3PA2 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF P DOMAIN FROM NORWALK VIRUS STRAIN VIETNAM 026 IN COMPLEX WITH HBGA TYPE LEY

Authors :   G. S. Hansman, C. Biertumpfel, L. Chen, I. Georgiev, J. S. Mclellan, K. K P. D. Kwong

Date :   18 Oct 10 (Deposition) - 11 May 11 (Release) - 29 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.48

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)

Keywords :   Norovirus, P-Domain, Capsid, Receptor, Histo Blood Group Antigen (Hbga), Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. S. Hansman, C. Biertumpfel, I. Georgiev, J. S. Mclellan, L. Chen, T. Zhou, K. Katayama, P. D. Kwong
Crystal Structures Of Gii. 10 And Gii. 12 Norovirus Protrudin Domains In Complex With Histo-Blood Group Antigens Reveal Details For A Potential Site Of Vulnerability.
J. Virol. V. 85 6687 2011
PubMed-ID: 21525337 | Reference-DOI: 10.1128/JVI.00246-11

Molecule 1 - CAPSID PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	MBP-HTSHP
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	P-DOMAIN-026 (UNP RESIDUES 224 TO 538)
	Gene	:	CAPSID PROTEIN
	Organism Scientific	:	NORWALK VIRUS
	Organism Taxid	:	11983
	Strain	:	VIETNAM 026

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 27)

No.	Name	Count	Type	Full Name
1	EDO	22	Ligand/Ion	1,2-ETHANEDIOL
2	FUC	2	Ligand/Ion	ALPHA-L-FUCOSE
3	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
4	IMD	1	Ligand/Ion	IMIDAZOLE
5	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (5, 27)

No.	Name	Count	Type	Full Name
1	EDO	22	Ligand/Ion	1,2-ETHANEDIOL
2	FUC	2	Ligand/Ion	ALPHA-L-FUCOSE
3	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
4	IMD	1	Ligand/Ion	IMIDAZOLE
5	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (5, 20)

No.	Name	Count	Type	Full Name
1	EDO	15	Ligand/Ion	1,2-ETHANEDIOL
2	FUC	2	Ligand/Ion	ALPHA-L-FUCOSE
3	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
4	IMD	1	Ligand/Ion	IMIDAZOLE
5	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 3 (1, 7)

