NCBI Class编号 ncbi_taxonomy_id	11033
宿主生物 host_organism	Mesocricetus auratus

Entity 4 Entity 4 polymer

Description description	Envelope glycoprotein E2
Molecular weight formula_weight	46870.3 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J,K,L

SVSQHFNVYKATRPYIAYCADCGAGHSCHSPVAIEAVRSEATDGMLKIQFSAQIGIDKSDNHDYTKIRYADGHAIENAVRSSLKVATSGDCFVHGTMGHFILAKCPPGEFLQVSIQDTRNAVRACRIQYHHDPQPVGREKFTIRPHYGKEIPCTTYQQTTAKTVEEIDMHMPPDTPDRTLLSQQSGNVKITVGGKKVKYNCTCGTGNVGTTNSDMTINTCLIEQCHVSVTDHKKWQFNSPFVPRADEPARKGKVHIPFPLDNITCRVPMAREPTVIHGKREVTLHLHPDHPTLFSYRTLGEDPQYHEEWVTAAVERTIPVPVDGMEYHWGNNDPVRLWSQLTTEGKPHGWPHQIVQYYYGLYPAATVSAVVGMSLLALISIFASCYMLVAARSKCLTPYALTPGAAVPWTLGILCCAPRAHA

来源 Source

来源生物 organism	Semliki Forest virus
NCBI Class编号 ncbi_taxonomy_id	11033
宿主生物 host_organism	Mesocricetus auratus

Entity 5 Entity 5 polymer

Description description	Capsid protein
Molecular weight formula_weight	29920.7 kDa
EC 编号 ec_number	3.4.21.90
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M,N,O

MNYIPTQTFYGRRWRPRPAARPWPLQATPVAPVVPDFQAQQMQQLISAVNALTMRQNAIAPARPPKPKKKKTTKPKPKTQPKKINGKTQQQKKKDKQADKKKKKPGKRERMCMKIENDCIFEVKHEGKVTGYACLVGDKVMKPAHVKGVIDNADLAKLAFKKSSKYDLECAQIPVHMRSDASKYTHEKPEGHYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLGGANEGSRTALSVVTWNKDMVTRVTPEGSEEW

来源 Source

来源生物 organism	Semliki Forest virus
NCBI Class编号 ncbi_taxonomy_id	11033
宿主生物 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)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	748.7 kDa
Source method src_method	man
Copy count entity_count	3

Entity 7 Entity 7 branched

Description description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	627.6 kDa
Source method src_method	man
Copy count entity_count	3

Entity 8 Entity 8 branched

Description description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	830.8 kDa
Source method src_method	man
Copy count entity_count	3

Entity 9 Entity 9 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

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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	2.70 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	2344552

fit	/app/data/saxs_computation/rb/9rbq/9rbq.fit
pddf	/app/data/pr_computation/rb/9rbq/9rbq.pr.out
profile	/app/data/saxs_computation/rb/9rbq/9rbq.dat

Semliki Forest virus trimer 1 in complex with ApoER2 LA5

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

LDL receptor related protein 8,Ig gamma-2A chain C region, A allele

State in the Current Structure

Other States of the Same Protein in the Database

LDL receptor related protein 8,Ig gamma-2A chain C region, A allele

State in the Current Structure

Other States of the Same Protein in the Database

Protein E3

State in the Current Structure

Other States of the Same Protein in the Database

Structural polyprotein

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 (9)

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 polymer

Polymer Polymer

来源 Source

Entity 6 Entity 6 branched

Entity 7 Entity 7 branched

Entity 8 Entity 8 branched

Entity 9 Entity 9 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)