8YW2 | pdb_00008yw2

Semliki Forest virus viron in complex with VLDLR

PDB DOI: https://doi.org/10.2210/pdb8YW2/pdb
EM Map EMD-39620: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Semliki Forest virus 4, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-03-29 Released: 2024-12-11
Deposition Author(s): Wang, J., Zheng, T., Yang, D.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structure of Semliki Forest virus in complex with VLDLR

Zheng, T.

To be published.

Macromolecule Content

Total Structure Weight: 1,927.32 kDa
Atom Count: 134,901
Modeled Residue Count: 17,266
Deposited Residue Count: 17,266
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein E3	A [auth 0] AA [auth M] BA [auth N] C [auth 2] GA [auth S] A [auth 0], AA [auth M], BA [auth N], C [auth 2], GA [auth S], HB [auth u], IB [auth v], JB [auth w], L [auth AA], M [auth AB], OA [auth a], PA [auth b], QA [auth c], UA [auth g], YA [auth l], Z [auth L]	52	Semliki Forest virus 4	Mutation(s): 0
UniProt
Find proteins for P03315 (Semliki forest virus) Explore P03315 Go to UniProtKB: P03315
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03315
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
capsid protein, partial	AB [auth n] B [auth 1] CA [auth O] D [auth 3] DA [auth P] AB [auth n], B [auth 1], CA [auth O], D [auth 3], DA [auth P], EA [auth Q], HA [auth T], KB [auth x], LB [auth y], N [auth AC], O [auth AD], P [auth AE], R [auth D], RA [auth d], SA [auth e], TA [auth f]	161	Semliki Forest virus 4	Mutation(s): 0
UniProt
Find proteins for P03315 (Semliki forest virus) Explore P03315 Go to UniProtKB: P03315
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03315
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein E1	BB [auth o] CB [auth p] DB [auth q] E [auth 4] F [auth 5] BB [auth o], CB [auth p], DB [auth q], E [auth 4], F [auth 5], G [auth 6], IA [auth U], JA [auth V], KA [auth W], S [auth E], T [auth F], U [auth G], V [auth H], VA [auth h], WA [auth i], ZA [auth m]	438	Semliki Forest virus 4	Mutation(s): 0
UniProt
Find proteins for P03315 (Semliki forest virus) Explore P03315 Go to UniProtKB: P03315
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03315
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain BB [auth o] Focus chain CB [auth p] Focus chain DB [auth q] Focus chain E [auth 4] Focus chain F [auth 5] Focus chain G [auth 6] Focus chain IA [auth U] Focus chain JA [auth V] Focus chain KA [auth W] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth G] Focus chain V [auth H] Focus chain VA [auth h] Focus chain WA [auth i] Focus chain ZA [auth m]
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein E2	EB [auth r] FA [auth R] FB [auth s] GB [auth t] H [auth 7] EB [auth r], FA [auth R], FB [auth s], GB [auth t], H [auth 7], I [auth 8], J [auth 9], LA [auth X], MA [auth Y], MB [auth z], NA [auth Z], Q [auth B], W [auth I], X [auth J], XA [auth j], Y [auth K]	418	Semliki Forest virus 4	Mutation(s): 0
UniProt
Find proteins for P03315 (Semliki forest virus) Explore P03315 Go to UniProtKB: P03315
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03315
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain EB [auth r] Focus chain FA [auth R] Focus chain FB [auth s] Focus chain GB [auth t] Focus chain H [auth 7] Focus chain I [auth 8] Focus chain J [auth 9] Focus chain LA [auth X] Focus chain MA [auth Y] Focus chain MB [auth z] Focus chain NA [auth Z] Focus chain Q [auth B] Focus chain W [auth I] Focus chain X [auth J] Focus chain XA [auth j] Focus chain Y [auth K]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Very low-density lipoprotein receptor	K [auth A]	162	Homo sapiens	Mutation(s): 0 Gene Names: VLDLR