No.	Name	Count	Type	Full Name
1	EDO	7	Ligand/Ion	1,2-ETHANEDIOL
2	FUC	-1	Ligand/Ion	ALPHA-L-FUCOSE
3	GAL	-1	Ligand/Ion	BETA-D-GALACTOSE
4	IMD	-1	Ligand/Ion	IMIDAZOLE
5	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (27, 27)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GAL A:2 , NAG A:3 , FUC A:4 , ALA A:354 , ASN A:355 , ARG A:356 , ASP A:385 , PHE A:532 , GLY B:451 , TYR B:452	BINDING SITE FOR RESIDUE FUC A 1
02	AC2	SOFTWARE	FUC A:1 , NAG A:3 , FUC A:4 , PHE A:532 , THR A:534 , HOH A:577 , HOH A:581 , HOH A:598 , HOH A:604 , HOH A:843	BINDING SITE FOR RESIDUE GAL A 2
03	AC3	SOFTWARE	FUC A:1 , GAL A:2 , FUC A:4 , PHE A:532 , HOH A:581 , ALA B:400 , SER B:401 , GLY B:451 , HOH B:567 , HOH B:728	BINDING SITE FOR RESIDUE NAG A 3
04	AC4	SOFTWARE	FUC A:1 , GAL A:2 , NAG A:3 , HOH A:557 , HOH A:581 , HOH A:649 , TRP B:381 , LYS B:449	BINDING SITE FOR RESIDUE FUC A 4
05	AC5	SOFTWARE	HOH A:79 , HOH A:109 , THR A:281 , ARG A:287 , LEU A:310	BINDING SITE FOR RESIDUE EDO A 539
06	AC6	SOFTWARE	HOH A:45 , HOH A:129 , HOH A:131 , PRO A:245 , ILE A:246 , HOH A:795 , ASN B:311	BINDING SITE FOR RESIDUE EDO A 540
07	AC7	SOFTWARE	HOH A:37 , HOH A:51 , HOH A:148 , ASN A:309 , LEU A:310 , ASN A:311 , LEU A:325	BINDING SITE FOR RESIDUE EDO A 541
08	AC8	SOFTWARE	ARG A:299 , SER A:379 , THR A:380 , TRP A:381 , HOH A:553	BINDING SITE FOR RESIDUE EDO A 5
09	AC9	SOFTWARE	EDO A:22 , GLU A:255 , ASP A:409 , GLN A:410 , TRP A:411 , HOH A:560 , HOH A:564 , HOH A:709	BINDING SITE FOR RESIDUE EDO A 6
10	BC1	SOFTWARE	PRO A:230 , GLU A:464 , HIS A:468 , HOH A:646 , HOH A:770 , HOH B:187	BINDING SITE FOR RESIDUE EDO A 8
11	BC2	SOFTWARE	GLY A:451 , TYR A:452 , HOH A:642 , HOH B:213 , ALA B:354 , ASN B:355 , HOH B:772	BINDING SITE FOR RESIDUE EDO A 13
12	BC3	SOFTWARE	HOH A:49 , ASP A:247 , HOH A:670 , EDO B:7 , HOH B:177 , ARG B:287	BINDING SITE FOR RESIDUE EDO A 16
13	BC4	SOFTWARE	EDO A:18 , ARG A:341 , HOH A:547 , HOH A:569 , PHE B:445 , PRO B:447	BINDING SITE FOR RESIDUE EDO A 17
14	BC5	SOFTWARE	EDO A:17 , HOH A:155 , ARG A:287 , HOH A:710 , HOH B:78 , ASP B:247	BINDING SITE FOR RESIDUE EDO A 18
15	BC6	SOFTWARE	HOH A:180 , ILE A:258 , GLN A:260 , TRP A:411 , HOH A:842	BINDING SITE FOR RESIDUE EDO A 19
16	BC7	SOFTWARE	GLU A:359 , TRP A:381 , LYS A:449 , HOH A:591 , HOH A:641 , HOH A:701	BINDING SITE FOR RESIDUE EDO A 20
17	BC8	SOFTWARE	GLN A:277 , LEU A:278 , HOH A:573 , HOH A:738 , HOH B:74 , GLU B:236	BINDING SITE FOR RESIDUE EDO A 21
18	BC9	SOFTWARE	EDO A:6 , HOH A:145 , PHE A:408 , GLN A:410 , PRO A:455 , ALA A:456 , HOH A:560 , HOH A:763	BINDING SITE FOR RESIDUE EDO A 22
19	CC1	SOFTWARE	HOH A:39 , HOH A:40 , HOH A:144 , HOH A:159 , PRO A:243 , PRO A:280 , THR A:281 , PRO B:280 , THR B:281	BINDING SITE FOR RESIDUE EDO A 23
20	CC2	SOFTWARE	LEU A:272 , GLN A:273 , GLY A:274 , THR A:276 , LEU A:325	BINDING SITE FOR RESIDUE IMD A 24
21	CC3	SOFTWARE	HOH A:131 , HOH B:63 , THR B:281 , ARG B:287	BINDING SITE FOR RESIDUE EDO B 1
22	CC4	SOFTWARE	EDO A:16 , PHE A:445 , HOH B:113 , ARG B:287 , ARG B:341 , HOH B:540 , HOH B:669	BINDING SITE FOR RESIDUE EDO B 7
23	CC5	SOFTWARE	LEU B:272 , GLN B:273 , GLY B:274 , THR B:276 , LEU B:325 , HOH B:672	BINDING SITE FOR RESIDUE EDO B 10
24	CC6	SOFTWARE	HOH B:41 , ASN B:309 , LEU B:310 , ASN B:311 , LEU B:325 , HOH B:542 , HOH B:544	BINDING SITE FOR RESIDUE EDO B 11
25	CC7	SOFTWARE	PRO B:317 , THR B:318 , GLU B:319 , ASP B:320 , LYS B:372 , ASN B:425	BINDING SITE FOR RESIDUE EDO B 12
26	CC8	SOFTWARE	SER B:379 , THR B:380 , HOH B:671 , HOH B:728	BINDING SITE FOR RESIDUE EDO B 14
27	CC9	SOFTWARE	HOH B:163 , HOH B:187 , GLU B:464 , HIS B:468	BINDING SITE FOR RESIDUE EDO B 15

(no "SS Bond" information available for 3PA2)

(no "Cis Peptide Bond" information available for 3PA2)

(no "SAP(SNP)/Variant" information available for 3PA2)

(no "PROSITE Motif" information available for 3PA2)

(no "Exon" information available for 3PA2)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:315
 aligned with Q5F4T5_9CALI | Q5F4T5 from UniProtKB/TrEMBL  Length:548

    Alignment length:315
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533     
         Q5F4T5_9CALI   224 SKPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVQDEHRGTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNTNTVPGEGNLPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 538
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh..........eeee...........................hhhhh..eeeeeeeee......eeeeeee.........................eeeeeeeee....hhhhh...eeeeeeeeee......hhhh.eeeeee..........eeeeeeeee...hhhhh.............................eeeeeeeee....eee...eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee....eee......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pa2 A 224 SKPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVQDEHRGTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNTNTVPGEGNLPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 538
                                   233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533

Chain B from PDB  Type:PROTEIN  Length:310
 aligned with Q5F4T5_9CALI | Q5F4T5 from UniProtKB/TrEMBL  Length:548

    Alignment length:316
                                   232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532      
         Q5F4T5_9CALI   223 KSKPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVQDEHRGTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNTNTVPGEGNLPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 538
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Calici_coat-3pa2B01 B:224-291                                       ---------------Calici_coat_C-3pa2B03 B:307-538                                                                                                                                                                                                          Pfam domains (1)
           Pfam domains (2) -Calici_coat-3pa2B02 B:224-291                                       ---------------Calici_coat_C-3pa2B04 B:307-538                                                                                                                                                                                                          Pfam domains (2)
         Sec.struct. author ..........hhhhh..........eeee...........................hhhhh..eeeeeeeeee.....eeeeeee.........................eeeeeeeee...------...eeeeeeeeee......hhhh.eeeeee..........eeeeeeeee...hhhhh.............................eeeeeeeee....eee...eeee..hhhhhhhhhhhh......eeeeeee......eeeeeeee...eeeee....eee......eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pa2 B 223 SSKPFTLPILTLGELTNSRFPLPIDVLYTNPNESAIVQCQNGRCTLDGELQGTTQLLPTGICAFRGKVTQQVQDEHRGTHWNMTVTNLNGTPFDPTEDVPAPLGTPDFSGQIYGVISQRNTN------NLPANRAHEAVIATYSPKFTPKLGNIQFSTWETQDVSSGQPTKFTPVGLASVDANSHFDQWTLPSYSGALTLNMNLAPSVAPVFPGECLLFFRSFIPLKGGYGNPAIDCLMPQEWVQHLYQESAPSLSDVALVRYVNPETGRTLFEAKLHRNGFLTVARNSAGPVVAPTNGYFRFDSWVNQFYTLAPM 538
                                   232       242       252       262       272       282       292       302       312       322       332       342 |     352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532      
                                                                                                                                                   344    351

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 3PA2)

(no "CATH Domain" information available for 3PA2)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Viral_ssRNA_CP (106)

Family: Calici_coat (20)

Norwalk virus (9)

1a	Calici_coat-3pa2B01	B:224-291
1b	Calici_coat-3pa2B02	B:224-291

Clan: no clan defined [family: Calici_coat_C] (19)

Family: Calici_coat_C (19)

Norwalk virus (9)

2a	Calici_coat_C-3pa2B03	B:307-538
2b	Calici_coat_C-3pa2B04	B:307-538

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 3PA2)

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Description

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Ligands, Modified Residues, Ions (5, 27)

Sites (27, 27)

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