SAXSdb — 9rbr

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

Protein E3

Semliki Forest 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 × 12 其他Polymer 9 PDB declaration: dodecameric（12） 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	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	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.

Other PDB	Difference from Current Entry 9RBR	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 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
9RBQ Semliki Forest virus trimer 1 in complex with ApoER2 LA5 Deposited 2025-05-27	Different oligomeric state Different ligand/ion	Assembly 1 Insufficient information Heteromer；Protein × 13 PDB declaration: 13-meric	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	CA CALCIUM ION × 1	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	1, 3, 4
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	Other combination Heteromer Protein × 12 其他Polymer 9 PDB declaration: dodecameric（12） Consistent with protein copy count	Chain G； UniProt 816–1253 Chain H； UniProt 816–1253 Chain I； UniProt 816–1253	Not recorded	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	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.

Other PDB	Difference from Current Entry 9RBR	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
9RBQ Semliki Forest virus trimer 1 in complex with ApoER2 LA5 Deposited 2025-05-27	Different oligomeric state Different ligand/ion	Assembly 1 Insufficient information Heteromer；Protein × 13 PDB declaration: 13-meric	Chain G 816–1253（438 aa） Chain H 816–1253（438 aa） Chain I 816–1253（438 aa）	Not recorded	CA CALCIUM ION × 1	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	2
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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9rbr
Deposition date deposition_date	2025-05-27
Structure title title	Semliki Forest virus trimer 2 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	61.09 Å
Radius of gyration Rg (electron density) rg_electron	60.70 Å
Forward intensity I(0) i0	1908520000.00
Molecular weight molecular_weight	360390.0 kDa
Excluded volume excluded_volume	448120 Å³
Envelope volume envelope_volume	750700 Å³
Hydration-shell volume shell_volume	103530 Å³
Envelope diameter envelope_diameter	192.5 Å
Shell Rg shell_rg	63.29 Å
Envelope Rg envelope_rg	58.69 Å
Shape Rg shape_rg	60.62 Å
Total Rg total_rg	61.05 Å
Total atoms total_atoms	25272
Residues n_residues	3225
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	191.5 Å
Rg (real space) rg_real	61.05 Å
Rg uncertainty (real space) rg_real_error	1.78 Å
I(0) (real space) i0_real	1.9090e+09
I(0) uncertainty (real space) i0_real_error	3.9430e+07
Rg (reciprocal space) rg_reciprocal	61.08 Å
I(0) (reciprocal space) i0_reciprocal	1909000000.0000
Solution quality estimate total_estimate	0.8462
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	66.3 Å
Skewness Skewness skewness	0.232
Kurtosis Kurtosis kurtosis	-0.592
Angular range angular_range	— – 0.1300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	73100000.0000
Real-space data points n_real_points	27
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.089

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 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
Atom count atom_count	25272

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 2 Entity 2 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 3 Entity 3 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 4 Entity 4 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 5 Entity 5 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 6 Entity 6 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 7 Entity 7 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

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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	611068

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

Semliki Forest virus trimer 2 in complex with ApoER2 LA5

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

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 (7)

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 branched

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)