5E65 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   THE COMPLEX STRUCTURE OF HEMAGGLUTININ-ESTERASE-FUSION MUTANT PROTEIN FROM THE INFLUENZA D VIRUS WITH RECEPTOR ANALOG 9-O-AC-3'SLN (TR322)

Authors :   H. Song, J. Qi, Y. Shi, G. F. Gao

Date :   09 Oct 15 (Deposition) - 23 Mar 16 (Release) - 23 Mar 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Influenza Virus, Hef, Membrane, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Song, J. Qi, Z. Khedri, S. Diaz, H. Yu, X. Chen, A. Varki, Y. Shi, G. F. Gao
An Open Receptor-Binding Cavity Of Hemagglutinin-Esterase-Fusion Glycoprotein From Newly-Identified Influenza D Virus: Basis For Its Broad Cel Tropism
Plos Pathog. V. 12 05505 2016
PubMed-ID: 26954772 | Reference-DOI: 10.1371/JOURNAL.PPAT.1005505

Molecule 1 - HEMAGGLUTININ-ESTERASE
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Cell Line	:	HI5
	Expression System Plasmid	:	PFASTBAC1
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	UNP RESIDUES 19-445
	Gene	:	HEF
	Mutation	:	YES
	Organism Scientific	:	INFLUENZA D VIRUS (D/SWINE/OKLAHOMA/1334/2011)
	Organism Taxid	:	1173138
	Strain	:	D/SWINE/OKLAHOMA/1334/2011

Molecule 2 - HEMAGGLUTININ-ESTERASE
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Taxid	:	7108
	Fragment	:	UNP RESIDUES 456-621
	Gene	:	HEF
	Organism Scientific	:	INFLUENZA D VIRUS (D/SWINE/OKLAHOMA/1334/2011)
	Organism Taxid	:	1173138
	Strain	:	D/SWINE/OKLAHOMA/1334/2011

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (3x)	:	A	B
Biological Unit 2 (3x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 34)

No.	Name	Count	Type	Full Name
1	5N6	2	Ligand/Ion	(2~{R},4~{S},5~{R},6~{R})-5-ACETAMIDO-6-[(1~{R},2~{R})-3-ACETYLOXY-1,2-BIS(OXIDANYL)PROPYL]-2,4-BIS(OXIDANYL)OXANE-2-CARBOXYLIC ACID
2	BMA	3	Ligand/Ion	BETA-D-MANNOSE
3	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
4	MAN	9	Ligand/Ion	ALPHA-D-MANNOSE
5	NAG	18	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (5, 57)

No.	Name	Count	Type	Full Name
1	5N6	3	Ligand/Ion	(2~{R},4~{S},5~{R},6~{R})-5-ACETAMIDO-6-[(1~{R},2~{R})-3-ACETYLOXY-1,2-BIS(OXIDANYL)PROPYL]-2,4-BIS(OXIDANYL)OXANE-2-CARBOXYLIC ACID
2	BMA	6	Ligand/Ion	BETA-D-MANNOSE
3	GAL	3	Ligand/Ion	BETA-D-GALACTOSE
4	MAN	18	Ligand/Ion	ALPHA-D-MANNOSE
5	NAG	27	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (5, 45)

No.	Name	Count	Type	Full Name
1	5N6	3	Ligand/Ion	(2~{R},4~{S},5~{R},6~{R})-5-ACETAMIDO-6-[(1~{R},2~{R})-3-ACETYLOXY-1,2-BIS(OXIDANYL)PROPYL]-2,4-BIS(OXIDANYL)OXANE-2-CARBOXYLIC ACID
2	BMA	3	Ligand/Ion	BETA-D-MANNOSE
3	GAL	3	Ligand/Ion	BETA-D-GALACTOSE
4	MAN	9	Ligand/Ion	ALPHA-D-MANNOSE
5	NAG	27	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:12 , GLU A:13 , SER A:14 , MET A:28 , HOH A:808 , HOH A:860 , HOH A:945 , GLY B:19 , GLY B:20 , ALA B:22 , GLY B:23	binding site for Poly-Saccharide residues NAG A 713 through NAG A 714 bound to ASN A 12
02	AC2	SOFTWARE	ASN A:130 , GLN A:133 , LYS A:218 , ASN A:220 , ASN A:330 , ALA A:331 , GLU A:334 , LEU A:337 , GLN A:338 , LYS A:346 , NAG A:707 , NAG A:708 , MAN A:711 , HOH A:807 , HOH A:809 , HOH A:821 , HOH A:825 , HOH A:844 , HOH A:850 , HOH A:883 , HOH A:887 , HOH A:912 , HOH A:922 , HOH A:930 , HOH A:933 , HOH A:950 , HOH A:988	binding site for Poly-Saccharide residues NAG A 701 through MAN A 706 bound to ASN A 130
03	AC3	SOFTWARE	ASN A:330 , GLU A:333 , GLU A:334 , LEU A:337 , NAG A:702 , BMA A:703 , MAN A:705 , HOH A:805 , HOH A:809 , HOH A:844 , HOH A:846 , HOH A:854 , HOH A:887 , HOH A:896 , HOH A:938 , HOH A:965 , ASN C:47 , GLN C:48 , LYS C:49	binding site for Poly-Saccharide residues NAG A 707 through MAN A 712 bound to ASN A 330
04	AC4	SOFTWARE	ASN B:58 , ASN B:61 , GLU B:65 , HOH B:830	binding site for Mono-Saccharide NAG B 703 bound to ASN B 58
05	AC5	SOFTWARE	SER A:19 , GLY A:20 , PHE A:21 , ASN A:24 , GLN A:424 , GLY A:426 , GLN B:55 , LEU B:56 , ASP B:59 , ASN B:107 , ASN B:111 , HOH B:801 , HOH B:805 , HOH B:811 , HOH B:825 , HOH B:845 , HOH B:847	binding site for Poly-Saccharide residues NAG B 701 through NAG B 702 bound to ASN B 107
06	AC6	SOFTWARE	ASP A:64 , ASN C:12 , SER C:14 , MET C:28 , GLY D:19 , GLY D:20 , ALA D:22 , GLY D:23	binding site for Poly-Saccharide residues NAG C 709 through NAG C 710 bound to ASN C 12
07	AC7	SOFTWARE	ASN C:130 , GLN C:133 , LYS C:218 , ASN C:220 , ASN C:330 , GLU C:334 , GLN C:338 , LYS C:346 , NAG C:707 , NAG C:708 , HOH C:803 , HOH C:806 , HOH C:807 , HOH C:808 , HOH C:813 , HOH C:816 , HOH C:827 , HOH C:839 , HOH C:844 , HOH C:853 , HOH C:868 , HOH C:912 , HOH C:919	binding site for Poly-Saccharide residues NAG C 701 through MAN C 706 bound to ASN C 130
08	AC8	SOFTWARE	LYS A:49 , ASN C:330 , GLU C:333 , GLU C:334 , LEU C:337 , NAG C:702 , BMA C:703 , MAN C:704 , MAN C:705 , HOH C:803 , HOH C:807 , HOH C:893 , HOH C:918	binding site for Poly-Saccharide residues NAG C 707 through NAG C 708 bound to ASN C 330
09	AC9	SOFTWARE	ASN D:58 , ASN D:61 , GLU D:65	binding site for Mono-Saccharide NAG D 703 bound to ASN D 58
10	AD1	SOFTWARE	SER C:19 , GLY C:20 , PHE C:21 , ASN C:24 , GLN C:424 , GLY C:426 , GLN D:55 , LEU D:56 , ASP D:59 , SER D:102 , ASN D:107 , ASN D:111 , HOH D:822 , HOH D:830	binding site for Poly-Saccharide residues NAG D 701 through NAG D 702 bound to ASN D 107
11	AD2	SOFTWARE	PHE A:127 , GLY A:170 , THR A:171 , ALA A:172 , SER A:173 , TRP A:185 , TYR A:231 , PHE A:240 , PHE A:297	binding site for Poly-Saccharide residues 5N6 A 715 through GAL A 716
12	AD3	SOFTWARE	PHE C:127 , THR C:171 , ALA C:172 , SER C:173 , TRP C:185 , ALA C:187 , PHE C:229 , TYR C:231 , PHE C:240 , VAL C:275 , PHE C:297 , HOH C:888 , HOH C:899	binding site for Poly-Saccharide residues 5N6 C 711 through GAL C 712

Asymmetric Unit

No.	Residues
1	A:6	-	B:138
2	A:106	-	A:151
3	A:126	-	A:175
4	A:200	-	A:242
5	A:219	-	A:306
6	A:227	-	A:279
7	A:336	-	A:342
8	A:378	-	A:404
9	B:146	-	B:150
10	C:6	-	D:138
11	C:106	-	C:151
12	C:126	-	C:175
13	C:200	-	C:242
14	C:219	-	C:306
15	C:227	-	C:279
16	C:336	-	C:342
17	C:378	-	C:404
18	D:146	-	D:150

Asymmetric Unit

No.	Residues
1	Phe A:66	-	Pro A:67
2	Ser A:182	-	Pro A:183
3	Pro A:398	-	Pro A:399
4	Gly B:34	-	Gly B:35
5	Gly B:128	-	Gly B:129
6	Phe C:66	-	Pro C:67
7	Ser C:182	-	Pro C:183
8	Leu C:371	-	Gly C:372
9	Pro C:398	-	Pro C:399
10	Gly D:34	-	Gly D:35
11	Gly D:128	-	Gly D:129

(no "SAP(SNP)/Variant" information available for 5E65)

(no "PROSITE Motif" information available for 5E65)

(no "Exon" information available for 5E65)

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:424
                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eee.....eeeeeeeee..................eeeee.hhhh............hhhhhh.eee....hhhhhhhh.........eee..eeeee.....hhhhh......hhhhhhhhhhhhhhhhhhh..eeeee...eeee.....ee..hhhhh.......eeee.............eeeeeee..ee..ee..eeeee..eee..hhhhhh.......eeeee.....eeeeee..............eee..eeee..eeeeeee...eeee...eeee.......eeee...........hhhhhhhhh...eeee.......eeee..eeehhhhhhhhhhhh....eee..eee.....ee.......eeee..ee.hhhhh.eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e65 A   3 ELICIVQRVNESFSLHSGFGGNVYSMKTEPMTGFTNVTKGASVINQKDWIGFGDARTDLTNDQFPASSDVPLAVAKKFRSLSGASLMLSAFGPPGKVDYLYQGCGKEKVFYEGVNWSPEAGIDCFGSNWTQTKKDFYSRIYEAARSSTCMTLVNSLDTKISSTTATAGTASSCSSSWMKSPLWYAESSVNPPQVCGTEQSATFTLPTSFGIYKCNKHVVQLCYFVYENKAKFNTFGCGDYYQNYYDGNGNLIGGMDNRVAAYRGIANAGVKIECPSKILNPGTYSIKSTPRFLLVPKRSYCFDTDGGYPIQVVQSEWSASRRSDNATEEACLQTEGCIFIKKTTPYVGEAADNAGDIEMRQLLSGLGNNDTVCVSQSGYTKGETPFVKDYLSPPKYGRCQLKTDSGRIPTLPSGLIIPQAGTDS 429
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192||     205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425    
                                                                                                                                                                                                                        193|                                                                                                                                                                                                                                        
                                                                                                                                                                                                                         197

Chain B from PDB  Type:PROTEIN  Length:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.......eeeeee................hhhhhhhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eee.......hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e65 B   9 FGLLFVGFVAGGVAGGYFWGRSNGGGGGASVSSTQAGFDKIGKDIQQLRNDTNAAIEGFNGRIAHDEQAIKNLAKEIEDARAEALVGELGIIRSLIVANISMNLKESLYELANQITKRGGGIAQEAGPGCWYVDSENCDASCKEYIFNF 157
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148

Chain C from PDB  Type:PROTEIN  Length:424
                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eee.....eeeeeeeee..................eeeee.hhhh............hhhhhh.eee....hhhhhhhh.........eee..eeeee.....hhhhh......hhhhhhhhhhhhhhhhhhh..eeeee...eeee.....ee..hhhhh.......eeee.............eeeeeee..ee..ee..eeeee..eee..hhhhhh.......eeeee.....eeeeee..............eee..eeee..eeeeeee...eeee...eeee.......eeee...........hhhhhhhhh...eeee...............hhhhhhhhhhhhh..eeeee..eeee....ee.......eeee..ee.hhhhh.eeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e65 C   3 ELICIVQRVNESFSLHSGFGGNVYSMKTEPMTGFTNVTKGASVINQKDWIGFGDARTDLTNDQFPASSDVPLAVAKKFRSLSGASLMLSAFGPPGKVDYLYQGCGKEKVFYEGVNWSPEAGIDCFGSNWTQTKKDFYSRIYEAARSSTCMTLVNSLDTKISSTTATAGTASSCSSSWMKSPLWYAESSVNPPQVCGTEQSATFTLPTSFGIYKCNKHVVQLCYFVYENKAKFNTFGCGDYYQNYYDGNGNLIGGMDNRVAAYRGIANAGVKIECPSKILNPGTYSIKSTPRFLLVPKRSYCFDTDGGYPIQVVQSEWSASRRSDNATEEACLQTEGCIFIKKTTPYVGEAADNAGDIEMRQLLSGLGNNDTVCVSQSGYTKGETPFVKDYLSPPKYGRCQLKTDSGRIPTLPSGLIIPQAGTDS 429
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192||     205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425    
                                                                                                                                                                                                                        193|                                                                                                                                                                                                                                        
                                                                                                                                                                                                                         197

Chain D from PDB  Type:PROTEIN  Length:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee.......eeeee.................hhhhhhhhhhhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eee.........hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e65 D   9 FGLLFVGFVAGGVAGGYFWGRSNGGGGGASVSSTQAGFDKIGKDIQQLRNDTNAAIEGFNGRIAHDEQAIKNLAKEIEDARAEALVGELGIIRSLIVANISMNLKESLYELANQITKRGGGIAQEAGPGCWYVDSENCDASCKEYIFNF 157
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148

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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 5E65)

(no "CATH Domain" information available for 5E65)

(no "Pfam Domain" information available for 5E65)

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Asymmetric Unit
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	Cis Peptide Bonds
		Gly B:128 - Gly B:129	[ RasMol ]
		Gly B:34 - Gly B:35	[ RasMol ]
		Gly D:128 - Gly D:129	[ RasMol ]
		Gly D:34 - Gly D:35	[ RasMol ]
		Leu C:371 - Gly C:372	[ RasMol ]
		Phe A:66 - Pro A:67	[ RasMol ]
		Phe C:66 - Pro C:67	[ RasMol ]
		Pro A:398 - Pro A:399	[ RasMol ]
		Pro C:398 - Pro C:399	[ RasMol ]
		Ser A:182 - Pro A:183	[ RasMol ]
		Ser C:182 - Pro C:183	[ RasMol ]

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	5e65
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	K9LG83_9ORTO \| K9LG83
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	K9LG83_9ORTO \| K9LG83	:	5e5w 5e62 5e64 5e66

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 34)

Sites (12, 12)

SS Bonds (18, 18)

Cis Peptide Bonds (11, 11)

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SAPs(SNPs)/Variants (0, 0)

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