3N43 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURES OF THE MATURE ENVELOPE GLYCOPROTEIN COMPLEX (TRYPSIN CLEAVAGE) 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 :   2.58

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 268-318
	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 332-667
	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
	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, 4)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	NDG	1	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN B:263 , THR F:116	BINDING SITE FOR RESIDUE NAG B 2001
2	AC2	SOFTWARE	ARG F:134 , GLY F:139 , ASN F:141 , HOH F:534 , NDG F:1002	BINDING SITE FOR RESIDUE NAG F 1001
3	AC3	SOFTWARE	NAG F:1001	BINDING SITE FOR RESIDUE NDG F 1002
4	AC4	SOFTWARE	SER F:77 , CYS F:78 , LYS F:79 , LEU F:219 , LEU F:221	BINDING SITE FOR RESIDUE ACT F 452

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	Gly F:164	-	Pro F:165
3	Asn F:264	-	Pro F:265

(no "SAP(SNP)/Variant" information available for 3N43)

(no "PROSITE Motif" information available for 3N43)

(no "Exon" information available for 3N43)

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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:51
 aligned with Q1H8W5_CHIKV | Q1H8W5 from UniProtKB/TrEMBL  Length:1248

    Alignment length:51
                                   277       287       297       307       317 
        Q1H8W5_CHIKV    268 MCLLANTTFPCSQPPCTPCCYEKEPEETLRMLEDNVMRPGYYQLLQASLTC  318
               SCOP domains --------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains Alpha_E3_glycop-3n43A01 A:7-57                      Pfam domains
         Sec.struct. author .eee..eee.........hhhhhhhhhhhhhhhhh....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                3n43 A    7 MCLLANTTFPCSQPPCTPCCYEKEPEETLRMLEDNVMRPGYYQLLQASLTC   57
                                    16        26        36        46        56

Chain B from PDB  Type:PROTEIN  Length:336
 aligned with Q1H8W5_CHIKV | Q1H8W5 from UniProtKB/TrEMBL  Length:1248

    Alignment length:336
                                   341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661      
        Q1H8W5_CHIKV    332 NVYKATRPYLAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDDSHDWTKLRYMDNHMPADAERAGLFVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKISHSCTHPFHHDPPVIGREKFHSRPQHGKELPCSTYVQSTAATTEEIEVHMPPDTPDRTLMSQQSGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSPLVPRNAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNMGEEPNYQEEWVMHKKEVVLTVPTEGLEVTWGNNEPYKYWPQL  667
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------Alpha_E2_glycop-3n43B01 B:14-342                                                                                                                                                                                                                                                                                                          Pfam domains
         Sec.struct. author ..........eee........eee...eeeee.......eeeeeeeeeee.....eeeeeeeeee..eeeeee....eee.....eeeeeeeeeeeee......eeeeee.....eeeeee.....................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
                3n43 B    7 NVYKATRPYLAHCPDCGEGHSCHSPVALERIRNEATDGTLKIQVSLQIGIKTDDSHDWTKLRYMDNHMPADAERAGLFVRTSAPCTITGTMGHFILARCPKGETLTVGFTDSRKISHSCTHPFHHDPPVIGREKFHSRPQHGKELPCSTYVQSTAATTEEIEVHMPPDTPDRTLMSQQSGNVKITVNGQTVRYKCNCGGSNEGLTTTDKVINNCKVDQCHAAVTNHKKWQYNSPLVPRNAELGDRKGKIHIPFPLANVTCRVPKARNPTVTYGKNQVIMLLYPDHPTLLSYRNMGEEPNYQEEWVMHKKEVVLTVPTEGLEVTWGNNEPYKYWPQL  342
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336

Chain F from PDB  Type:PROTEIN  Length:393
 aligned with Q1H8W5_CHIKV | Q1H8W5 from UniProtKB/TrEMBL  Length:1248

    Alignment length:393
                                   817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167      1177      1187      1197   
        Q1H8W5_CHIKV    808 SAYEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYVKCCGTAECKDKNLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFASAYRAHTASASAKLRVLYQGNNITVTAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVYKGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSGFKYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNMPISIDIPEAAFTRVVDAPSLTDMSCEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFSTALASAEFRVQVCSTQVHCAAECHPPKDHIVNYP 1200
               SCOP domains d3n43f1 F:-1-292 automated matches                                                                                                                                                                                                                                                                    d3n43f2 F:293-391 automated matches                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --Alpha_E1_glycop-3n43F01 F:1-391                                                                                                                                                                                                                                                                                                                                                                         Pfam domains
         Sec.struct. author .eeeeeeeee......eeeee.......eeeeeeeeeeeeee...eeeee..eeee....eee...............eeeeee....ee..ee........eeeeeeeeee.hhhhh..eeeee...eeeeeeeeeee..eeeeeeee.....eeee..eeeee............eeeee..eeee................ee.........ee....ee...........ee...hhhhhhhhhh..hhhhhhhhhheee....eee.....eeeeeeeee.hhh........eeeeeeeeeee.......eeeeeeeee...eeeeeee.....ee...eeee..eeeeeeeee....eeeeeeee..eeeeeeee.......ee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3n43 F   -1 GGYEHVTVIPNTVGVPYKTLVNRPGYSPMVLEMELLSVTLEPTLSLDYITCEYKTVIPSPYVKCCGTAECKDKNLPDYSCKVFTGVYPFMWGGAYCFCDAENTQLSEAHVEKSESCKTEFASAYRAHTASASAKLRVLYQGNNITVTAYANGDHAVTVKDAKFIVGPMSSAWTPFDNKIVVYKGDVYNMDYPPFGAGRPGQFGDIQSRTPESKDVYANTQLVLQRPAAGTVHVPYSQAPSGFKYWLKERGASLQHTAPFGCQIATNPVRAVNCAVGNMPISIDIPEAAFTRVVDAPSLTDMSCEVPACTHSSDFGGVAIIKYAASKKGKCAVHSMTNAVTIREAEIEVEGNSQLQISFSTALASAEFRVQVCSTQVHCAAECHPPKDHIVNYP  391
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388

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 3N43)

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 ]
		Thr A:23 - Pro A:24	[ RasMol ]

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

1rer	CRYSTAL STRUCTURE OF THE HOMOTRIMER OF FUSION GLYCOPROTEIN E1 FROM SEMLIKI FOREST VIRUS. RELATED ID: EMD-1121 RELATED DB: EMDB MAPPING THE STRUCTURE AND FUNCTION OF THE E1 AND E2 GLYCOPROTEINS IN ALPHAVIRUSES (SINDBIS VIRUS). RELATED ID: EMD-1015 RELATED DB: EMDB CRYO-ELECTRON MICROSCOPY REVEALS THE FUNCTIONAL ORGANIZATION OF AN ENVELOPED VIRUS, SEMLIKI FOREST VIRUS.
2ala	CRYSTAL STRUCTURE OF THE SEMLIKI FOREST VIRUS ENVELOPE PROTEIN E1 IN ITS MONOMERIC CONFORMATION.
3muu	CRYSTAL STRUCTURE OF THE SINDBIS VIRUS E2-E1 HETERODIMER AT LOW PH.
3muw	PSEUDO-ATOMIC STRUCTURE OF THE E2-E1 PROTEIN SHELL IN SINDBIS VIRUS.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (17, 17)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (3, 3)

Gene Ontology (18, 18)

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