3N44 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE MATURE ENVELOPE GLYCOPROTEIN COMPLEX (TRYPSIN CLEAVAGE; OSMIUM SOAK) OF CHIKUNGUNYA VIRUS.

Authors :   J. Voss, M. C. Vaney, S. Duquerroy, F. A. Rey

Date :   21 May 10 (Deposition) - 01 Dec 10 (Release) - 15 Dec 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.35

Chains :   Asym./Biol. Unit : A,B,F

Keywords :   Viral Protein, Immature Heterodimer, Alphavirus, Receptor Binding, Membrane Fusion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. E. Voss, M. C. Vaney, S. Duquerroy, C. Vonrhein, C. Girard-Blanc, E. Crublet, A. Thompson, G. Bricogne, F. A. Rey
Glycoprotein Organization Of Chikungunya Virus Particles Revealed By X-Ray Crystallography.
Nature V. 468 709 2010
PubMed-ID: 21124458 | Reference-DOI: 10.1038/NATURE09555
(for further references see the PDB file header)

Molecule 1 - E3 ENVELOPE GLYCOPROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Cell Line	:	SCHNEIDER 2
	Expression System Plasmid	:	PMRBIP/V5 HISA
	Expression System Taxid	:	7227
	Expression System Vector Type	:	PLASMID
	Fragment	:	POLYPROTEIN FRAGMENT RESIDUES 266-319
	Organism Common	:	CHIKV
	Organism Scientific	:	CHIKUNGUNYA VIRUS
	Organism Taxid	:	37124
	Strain	:	05-115

Molecule 2 - E2 ENVELOPE GLYCOPROTEIN
	Chains	:	B
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Cell Line	:	SCHNEIDER 2
	Expression System Plasmid	:	PMRBIP/V5 HISA
	Expression System Taxid	:	7227
	Expression System Vector Type	:	PLASMID
	Fragment	:	POLYPROTEIN FRAGMENT RESIDUES 329-666
	Organism Common	:	CHIKV
	Organism Scientific	:	CHIKUNGUNYA VIRUS
	Organism Taxid	:	37124
	Strain	:	05-115

Molecule 3 - E1 ENVELOPE GLYCOPROTEIN
	Chains	:	F
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Cell Line	:	SCHNEIDER 2
	Expression System Plasmid	:	PMRBIP/V5 HISA
	Expression System Taxid	:	7227
	Expression System Vector Type	:	PLASMID
	Fragment	:	POLYPROTEIN FRAGMENT RESIDUES 810-1200
	Mutation	:	YES
	Organism Common	:	CHIKV
	Organism Scientific	:	CHIKUNGUNYA VIRUS
	Organism Taxid	:	37124
	Strain	:	05-115

		1	2	3
Asymmetric/Biological Unit	:	A	B	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 11)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	OS	6	Ligand/Ion	OSMIUM ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:32 , THR B:196 , HIS B:232	BINDING SITE FOR RESIDUE ACT A 65
2	AC2	SOFTWARE	ASN B:263	BINDING SITE FOR RESIDUE NAG B 2001
3	AC3	SOFTWARE	HIS B:18	BINDING SITE FOR RESIDUE OS B 361
4	AC4	SOFTWARE	HIS B:142	BINDING SITE FOR RESIDUE OS B 362
5	AC5	SOFTWARE	HIS B:130	BINDING SITE FOR RESIDUE OS B 363
6	AC6	SOFTWARE	ARG F:134 , GLY F:139 , ASN F:141 , HOH F:563	BINDING SITE FOR RESIDUE NAG F 1001
7	AC7	SOFTWARE	ASP F:158 , ARG F:223 , ASP F:281	BINDING SITE FOR RESIDUE ACT F 452
8	AC8	SOFTWARE	SER F:77 , LYS F:79 , LEU F:219 , VAL F:220 , LEU F:221	BINDING SITE FOR RESIDUE ACT F 453
9	AC9	SOFTWARE	HIS B:73	BINDING SITE FOR RESIDUE OS F 454

Asymmetric/Biological Unit

No.	Residues
1	A:8	-	A:17
2	A:22	-	A:26
3	A:25	-	A:57
4	B:19	-	B:125
5	B:22	-	B:28
6	B:91	-	B:105
7	B:153	-	B:266
8	B:201	-	B:225
9	B:203	-	B:220
10	F:49	-	F:114
11	F:62	-	F:94
12	F:63	-	F:96
13	F:68	-	F:78
14	F:259	-	F:271
15	F:301	-	F:376
16	F:306	-	F:380
17	F:328	-	F:370

Asymmetric/Biological Unit

No.	Residues
1	Thr A:23	-	Pro A:24
2	Ser B:185	-	Gly B:186
3	Gly F:164	-	Pro F:165
4	Asn F:264	-	Pro F:265

(no "SAP(SNP)/Variant" information available for 3N44)

(no "PROSITE Motif" information available for 3N44)

(no "Exon" information available for 3N44)

Asymmetric/Biological 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:54
 aligned with Q1H8W5_CHIKV | Q1H8W5 from UniProtKB/TrEMBL  Length:1248

