5LCV - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURAL BASIS OF ZIKA AND DENGUE VIRUS POTENT ANTIBODY CROSS-NEUTRALIZATION

Authors :   G. Barba-Spaeth

Date :   22 Jun 16 (Deposition) - 06 Jul 16 (Release) - 17 Aug 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.64

Chains :   Asym./Biol. Unit : A,B,H,L

Keywords :   Immune System-Viral Protein Complex, Zika Virus, Broadly Neutralizing Antibody, Viral Protein, Immune System, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Barba-Spaeth, W. Dejnirattisai, A. Rouvinski, M. C. Vaney, I. Medits, A. Sharma, E. Simon-Loriere, A. Sakuntabhai, V. M. Cao-Lormeau, A. Haouz, P. England, K. Stiasny, J. Mongkolsapaya F. X. Heinz, G. R. Screaton, F. A. Rey
Structural Basis Of Potent Zika-Dengue Virus Antibody Cross-Neutralization.
Nature V. 536 48 2016
PubMed-ID: 27338953 | Reference-DOI: 10.1038/NATURE18938
(for further references see the PDB file header)

Molecule 1 - POLYPROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Cell	:	SCHNEIDER 2
	Expression System Plasmid	:	PT389
	Expression System Taxid	:	7227
	Expression System Vector Type	:	PMT-BIP-STREP
	Organism Common	:	ZIKV
	Organism Scientific	:	ZIKA VIRUS
	Organism Taxid	:	64320
	Strain	:	MR 766

Molecule 2 - BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11
	Chains	:	H
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Cell	:	SCHNEIDER 2
	Expression System Taxid	:	7227
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	FAB FRAGMENT, HEAVY CHAIN

Molecule 3 - BROADLY NEUTRALIZING HUMAN ANTIBODY EDE2 A11
	Chains	:	L
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Cell	:	SCHNEIDER 2
	Expression System Taxid	:	7227
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	FAB FRAGMENT, LIGHT CHAIN

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	H	L

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 9)

No.	Name	Count	Type	Full Name
1	BMA	1	Ligand/Ion	BETA-D-MANNOSE
2	FMT	1	Ligand/Ion	FORMIC ACID
3	FUC	1	Ligand/Ion	ALPHA-L-FUCOSE
4	GOL	3	Ligand/Ion	GLYCEROL
5	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:37 , LYS A:38 , LEU A:298 , ARG A:299 , LEU A:300 , HIS B:398	binding site for residue GOL A 502
2	AC2	SOFTWARE	HIS A:323 , THR A:325 , ARG A:357 , ASP A:379 , ARG A:402	binding site for residue GOL A 503
3	AC3	SOFTWARE	GLU A:79 , ARG A:94 , THR A:95 , LEU A:96 , SER A:112	binding site for residue FMT A 504
4	AC4	SOFTWARE	PHE B:11 , HIS B:323 , ARG B:357 , ASP B:379	binding site for residue GOL B 505
5	AC5	SOFTWARE	GLY A:150 , MET A:151 , VAL A:153 , ASN A:154	binding site for Mono-Saccharide NAG A 501 bound to ASN A 154
6	AC6	SOFTWARE	HIS B:148 , GLY B:150 , MET B:151 , VAL B:153 , ASN B:154 , ASP B:161 , SER H:28 , ASN H:31 , PHE H:99	binding site for Poly-Saccharide residues NAG B 501 through FUC B 504 bound to ASN B 154

Asymmetric/Biological Unit

No.	Residues
1	A:3	-	A:30
2	A:60	-	A:121
3	A:74	-	A:105
4	A:92	-	A:116
5	A:190	-	A:291
6	A:308	-	A:339
7	B:3	-	B:30
8	B:60	-	B:121
9	B:74	-	B:105
10	B:92	-	B:116
11	B:190	-	B:291
12	B:308	-	B:339
13	H:22	-	H:92
14	H:140	-	H:196
15	L:23	-	L:88
16	L:135	-	L:194

Asymmetric/Biological Unit

No.	Residues
1	Gly A:337	-	Pro A:338
2	Gly B:337	-	Pro B:338
3	Phe H:146	-	Pro H:147
4	Glu H:148	-	Pro H:149
5	Tyr L:141	-	Pro L:142

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

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

(no "Exon" information available for 5LCV)

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:406
                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee......eeeeeee..eeeeee......eeeeeeeeee...eeeeeeeeeeeeeeeeeee.........hhhhhh..eeeeeeeeee.........eeeeeeeeeeeeeeeeeeeee.....eeeeeeeee....hhhhh...........eeeeee.....eeeee.hhh.eeeeeee.....hhh.eeeee....eeeeehhhhh.....eee......hhhh.eeeeee...eeeeee...hhhhhhhhh...eeeeee..eeee...eeeeeee.................eee....ee.....eeeeeee......ee..eeee.......ee.ee.....ee......eeeeeeee...eeeeeee.hhhhheeeeeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5lcv A    1 IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATLGGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGAPHWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGWSHPQF  425
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       419      
                                                                                                                                                                                                                                                              229|                                                                                                                                                                      403|      
                                                                                                                                                                                                                                                               234                                                                                                                                                                       419

Chain B from PDB  Type:PROTEIN  Length:405
                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...eeeeeee...eeeee......eeeeeeeeee...eeeeeeeeeeeeeeeeeee.........hhhhhh..eeeeeeeeee.........eeeeeeeeeeeeeeeeeeeee.....eeeeeeeee....hhhhh...........eeeeee.....eeeee.hhh.eeeeeee.....hhh.eeeee....eeeeehhhhh.....eee..........hhhh.eeeee.....eeeee...hhhhhhhhh...eeeeee..eeee...eeeeeee.................eee....ee.....eeeeeee......ee..eeee.......ee.ee.....ee......eeeeeeee...eeeeeee.hhhhheeeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5lcv B    1 IRCIGVSNRDFVEGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATLGGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTGTPHWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGWSHP  423
                                    10   ||   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       343       353       363       373       383       393       403|    
                                        14|                                                                                                                                                                                                                                                                                                                                                                                              403|    
                                         18                                                                                                                                                                                                                                                                                                                                                                                               419

Chain H from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeehhhhhhhh...............ee...eeeee........eeeee....eeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeee.........eeeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5lcv H    1 EVQLVESGGGLVRPGGSLRLSCAASGFSYSNHWMHWVRQAPGKGLVWVSRINSDGSTRNYADFVKGRFTISRDNAENTLYLEMNSLTADDTAVYYCVRDGVRFYYDSTGYYPDSFFKYGMDVWGQGTTVTVSSASTKGPSVFPLAPSTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP  213
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||||||100P       110       120      |137       147       157       167       177       187       197       207      
                                                                              52A                            82A||               100A|||||100J||||||                        127|                                                                              
                                                                                                              82B|                100B|||||100K|||||                         135                                                                              
                                                                                                               82C                 100C|||||100L||||                                                                                                          
                                                                                                                                    100D|||||100M|||                                                                                                          
                                                                                                                                     100E|||| 100N||                                                                                                          
                                                                                                                                      100F|||  100O|                                                                                                          
                                                                                                                                       100G||   100P                                                                                                          
                                                                                                                                        100H|                                                                                                                 
                                                                                                                                         100I

Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                     
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...eeee.....eeeeeeee..hhhhhhh.eeeee......eeee.............eeeee...eeeeee...hhhhheeeeeeeeee..eeee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhh...eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5lcv L    2 SVLTQPVSVSGSPGQSITISCTGTSSNADTYNLVSWYQQRPGKAPKLMIYEGTKRPSGVSNRFSASKSATAASLTISGLQPEDEADYYCCSYATSRTLVFGGGTKLTVVGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  210
                                   |12        22     |||29        39        49        59        69        79        89      | 98       108       118       128       138       148       158       168       178       188       198       208  
                                   9|              27A||                                                                  95A                                                                                                                   
                                   11               27B|                                                                                                                                                                                        
                                                     27C

Legend:		→ Mismatch	(orange background)
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		→ 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 "SCOP Domain" information available for 5LCV)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

(no "Gene Ontology" information available for 5LCV)

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu H:148 - Pro H:149	[ RasMol ]
		Gly A:337 - Pro A:338	[ RasMol ]
		Gly B:337 - Pro B:338	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Tyr L:141 - Pro L:142	[ RasMol ]

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	5lcv
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5lbs	5LBS CONTAINS THE ZIKA VIRUS ENVELOPE PROTEIN E COMPLEXED WITH BROADLY NEUTRALIZING ANTIBODY EDE1 C8 SCFV FRAGMENT
5lbv	5LBV CONTAINS THE APO PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 9)

Sites (6, 6)

SS Bonds (16, 16)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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