8ua8

Structure of Semliki Forest virus VLP in complex with VLDLR LA2

Method: ELECTRON MICROSCOPY

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

Glycoprotein E1

Semliki Forest virus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 17 其他Polymer 12	Glycoprotein E2 × 4 （A0A0E3T652） Assembly protein E3 × 4 （P03315） Capsid protein × 4 （P03315） Very low-density lipoprotein receptor × 1 （P98155） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CALCIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0F6PP03_SFV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–438； UniProt 816–1253 Author chain E； PDBConstruct 1–438； UniProt 816–1253 Author chain I； PDBConstruct 1–438； UniProt 816–1253 Author chain M； PDBConstruct 1–438； UniProt 816–1253

Glycoprotein E2

Semliki Forest virus

UniProt A0A0E3T652

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 17 其他Polymer 12	Glycoprotein E1 × 4 （A0A0F6PP03） Assembly protein E3 × 4 （P03315） Capsid protein × 4 （P03315） Very low-density lipoprotein receptor × 1 （P98155） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CALCIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A0E3T652_SFV
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–417； UniProt 339–755 Author chain F； PDBConstruct 1–417； UniProt 339–755 Author chain J； PDBConstruct 1–417； UniProt 339–755 Author chain N； PDBConstruct 1–417； UniProt 339–755

Assembly protein E3

Semliki Forest virus

UniProt P03315

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 17 其他Polymer 12	Glycoprotein E1 × 4 （A0A0F6PP03） Glycoprotein E2 × 4 （A0A0E3T652） Very low-density lipoprotein receptor × 1 （P98155） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CALCIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POLS_SFV
Isoform	—
PDB entities	3, 4
Chains and sequence ranges	Author chain C； PDBConstruct 1–54； UniProt 273–326 Author chain G； PDBConstruct 1–54； UniProt 273–326 Author chain K； PDBConstruct 1–54； UniProt 273–326 Author chain O； PDBConstruct 1–54； UniProt 273–326 Author chain D； PDBConstruct 1–153； UniProt 115–267 Author chain H； PDBConstruct 1–153； UniProt 115–267 Author chain L； PDBConstruct 1–153； UniProt 115–267 Author chain P； PDBConstruct 1–153； UniProt 115–267

Very low-density lipoprotein receptor

Homo sapiens

UniProt P98155

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 17 其他Polymer 12	Glycoprotein E1 × 4 （A0A0F6PP03） Glycoprotein E2 × 4 （A0A0E3T652） Assembly protein E3 × 4 （P03315） Capsid protein × 4 （P03315） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 6 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CALCIUM ION × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VLDLR_HUMAN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain R； PDBConstruct 1–37； UniProt 72–108

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	8ua8
Deposition date deposition_date	2023-09-20
Structure title title	Structure of Semliki Forest virus VLP in complex with VLDLR LA2
Keywords keywords	Semliki Forest Virus, Receptor, VIRUS LIKE PARTICLE; VIRUS LIKE PARTICLE
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

8ua8__assembly_1__model_1

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

Download this curve (.dat)

8ua8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8ua8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	66.02 Å
Rg (electron density)	65.38 Å
Total Rg	65.61 Å
Atom count	33212
Residues	4267
Excluded volume	588670 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8ua8__assembly_1__model_1`	heptadecameric （17）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Glycoprotein E1
Molecular weight formula_weight	47489.8 kDa
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	33212

YEHSTVMPNVVGFPYKAHIERPGYSPLTLQMQVVETSLEPTLNLEYITCEYKTVVPSPYVKCCGASECSTKEKPDYQCKVYTGVYPFMWGGAYCFCDSENTQLSEAYVDRSDVCRHDHASAYKAHTASLKAKVRVMYGNVNQTVDVYVNGDHAVTIGGTQFIFGPLSSAWTPFDNKIVVYKDEVFNQDFPPYGSGQPGRFGDIQSRTVESNDLYANTALKLARPSPGMVHVPYTQTPSGFKYWLKEKGTALNTKAPFGCQIKTNPVRAMNCAVGNIPVSMNLPDSAFTRIVEAPTIIDLTCTVATCTHSSDFGGVLTLTYKTDKNGDCSVHSHSNVATLQEATAKVKTAGKVTLHFSTASASPSFVVSLCSARATCSASCEPPKDHIVPYAASHSNVVFPDMSGTALSWVQKISGGLGAFAIGAILVLVVVTCIGLRR

Source Source

Source organism organism	Semliki Forest virus
NCBI taxonomy ID ncbi_taxonomy_id	11033
Host organism host_organism	Homo sapiens

Entity 2 Entity 2 polymer

Description description	Glycoprotein E2
Molecular weight formula_weight	46330.7 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

FNVYKATRPYIAYCADCGAGHSCHSPVAIEAVRSEATDGMLKIQFSAQIGIDKSDNHDYTKIRYADGHAIENAVRSSLKVATSGDCFVHGTMGHFILAKCPPGEFLQVSIQDTRNAVRACRIQYHHDPQPVGREKFTIRPHYGKEIPCTTYQQTTAKTVEEIDMHMPPDTPDRTLLSQQSGNVKITVGGKKVKYNCTCGTGNVGTTNSDMTINTCLIEQCHVSVTDHKKWQFNSPFVPRADEPARKGKVHIPFPLDNITCRVPMAREPTVIHGKREVTLHLHPDHPTLFSYRTLGEDPQYHEEWVTAAVERTIPVPVDGMEYHWGNNDPVRLWSQLTTEGKPHGWPHQIVQYYYGLYPAATVSAVVGMSLLALISIFASCYMLVAARSKCLTPYALTPGAAVPWTLGILCCAPRAHA

Source Source

Source organism organism	Semliki Forest virus
NCBI taxonomy ID ncbi_taxonomy_id	11033
Host organism host_organism	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Assembly protein E3
Molecular weight formula_weight	6020.9 kDa
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

TAMCVLANATFPCFQPPCVPCCYENNAEATLRMLEDNVDRPGYYDLLQAALTCR

Source Source

Source organism organism	Semliki Forest virus
NCBI taxonomy ID ncbi_taxonomy_id	11033
Host organism host_organism	Homo sapiens

Entity 4 Entity 4 polymer

Description description	Capsid protein
Molecular weight formula_weight	16723.9 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	D,H,L,P

IENDCIFEVKHEGKVTGYACLVGDKVMKPAHVKGVIDNADLAKLAFKKSSKYDLECAQIPVHMRSDASKYTHEKPEGHYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLGGANEGSRTALSVVTWNKDMVTRVTPEGSEEW

Source Source

Source organism organism	Semliki Forest virus
NCBI taxonomy ID ncbi_taxonomy_id	11033
Host organism host_organism	Homo sapiens

Entity 5 Entity 5 polymer

Description description	Very low-density lipoprotein receptor
Molecular weight formula_weight	4028.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	R

CAESDFVCNNGQCVPSRWKCDGDPDCEDGSDESPEQC

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Homo sapiens

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	6

Entity 7 Entity 7 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	syn
Copy count entity_count	6

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	2

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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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	3.70 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	439486

Structure of Semliki Forest virus VLP in complex with VLDLR LA2

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

Glycoprotein E1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Glycoprotein E2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Assembly protein E3

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Very low-density lipoprotein receptor

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8ua8__assembly_1__model_1

8ua8__assembly_1__model_1 | I(q)

8ua8__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 branched

Entity 7 Entity 7 branched

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

7. Citations (1)