SAXSdb — 8yw2

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

Spike glycoprotein E3

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 65 其他Polymer 48	Very low-density lipoprotein receptor × 1 （P98155） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 48	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	1, 2, 3, 4
Chains and sequence ranges	Author chain 0； PDBConstruct 1–52； UniProt 275–326 Author chain 2； PDBConstruct 1–52； UniProt 275–326 Author chain AA； PDBConstruct 1–52； UniProt 275–326 Author chain AB； PDBConstruct 1–52； UniProt 275–326 Author chain L； PDBConstruct 1–52； UniProt 275–326 Author chain M； PDBConstruct 1–52； UniProt 275–326 Author chain N； PDBConstruct 1–52； UniProt 275–326 Author chain S； PDBConstruct 1–52； UniProt 275–326 Author chain a； PDBConstruct 1–52； UniProt 275–326 Author chain b； PDBConstruct 1–52； UniProt 275–326 Author chain c； PDBConstruct 1–52； UniProt 275–326 Author chain g； PDBConstruct 1–52； UniProt 275–326 Author chain l； PDBConstruct 1–52； UniProt 275–326 Author chain u； PDBConstruct 1–52； UniProt 275–326 Author chain v； PDBConstruct 1–52； UniProt 275–326 Author chain w； PDBConstruct 1–52； UniProt 275–326 Author chain 1； PDBConstruct 1–161； UniProt 107–267 Author chain 3； PDBConstruct 1–161； UniProt 107–267 Author chain AC； PDBConstruct 1–161； UniProt 107–267 Author chain AD； PDBConstruct 1–161； UniProt 107–267 Author chain AE； PDBConstruct 1–161； UniProt 107–267 Author chain D； PDBConstruct 1–161； UniProt 107–267 Author chain O； PDBConstruct 1–161； UniProt 107–267 Author chain P； PDBConstruct 1–161； UniProt 107–267 Author chain Q； PDBConstruct 1–161； UniProt 107–267 Author chain T； PDBConstruct 1–161； UniProt 107–267 Author chain d； PDBConstruct 1–161； UniProt 107–267 Author chain e； PDBConstruct 1–161； UniProt 107–267 Author chain f； PDBConstruct 1–161； UniProt 107–267 Author chain n； PDBConstruct 1–161； UniProt 107–267 Author chain x； PDBConstruct 1–161； UniProt 107–267 Author chain y； PDBConstruct 1–161； UniProt 107–267 Author chain 4； PDBConstruct 1–438； UniProt 816–1253 Author chain 5； PDBConstruct 1–438； UniProt 816–1253 Author chain 6； PDBConstruct 1–438； UniProt 816–1253 Author chain E； PDBConstruct 1–438； UniProt 816–1253 Author chain F； PDBConstruct 1–438； UniProt 816–1253 Author chain G； PDBConstruct 1–438； UniProt 816–1253 Author chain H； PDBConstruct 1–438； UniProt 816–1253 Author chain U； PDBConstruct 1–438； UniProt 816–1253 Author chain V； PDBConstruct 1–438； UniProt 816–1253 Author chain W； PDBConstruct 1–438； UniProt 816–1253 Author chain h； PDBConstruct 1–438； UniProt 816–1253 Author chain i； PDBConstruct 1–438； UniProt 816–1253 Author chain m； PDBConstruct 1–438； UniProt 816–1253 Author chain o； PDBConstruct 1–438； UniProt 816–1253 Author chain p； PDBConstruct 1–438； UniProt 816–1253 Author chain q； PDBConstruct 1–438； UniProt 816–1253 Author chain 7； PDBConstruct 1–418； UniProt 338–755 Author chain 8； PDBConstruct 1–418； UniProt 338–755 Author chain 9； PDBConstruct 1–418； UniProt 338–755 Author chain B； PDBConstruct 1–418； UniProt 338–755 Author chain I； PDBConstruct 1–418； UniProt 338–755 Author chain J； PDBConstruct 1–418； UniProt 338–755 Author chain K； PDBConstruct 1–418； UniProt 338–755 Author chain R； PDBConstruct 1–418； UniProt 338–755 Author chain X； PDBConstruct 1–418； UniProt 338–755 Author chain Y； PDBConstruct 1–418； UniProt 338–755 Author chain Z； PDBConstruct 1–418； UniProt 338–755 Author chain j； PDBConstruct 1–418； UniProt 338–755 Author chain r； PDBConstruct 1–418； UniProt 338–755 Author chain s； PDBConstruct 1–418； UniProt 338–755 Author chain t； PDBConstruct 1–418； UniProt 338–755 Author chain z； PDBConstruct 1–418； UniProt 338–755

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 65 其他Polymer 48	Spike glycoprotein E3 × 16 （A0A0E3T652） capsid protein, partial × 16 （A0A0E3T652） Spike glycoprotein E1 × 16 （A0A0E3T652） Spike glycoprotein E2 × 16 （A0A0E3T652） beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 48	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 A； PDBConstruct 1–162； UniProt 70–231

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	8yw2
Deposition date deposition_date	2024-03-29
Structure title title	Semliki Forest virus viron in complex with VLDLR
Keywords keywords	Semliki Forest virus viron, VLDLR, 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.

8yw2__assembly_1__model_1

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

Download this curve (.dat)

8yw2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8yw2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	0.00 Å
Rg (electron density)	109.90 Å
Total Rg	110.10 Å
Atom count	134901
Residues	17266
Excluded volume	2391200 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8yw2__assembly_1__model_1`	65-meric （65）	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 (6)

Entity 1 Entity 1 polymer

Description description	Spike glycoprotein E3
Molecular weight formula_weight	5848.7 kDa
Source method src_method	nat
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	0,2,AA,AB,L,M,N,S,a,b,c,g,l,u,v,w
Atom count atom_count	134901

MCVLANATFPCFQPPCVPCCYENNAEATLRMLEDNVDRPGYYDLLQAALTCR

Entity 2 Entity 2 polymer

Description description	capsid protein, partial
Molecular weight formula_weight	17791.3 kDa
Source method src_method	nat
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1,3,AC,AD,AE,D,O,P,Q,T,d,e,f,n,x,y

KRERMCMKIENDCIFEVKHEGKVTGYACLVGDKVMKPAHVKGVIDNADLAKLAFKKSSKYDLECAQIPVHMRSDASKYTHEKPEGHYNWHHGAVQYSGGRFTIPTGAGKPGDSGRPIFDNKGRVVAIVLGGANEGSRTALSVVTWNKDMVTRVTPEGSEEW

Entity 3 Entity 3 polymer

Description description	Spike glycoprotein E1
Molecular weight formula_weight	47489.8 kDa
Source method src_method	nat
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	4,5,6,E,F,G,H,U,V,W,h,i,m,o,p,q

YEHSTVMPNVVGFPYKAHIERPGYSPLTLQMQVVETSLEPTLNLEYITCEYKTVVPSPYVKCCGASECSTKEKPDYQCKVYTGVYPFMWGGAYCFCDSENTQLSEAYVDRSDVCRHDHASAYKAHTASLKAKVRVMYGNVNQTVDVYVNGDHAVTIGGTQFIFGPLSSAWTPFDNKIVVYKDEVFNQDFPPYGSGQPGRFGDIQSRTVESNDLYANTALKLARPSPGMVHVPYTQTPSGFKYWLKEKGTALNTKAPFGCQIKTNPVRAMNCAVGNIPVSMNLPDSAFTRIVEAPTIIDLTCTVATCTHSSDFGGVLTLTYKTDKNGDCSVHSHSNVATLQEATAKVKTAGKVTLHFSTASASPSFVVSLCSARATCSASCEPPKDHIVPYAASHSNVVFPDMSGTALSWVQKISGGLGAFAIGAILVLVVVTCIGLRR

Entity 4 Entity 4 polymer

Description description	Spike glycoprotein E2
Molecular weight formula_weight	46468.9 kDa
Source method src_method	nat
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	7,8,9,B,I,J,K,R,X,Y,Z,j,r,s,t,z

HFNVYKATRPYIAYCADCGAGHSCHSPVAIEAVRSEATDGMLKIQFSAQIGIDKSDNHDYTKIRYADGHAIENAVRSSLKVATSGDCFVHGTMGHFILAKCPPGEFLQVSIQDTRNAVRACRIQYHHDPQPVGREKFTIRPHYGKEIPCTTYQQTTAKTVEEIDMHMPPDTPDRTLLSQQSGNVKITVGGKKVKYNCTCGTGNVGTTNSDMTINTCLIEQCHVSVTDHKKWQFNSPFVPRADEPARKGKVHIPFPLDNITCRVPMAREPTVIHGKREVTLHLHPDHPTLFSYRTLGEDPQYHEEWVTAAVERTIPVPVDGMEYHWGNNDPVRLWSQLTTEGKPHGWPHQIVQYYYGLYPAATVSAVVGMSLLALISIFASCYMLVAARSKCLTPYALTPGAAVPWTLGILCCAPRAHA

Entity 5 Entity 5 polymer

Description description	Very low-density lipoprotein receptor
Molecular weight formula_weight	17585.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

KTCAESDFVCNNGQCVPSRWKCDGDPDCEDGSDESPEQCHMRTCRIHEISCGAHSTQCIPVSWRCDGENDCDSGEDEENCGNITCSPDEFTCSSGRCISRNFVCNGQDDCSDGSDELDCAPPTCGAHEFQCSTSSCIPISWVCDDDADCSDQSDESLEQCGR

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	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	man
Copy count entity_count	48

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Resolution resolution	3.70 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	33471

Semliki Forest virus viron in complex with VLDLR

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

Spike glycoprotein E3

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

8yw2__assembly_1__model_1

8yw2__assembly_1__model_1 | I(q)

8yw2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 branched

7. Citations (1)

Semliki Forest virus viron in complex with VLDLR

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

Spike glycoprotein 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

8yw2__assembly_1__model_1

8yw2__assembly_1__model_1 | I(q)

8yw2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 branched

7. Citations (1)