UniProt & NIH Common Fund Data Resources
Find proteins for P98155 (Homo sapiens) Explore P98155 Go to UniProtKB: P98155
PHAROS: P98155 GTEx: ENSG00000147852
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P98155
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AC [auth MA], AD [auth mA], BC [auth NA], BD [auth nA], CC [auth OA], AC [auth MA], AD [auth mA], BC [auth NA], BD [auth nA], CC [auth OA], CD [auth oA], DC [auth PA], DD [auth pA], EC [auth QA], ED [auth qA], FC [auth RA], FD [auth rA], GC [auth SA], GD [auth sA], HC [auth TA], HD [auth tA], IC [auth UA], ID [auth uA], JC [auth VA], KC [auth WA], LC [auth XA], MC [auth YA], NB [auth C], NC [auth ZA], OB [auth k], OC [auth aA], PB [auth BA], PC [auth bA], QB [auth CA], QC [auth cA], RB [auth DA], RC [auth dA], SB [auth EA], SC [auth eA], TB [auth FA], TC [auth fA], UB [auth GA], UC [auth gA], VB [auth HA], VC [auth hA], WB [auth IA], WC [auth iA], XB [auth JA], XC [auth jA], YB [auth KA], YC [auth kA], ZB [auth LA], ZC [auth lA]	3		N-Glycosylation	Interactions Focus chain AC [auth MA] Focus chain AD [auth mA] Focus chain BC [auth NA] Focus chain BD [auth nA] Focus chain CC [auth OA] Focus chain CD [auth oA] Focus chain DC [auth PA] Focus chain DD [auth pA] Focus chain EC [auth QA] Focus chain ED [auth qA] Focus chain FC [auth RA] Focus chain FD [auth rA] Focus chain GC [auth SA] Focus chain GD [auth sA] Focus chain HC [auth TA] Focus chain HD [auth tA] Focus chain IC [auth UA] Focus chain ID [auth uA] Focus chain JC [auth VA] Focus chain KC [auth WA] Focus chain LC [auth XA] Focus chain MC [auth YA] Focus chain NB [auth C] Focus chain NC [auth ZA] Focus chain OB [auth k] Focus chain OC [auth aA] Focus chain PB [auth BA] Focus chain PC [auth bA] Focus chain QB [auth CA] Focus chain QC [auth cA] Focus chain RB [auth DA] Focus chain RC [auth dA] Focus chain SB [auth EA] Focus chain SC [auth eA] Focus chain TB [auth FA] Focus chain TC [auth fA] Focus chain UB [auth GA] Focus chain UC [auth gA] Focus chain VB [auth HA] Focus chain VC [auth hA] Focus chain WB [auth IA] Focus chain WC [auth iA] Focus chain XB [auth JA] Focus chain XC [auth jA] Focus chain YB [auth KA] Focus chain YC [auth kA] Focus chain ZB [auth LA] Focus chain ZC [auth lA] Interactions & Density Focus chain AC [auth MA] Focus chain AD [auth mA] Focus chain BC [auth NA] Focus chain BD [auth nA] Focus chain CC [auth OA] Focus chain CD [auth oA] Focus chain DC [auth PA] Focus chain DD [auth pA] Focus chain EC [auth QA] Focus chain ED [auth qA] Focus chain FC [auth RA] Focus chain FD [auth rA] Focus chain GC [auth SA] Focus chain GD [auth sA] Focus chain HC [auth TA] Focus chain HD [auth tA] Focus chain IC [auth UA] Focus chain ID [auth uA] Focus chain JC [auth VA] Focus chain KC [auth WA] Focus chain LC [auth XA] Focus chain MC [auth YA] Focus chain NB [auth C] Focus chain NC [auth ZA] Focus chain OB [auth k] Focus chain OC [auth aA] Focus chain PB [auth BA] Focus chain PC [auth bA] Focus chain QB [auth CA] Focus chain QC [auth cA] Focus chain RB [auth DA] Focus chain RC [auth dA] Focus chain SB [auth EA] Focus chain SC [auth eA] Focus chain TB [auth FA] Focus chain TC [auth fA] Focus chain UB [auth GA] Focus chain UC [auth gA] Focus chain VB [auth HA] Focus chain VC [auth hA] Focus chain WB [auth IA] Focus chain WC [auth iA] Focus chain XB [auth JA] Focus chain XC [auth jA] Focus chain YB [auth KA] Focus chain YC [auth kA] Focus chain ZB [auth LA] Focus chain ZC [auth lA]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE