9NAI | pdb_00009nai

LuIII VLP - Glycan [s(Lex)2]

PDB DOI: https://doi.org/10.2210/pdb9NAI/pdb
EM Map EMD-49195: EMDB EMDataResource

Classification: VIRUS
Organism(s): LuIII virus
Expression System: Baculoviridae sp.
Mutation(s): No

Deposited: 2025-02-12 Released: 2025-03-19
Deposition Author(s): Busuttil, K.B., Bennett, A.B.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.88 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9NAI

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

Literature

Mapping the Sialic Acid Binding Sites of LuIII and H-1 Parvovirus

Busuttil, K.B., Bennett, A.B.

To be published.

Macromolecule Content

Total Structure Weight: 3,774.86 kDa
Atom Count: 266,820
Modeled Residue Count: 33,060
Deposited Residue Count: 33,060
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	A AA [auth a] AB [auth 1] B BA [auth b] A, AA [auth a], AB [auth 1], B, BA [auth b], BB [auth 2], C, CA [auth c], CB [auth 3], D, DA [auth d], DB [auth 4], E, EA [auth e], EB [auth 5], F, FA [auth f], FB [auth 6], G, GA [auth g], GB [auth 7], H, HA [auth h], HB [auth 8], I, IA [auth i], J, JA [auth j], K, KA [auth k], L, LA [auth l], M, MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, QA [auth q], R, RA [auth r], S, SA [auth s], T, TA [auth t], U, UA [auth u], V, VA [auth v], W, WA [auth w], X, XA [auth x], Y, YA [auth y], Z, ZA [auth z]	551	LuIII virus	Mutation(s): 0
UniProt
Find proteins for P36310 (Parvovirus LuIII) Explore P36310 Go to UniProtKB: P36310
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P36310
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	AC [auth 0A], AD [auth GC], BC [auth 3A], BD [auth JC], CC [auth 6A], AC [auth 0A], AD [auth GC], BC [auth 3A], BD [auth JC], CC [auth 6A], CD [auth MC], DC [auth 9A], DD [auth PC], EC [auth CB], ED [auth SC], FC [auth FB], FD [auth VC], GC [auth IB], GD [auth YC], HC [auth LB], HD [auth bC], IB [auth 0], IC [auth OB], ID [auth eC], JB [auth BA], JC [auth RB], JD [auth hC], KB [auth EA], KC [auth UB], KD [auth kC], LB [auth HA], LC [auth XB], LD [auth nC], MB [auth KA], MC [auth aB], MD [auth qC], NB [auth NA], NC [auth dB], ND [auth tC], OB [auth QA], OC [auth gB], OD [auth wC], PB [auth TA], PC [auth jB], PD [auth zC], QB [auth WA], QC [auth mB], RB [auth ZA], RC [auth pB], SB [auth cA], SC [auth sB], TB [auth fA], TC [auth vB], UB [auth iA], UC [auth yB], VB [auth lA], VC [auth 1B], WB [auth oA], WC [auth 4B], XB [auth rA], XC [auth 7B], YB [auth uA], YC [auth AC], ZB [auth xA], ZC [auth DC]	3		N/A	Interactions Focus chain AC [auth 0A] Focus chain AD [auth GC] Focus chain BC [auth 3A] Focus chain BD [auth JC] Focus chain CC [auth 6A] Focus chain CD [auth MC] Focus chain DC [auth 9A] Focus chain DD [auth PC] Focus chain EC [auth CB] Focus chain ED [auth SC] Focus chain FC [auth FB] Focus chain FD [auth VC] Focus chain GC [auth IB] Focus chain GD [auth YC] Focus chain HC [auth LB] Focus chain HD [auth bC] Focus chain IB [auth 0] Focus chain IC [auth OB] Focus chain ID [auth eC] Focus chain JB [auth BA] Focus chain JC [auth RB] Focus chain JD [auth hC] Focus chain KB [auth EA] Focus chain KC [auth UB] Focus chain KD [auth kC] Focus chain LB [auth HA] Focus chain LC [auth XB] Focus chain LD [auth nC] Focus chain MB [auth KA] Focus chain MC [auth aB] Focus chain MD [auth qC] Focus chain NB [auth NA] Focus chain NC [auth dB] Focus chain ND [auth tC] Focus chain OB [auth QA] Focus chain OC [auth gB] Focus chain OD [auth wC] Focus chain PB [auth TA] Focus chain PC [auth jB] Focus chain PD [auth zC] Focus chain QB [auth WA] Focus chain QC [auth mB] Focus chain RB [auth ZA] Focus chain RC [auth pB] Focus chain SB [auth cA] Focus chain SC [auth sB] Focus chain TB [auth fA] Focus chain TC [auth vB] Focus chain UB [auth iA] Focus chain UC [auth yB] Focus chain VB [auth lA] Focus chain VC [auth 1B] Focus chain WB [auth oA] Focus chain WC [auth 4B] Focus chain XB [auth rA] Focus chain XC [auth 7B] Focus chain YB [auth uA] Focus chain YC [auth AC] Focus chain ZB [auth xA] Focus chain ZC [auth DC] Interactions & Density Focus chain AC [auth 0A] Focus chain AD [auth GC] Focus chain BC [auth 3A] Focus chain BD [auth JC] Focus chain CC [auth 6A] Focus chain CD [auth MC] Focus chain DC [auth 9A] Focus chain DD [auth PC] Focus chain EC [auth CB] Focus chain ED [auth SC] Focus chain FC [auth FB] Focus chain FD [auth VC] Focus chain GC [auth IB] Focus chain GD [auth YC] Focus chain HC [auth LB] Focus chain HD [auth bC] Focus chain IB [auth 0] Focus chain IC [auth OB] Focus chain ID [auth eC] Focus chain JB [auth BA] Focus chain JC [auth RB] Focus chain JD [auth hC] Focus chain KB [auth EA] Focus chain KC [auth UB] Focus chain KD [auth kC] Focus chain LB [auth HA] Focus chain LC [auth XB] Focus chain LD [auth nC] Focus chain MB [auth KA] Focus chain MC [auth aB] Focus chain MD [auth qC] Focus chain NB [auth NA] Focus chain NC [auth dB] Focus chain ND [auth tC] Focus chain OB [auth QA] Focus chain OC [auth gB] Focus chain OD [auth wC] Focus chain PB [auth TA] Focus chain PC [auth jB] Focus chain PD [auth zC] Focus chain QB [auth WA] Focus chain QC [auth mB] Focus chain RB [auth ZA] Focus chain RC [auth pB] Focus chain SB [auth cA] Focus chain SC [auth sB] Focus chain TB [auth fA] Focus chain TC [auth vB] Focus chain UB [auth iA] Focus chain UC [auth yB] Focus chain VB [auth lA] Focus chain VC [auth 1B] Focus chain WB [auth oA] Focus chain WC [auth 4B] Focus chain XB [auth rA] Focus chain XC [auth 7B] Focus chain YB [auth uA] Focus chain YC [auth AC] Focus chain ZB [auth xA] Focus chain ZC [auth DC]
Glycosylation Resources
GlyTouCan: G00065MO GlyCosmos: G00065MO GlyGen: G00065MO

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.88 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.10-2155_2155

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-03-19

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM082946

Revision History (Full details and data files)

Version 1.0: 2025-03-19
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.