8x0k

Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(2-fold)

Method: ELECTRON MICROSCOPY

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

Capsid protein

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 16 其他Polymer 8	Spike glycoprotein E2 × 4 （A0A0E3T652） Spike glycoprotein E1 × 4 （A0A0F6PP03） Very low-density lipoprotein receptor × 4 （P98155） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CALCIUM ION × 4	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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–162； UniProt 106–267 Author chain E； PDBConstruct 1–162； UniProt 106–267 Author chain I； PDBConstruct 1–162； UniProt 106–267 Author chain M； PDBConstruct 1–162； UniProt 106–267

Spike 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 16 其他Polymer 8	Capsid protein × 4 （P03315） Spike glycoprotein E1 × 4 （A0A0F6PP03） Very low-density lipoprotein receptor × 4 （P98155） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CALCIUM ION × 4	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 1–418； UniProt 334–751 Author chain F； PDBConstruct 1–418； UniProt 334–751 Author chain J； PDBConstruct 1–418； UniProt 334–751 Author chain N； PDBConstruct 1–418； UniProt 334–751

Spike glycoprotein E1

Semliki Forest virus

UniProt A0A0F6PP03

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 16 其他Polymer 8	Capsid protein × 4 （P03315） Spike glycoprotein E2 × 4 （A0A0E3T652） Very low-density lipoprotein receptor × 4 （P98155） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CALCIUM ION × 4	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	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–438； UniProt 816–1253 Author chain G； PDBConstruct 1–438； UniProt 816–1253 Author chain K； PDBConstruct 1–438； UniProt 816–1253 Author chain O； PDBConstruct 1–438； UniProt 816–1253

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 16 其他Polymer 8	Capsid protein × 4 （P03315） Spike glycoprotein E2 × 4 （A0A0E3T652） Spike glycoprotein E1 × 4 （A0A0F6PP03） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 8 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CALCIUM ION × 4	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	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–37； UniProt 113–149 Author chain H； PDBConstruct 1–37； UniProt 113–149 Author chain L； PDBConstruct 1–37； UniProt 113–149 Author chain P； PDBConstruct 1–37； UniProt 113–149

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8x0k
Deposition date deposition_date	2023-11-04
Structure title title	Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(2-fold)
Keywords keywords	VIRAL PROTEIN; VIRAL PROTEIN
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.

8x0k__assembly_1__model_1

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

Download this curve (.dat)

8x0k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8x0k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	68.42 Å
Rg (electron density)	67.79 Å
Total Rg	68.12 Å
Atom count	32740
Residues	4220
Excluded volume	579560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8x0k__assembly_1__model_1`	16-meric （16）	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 (7)

Entity 1 Entity 1 polymer

Description description	Capsid protein
Molecular weight formula_weight	17848.3 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	32740

GKRERMCMKIENDCIFEVKHEGKVTGYACLVGDKVMKPAHVKGVIDNADLAKLAFKKSSKYDLECAQIPVHMRSDASKYTHEKPEGHYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLGGANEGSRTALSVVTWNKDMVTRVTPEGSEEW

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	Spike glycoprotein E2
Molecular weight formula_weight	46432.8 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

SVSQHFNVYKATRPYIAYCADCGAGHSCHSPVAIEAVRSEATDGMLKIQFSAQIGIDKSDNHDYTKIRYADGHAIENAVRSSLKVATSGDCFVHGTMGHFILAKCPPGEFLQVSIQDTRNAVRACRIQYHHDPQPVGREKFTIRPHYGKEIPCTTYQQTTAKTVEEIDMHMPPDTPDRTLLSQQSGNVKITVGGKKVKYNCTCGTGNVGTTNSDMTINTCLIEQCHVSVTDHKKWQFNSPFVPRADEPARKGKVHIPFPLDNITCRVPMAREPTVIHGKREVTLHLHPDHPTLFSYRTLGEDPQYHEEWVTAAVERTIPVPVDGMEYHWGNNDPVRLWSQLTTEGKPHGWPHQIVQYYYGLYPAATVSAVVGMSLLALISIFASCYMLVAARSKCLTPYALTPGAAVPWTLGILCCAP

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	Spike 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	C,G,K,O

YEHSTVMPNVVGFPYKAHIERPGYSPLTLQMQVVETSLEPTLNLEYITCEYKTVVPSPYVKCCGASECSTKEKPDYQCKVYTGVYPFMWGGAYCFCDSENTQLSEAYVDRSDVCRHDHASAYKAHTASLKAKVRVMYGNVNQTVDVYVNGDHAVTIGGTQFIFGPLSSAWTPFDNKIVVYKDEVFNQDFPPYGSGQPGRFGDIQSRTVESNDLYANTALKLARPSPGMVHVPYTQTPSGFKYWLKEKGTALNTKAPFGCQIKTNPVRAMNCAVGNIPVSMNLPDSAFTRIVEAPTIIDLTCTVATCTHSSDFGGVLTLTYKTDKNGDCSVHSHSNVATLQEATAKVKTAGKVTLHFSTASASPSFVVSLCSARATCSASCEPPKDHIVPYAASHSNVVFPDMSGTALSWVQKISGGLGAFAIGAILVLVVVTCIGLRR

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	Very low-density lipoprotein receptor
Molecular weight formula_weight	4103.4 kDa
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

CRIHEISCGAHSTQCIPVSWRCDGENDCDSGEDEENC

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 5 Entity 5 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	man
Copy count entity_count	8

Entity 6 Entity 6 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

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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	3.50 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	787942

Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(2-fold)

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

Capsid protein

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

Spike glycoprotein E1

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8x0k__assembly_1__model_1

8x0k__assembly_1__model_1 | I(q)

8x0k__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 (7)

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 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)

Cryo-EM structure of Semliki Forest virus in complex with its receptor VLDLR(2-fold)

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

Capsid protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Spike 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

Spike 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

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

8x0k__assembly_1__model_1

8x0k__assembly_1__model_1 | I(q)

8x0k__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 (7)

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 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

7. Citations (1)