    Alignment length:54
                                   275       285       295       305       315    
        Q1H8W5_CHIKV    266 PVMCLLANTTFPCSQPPCTPCCYEKEPEETLRMLEDNVMRPGYYQLLQASLTCS  319
               SCOP domains ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains --Alpha_E3_glycop-3n44A01 A:7-58                       Pfam domains
         Sec.struct. author ..eeee..eeee........hhhhhhhhhhhhhhhh.....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                3n44 A    5 PVMCLLANTTFPCSQPPCTPCCYEKEPEETLRMLEDNVMRPGYYQLLQASLTCS   58
                                    14        24        34        44        54

Chain B from PDB  Type:PROTEIN  Length:338
 aligned with Q1H8W5_CHIKV | Q1H8W5 from UniProtKB/TrEMBL  Length:1248

    Alignment length:338
                                   338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658        
        Q1H8W5_CHIKV    329 DNFNVYKATRPYLAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDDSHDWTKLRYMDNHMPADAERAGLFVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKISHSCTHPFHHDPPVIGREKFHSRPQHGKELPCSTYVQSTAATTEEIEVHMPPDTPDRTLMSQQSGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSPLVPRNAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNMGEEPNYQEEWVMHKKEVVLTVPTEGLEVTWGNNEPYKYWPQ  666
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------Alpha_E2_glycop-3n44B01 B:14-341                                                                                                                                                                                                                                                                                                         Pfam domains
         Sec.struct. author ...hhhhh.....eee........eee...eeeee.......eeeeeeeeeee.....eeeeeeeeee..eeeeee.hhheee.....eeeeeeeeeeeee...eeeeeeeee.....eeeeeeeeee.................eeeeeeee.........eeeee....ee....eeee..eeee......eeeee......eeee...eee...hhh.eeeee......ee...............eeee....eeeeeeee......eeeee..eeeeee.....eeeeeee.......eeeee...eeeeee.....eeeee.....eeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3n44 B    4 DNFNVYKATRPYLAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDDSHDWTKLRYMDNHMPADAERAGLFVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKISHSCTHPFHHDPPVIGREKFHSRPQHGKELPCSTYVQSTAATTEEIEVHMPPDTPDRTLMSQQSGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSPLVPRNAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNMGEEPNYQEEWVMHKKEVVLTVPTEGLEVTWGNNEPYKYWPQ  341
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333

Chain F from PDB  Type:PROTEIN  Length:391
 aligned with Q1H8W5_CHIKV | Q1H8W5 from UniProtKB/TrEMBL  Length:1248

    Alignment length:391
                                   819       829       839       849       859       869       879       889       899       909       919       929       939       949       959       969       979       989       999      1009      1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199 
        Q1H8W5_CHIKV    810 YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYVKCCGTAECKDKNLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFASAYRAHTASASAKLRVLYQGNNITVTAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVYKGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSGFKYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNMPISIDIPEAAFTRVVDAPSLTDMSCEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFSTALASAEFRVQVCSTQVHCAAECHPPKDHIVNYP 1200
               SCOP domains d3n44f1 F:1-292 automated matches                                                                                                                                                                                                                                                                   d3n44f2 F:293-391 automated matches                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Alpha_E1_glycop-3n44F01 F:1-391                                                                                                                                                                                                                                                                                                                                                                         Pfam domains
         Sec.struct. author .eeeeeee......eeeee.......eeeeeeeeeeeee..eeeeeeee.eeee....eee...............eeeeee....ee..ee........eeeeeeeeee.hhhhh.eeeeeee...eeeeeeeeee..eeeeeeee.....eeee..eeeee............eeeee..eeee................ee.........ee....ee...........ee...hhhhhhhhhh..hhhhhhhhhheee....eee.....eeeeeee.hhhhh........eeeeeeeeeee.......eeeeeeeee...eeeeeee.....ee...eeee....eeeeeee....eeeeeeee..eeeeeeee.......ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3n44 F    1 YEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYVKCCGTAECKDKNLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFASAYRAHTASASAKLRVLYQGNNITVTAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVYKGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSGFKYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNMPISIDIPEAAFTRVVDAPSLTDMSCEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFSTALASAEFRVQVCSTQVHCAAECHPPKDHIVNYP  391
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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 "CATH Domain" information available for 3N44)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,F (Q1H8W5_CHIKV | Q1H8W5)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008236	serine-type peptidase activity	Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
	GO:0039654	fusion of virus membrane with host endosome membrane	Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
	GO:0039663	membrane fusion involved in viral entry into host cell	Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019028	viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asn F:264 - Pro F:265	[ RasMol ]
		Gly F:164 - Pro F:165	[ RasMol ]
		Ser B:185 - Gly B:186	[ RasMol ]
		Thr A:23 - Pro A:24	[ RasMol ]

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	3n44
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	Q1H8W5_CHIKV \| Q1H8W5	:	2xfb 2xfc 3j2w 3n40 3n41 3n42 3n43 5any

(no "Related Entries Specified in the PDB File" available for 3N44)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 11)

Sites (9, 9)

SS Bonds (17, 17)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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