Capsid protein - Norwalk virus

Preferred order of sections

Names and origin

Protein names	Submitted name: Capsid protein EMBL AAT12445.1
Organism	Norwalk virus EMBL AAT12445.1
Taxonomic identifier	11983 [NCBI]
Taxonomic lineage	Viruses › ssRNA viruses › ssRNA positive-strand viruses, no DNA stage › Caliciviridae › Norovirus

Protein attributes

Sequence length	548 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

Ontologies

Keywords
Technical term	3D-structure PDB 3Q6R PDB 3PA2 PDB 3Q6Q PDB 3Q38 PDB 3PA1 PDB 3Q39 PDB 3ONU PDB 3Q3A PDB 3ONY PDB 3RY8 PDB 3V7A
Gene Ontology (GO)
None. [Check GOA]

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Regions

Region

355 – 356

2

Fucose binding PDB 3PA2 PDB 3Q38 PDB 3PA1 PDB 3Q39 PDB 3ONY

Region

400 – 401

2

N-acetyl-D-glucosamine binding PDB 3PA2

Region

451 – 452

2

Fucose binding PDB 3PA2 PDB 3Q38 PDB 3PA1 PDB 3Q39 PDB 3ONY

Sites

Binding site

299

1

Galactose

Binding site

381

1

Fucose PDB 3PA2

Binding site

382

1

N-acetyl-D-glucosamine

Binding site

385

1

Fucose PDB 3PA2 PDB 3Q38 PDB 3PA1 PDB 3Q39 PDB 3ONY

Binding site

449

1

N-acetyl-D-glucosamine; via carbonyl oxygen

Sequences

Sequence

Length

Mass (Da)

Tools

Q5F4T5 [UniParc].

Last modified March 15, 2005. Version 1.
Checksum: FDB134B87D09A39B
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FASTA

548

59,900

        10         20         30         40         50         60 
MKMASNDAAP SNDGAAGLVP ESNNEVMALE PVAGASLAAP VTGQTNIIDP WIRMNFVQAP 

        70         80         90        100        110        120 
NGEFTVSPRN SPGEVLLNLE LGPELNPYLA HLSRMYNGYA GGMEVQIMLA GNAFTAGKLI 

       130        140        150        160        170        180 
FAAVPPHFPI ENLSPPQITM FPHVIIDVRT LEPVLLPMPD IRNSFFHFIQ RDEPKMRLVA 

       190        200        210        220        230        240 
MLYTPLRSNG SGDDVFTVSC RVLTRPTPDF DFTYLVPPTV ESKSKPFTLP ILTLGELTNS 

       250        260        270        280        290        300 
RFPLPIDVLY TNPNESAIVQ CQNGRCTLDG ELQGTTQLLP TGICAFRGKV TQQVQDEHRG 

       310        320        330        340        350        360 
THWNMTVTNL NGTPFDPTED VPAPLGTPDF SGQIYGVISQ RNTNTVPGEG NLPANRAHEA 

       370        380        390        400        410        420 
VIATYSPKFT PKLGNIQFST WETQDVSSGQ PTKFTPVGLA SVDANSHFDQ WTLPSYSGAL 

       430        440        450        460        470        480 
TLNMNLAPSV APVFPGECLL FFRSFIPLKG GYGNPAIDCL MPQEWVQHLY QESAPSLSDV 

       490        500        510        520        530        540 
ALVRYVNPET GRTLFEAKLH RNGFLTVARN SAGPVVAPTN GYFRFDSWVN QFYTLAPMGN 


GSGRRRMQ

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References

[1]	"Detection of norovirus and sapovirus infection among children with gastroenteritis in Ho Chi Minh City, Vietnam." Hansman G.S., Doan L.T., Kguyen T.A., Okitsu S., Katayama K., Ogawa S., Natori K., Takeda N., Kato Y., Nishio O., Noda M., Ushijima H. Arch. Virol. 149:1673-1688(2004) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE. Strain: Vietnam 026 EMBL AAT12445.1.
[2]	"Crystal structures of GII.10 and GII.12 norovirus protruding domains in complex with histo-blood group antigens reveal details for a potential site of vulnerability." Hansman G.S., Biertumpfel C., Georgiev I., McLellan J.S., Chen L., Zhou T., Katayama K., Kwong P.D. J. Virol. 85:6687-6701(2011) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.25 ANGSTROMS) OF 224-538 IN COMPLEX WITH FUCOSE; GALACTOSE AND N-ACETYL-D-GLUCOSAMINE.
[3]	"Structural basis for norovirus inhibition and fucose mimicry by citrate." Hansman G.S., Shahzad-Ul-Hussan S., McLellan J.S., Chuang G.Y., Georgiev I., Shimoike T., Katayama K., Bewley C.A., Kwong P.D. J. Virol. 86:284-292(2012) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.40 ANGSTROMS) OF 224-538.
[4]	"Structural basis for broad detection of genogroup II noroviruses by a monoclonal antibody that binds to a site occluded in the viral particle." Hansman G.S., Taylor D.W., McLellan J.S., Smith T.J., Georgiev I., Tame J.R., Park S.Y., Yamazaki M., Gondaira F., Miki M., Katayama K., Murata K., Kwong P.D. J. Virol. 86:3635-3646(2012) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (3.30 ANGSTROMS) OF 224-538.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

AF504671 Genomic RNA. Translation: AAT12445.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3ONU	X-ray	1.40	A/B	224-538	[»]
3ONY	X-ray	1.85	A/B/C	224-538	[»]
3PA1	X-ray	1.48	A/B	224-538	[»]
3PA2	X-ray	1.48	A/B	224-538	[»]
3Q38	X-ray	1.28	A/B	224-538	[»]
3Q39	X-ray	1.25	A/B	224-538	[»]
3Q3A	X-ray	1.40	A/B	224-538	[»]
3Q6Q	X-ray	1.43	A/B	224-538	[»]
3Q6R	X-ray	1.40	A/B	224-538	[»]
3RY8	X-ray	1.40	A/B	224-538	[»]
3V7A	X-ray	3.30	A/B	224-538	[»]

ProteinModelPortal

Q5F4T5.

ModBase

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Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Family and domain databases

InterPro

IPR004005. Calicivirus_coat.
IPR013643. Calicivirus_coat_C.
[Graphical view]

Pfam

PF00915. Calici_coat. 1 hit.
PF08435. Calici_coat_C. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

Q5F4T5.

Entry information

Entry name

Q5F4T5_9CALI

Accession

Primary (citable) accession number: Q5F4T5

Entry history

Integrated into UniProtKB/TrEMBL:	March 15, 2005
Last sequence update:	March 15, 2005
Last modified:	September 5, 2012
This is version 19 of the entry and version 1 of the sequence. [Complete history]

Entry status

Unreviewed (UniProtKB/TrEMBL)