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Biological Unit 2 (Jmol Viewer)

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

Authors :   M. C. Vaney, A. Rouvinski, G. Barba-Spaeth, F. A. Rey

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

Method :   X-RAY DIFFRACTION

Resolution :   2.41

Chains :   Asym. Unit : A,B,H,I,L,M
Biol. Unit 1: A,H,L  (2x)
Biol. Unit 2: B,I,M  (2x)

Keywords :   Immune System-Viral Protein Complex, Zika Virus, Broadly Neutralizing Antibody, Immune System-Viral Protein (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 - ENVELOPE PROTEIN E
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Cell	:	SCHNEIDER 2
	Expression System Common	:	FUIT FLY
	Expression System Taxid	:	7227
	Organism Common	:	ZIKV
	Organism Scientific	:	ZIKA VIRUS
	Organism Taxid	:	64320
	Strain	:	MR 766

Molecule 2 - BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8
	Chains	:	H, I
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Cell	:	SCHNEIDER 2
	Expression System Common	:	FUIT FLY
	Expression System Taxid	:	7227
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	SCFV FRAGMENT, HEAVY CHAIN

Molecule 3 - BROADLY NEUTRALIZING HUMAN ANTIBODY EDE1 C8
	Chains	:	L, M
	Engineered	:	YES
	Expression System	:	DROSOPHILA MELANOGASTER
	Expression System Cell	:	SCHNEIDER 2
	Expression System Common	:	FRUIT FLY
	Expression System Taxid	:	7227
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	SCFV FRAGMENT, LIGHT CHAIN

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	H	I	L	M
Biological Unit 1 (2x)	:	A		H		L
Biological Unit 2 (2x)	:		B		I		M

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 14)

No.	Name	Count	Type	Full Name
1	EDO	11	Ligand/Ion	1,2-ETHANEDIOL
2	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 18)

No.	Name	Count	Type	Full Name
1	EDO	16	Ligand/Ion	1,2-ETHANEDIOL
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 10)

No.	Name	Count	Type	Full Name
1	EDO	6	Ligand/Ion	1,2-ETHANEDIOL
2	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:323 , ARG A:357 , ASP A:379 , ARG A:402	binding site for residue EDO A 801
02	AC2	SOFTWARE	HIS A:398 , HIS A:399	binding site for residue EDO A 802
03	AC3	SOFTWARE	ILE A:1 , ARG A:164	binding site for residue EDO A 803
04	AC4	SOFTWARE	ARG A:299 , LEU A:300 , GLY A:302 , VAL A:303 , SER A:304 , TYR A:305	binding site for residue SO4 A 804
05	AC5	SOFTWARE	LYS B:340 , TRP B:440 , SER B:441 , ARG M:18	binding site for residue SO4 B 501
06	AC6	SOFTWARE	SER A:66 , ASP A:67 , MET A:68 , GLY H:54	binding site for residue EDO H 201
07	AC7	SOFTWARE	TYR H:32 , TYR H:96 , MET H:100E	binding site for residue EDO H 202
08	AC8	SOFTWARE	TYR I:32 , GLY I:95 , TYR I:96 , MET I:100E	binding site for residue EDO I 201
09	AC9	SOFTWARE	THR H:108 , THR I:107 , THR I:108	binding site for residue SO4 I 202
10	AD1	SOFTWARE	ILE A:317 , ARG L:66 , HOH L:305	binding site for residue EDO L 201
11	AD2	SOFTWARE	ARG L:45 , PRO L:59 , ARG L:61 , GLU L:81	binding site for residue EDO L 202
12	AD3	SOFTWARE	LEU H:45 , GLU H:46 , TYR H:47 , THR L:97 , PHE L:98 , HOH L:303	binding site for residue EDO L 203
13	AD4	SOFTWARE	SER M:67 , THR M:69 , ASP M:70	binding site for residue EDO M 801
14	AD5	SOFTWARE	ILE B:317 , SER M:30 , ARG M:66	binding site for residue EDO M 802

Asymmetric 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	I:22	-	I:92
15	L:23	-	L:88
16	M:23	-	M:88

Asymmetric Unit

No.	Residues
1	Gly B:337	-	Pro B:338
2	Ser L:7	-	Pro L:8
3	Pro L:95	-	Pro L:95A
4	Ser M:7	-	Pro M:8
5	Pro M:95	-	Pro M:95A

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

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

(no "Exon" information available for 5LBS)

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
	(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:394
                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.....eeeeeee...eeeeee.....eeeeeeeeeee..eeeeeeeeeeeeeeeeeee.........hhhhh...eeeeeeeeeehhhhh....eeeeeeeeeeeeeeeeeeeee.hhh.eeeeeeeee........eeeeee.....eeeee.hhh.eeeeee.....eeeeee..eeeeeehhhhhh....eee........hhhh.eeeeee...eeeeee...hhhhhhhhh...eee.....eee....eeeeeee.hhh.......ee....eee....ee.....eeeeeee......ee..eeee..........ee.....ee......eeeeeeee...eeeeeee......eeeeeee........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5lbs A    1 IRCIGVSNRDFVEGMSGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSQHDENRAKVEITPNSPRAEATLGGFGSLGLDCEPFSDLYYLTMNNKHWLVHKEWFHDIPLPWHAGADTPHWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGGSWSHPQFE  446
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       162       172       182       192|      207       217       227  ||   239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399   ||  442    
                                                                                                                                                                             148|                            192|                             230|                                                                                                                                                                       403|         
                                                                                                                                                                              161                             198                              233                                                                                                                                                                        437

Chain B from PDB  Type:PROTEIN  Length:386
                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee..eeeeeee...eeeeee.....eeeeeeeeeee..eeeeeeeeeeeeeeeeeee.........hhhhh...eeeeeeeeeehhhhh....eeeeeeeeeeeeeeeeeeeee.hhh.eeeeeeeee......eeeeee.....eeeee.hhh.eeeeee.hhhh.hhh.eeeeee..eeeeeehhhhhh....ee....hhhh.eeeeee...eeeeee...hhhhhhhhh...eee.....eee....eeeeeee.hhh.......ee....eee....ee.....eeeeeee......ee..eeee..........ee.....ee......eeeeeeee...eeeeeee......eeeeeee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5lbs B    1 IRCIGVSNRDFVEGGTWVDVVLEHGGCVTVMAQDKPTVDIELVTTTVSNMAEVRSYCYEASISDMASDSRCPTQGEAYLDKQSDTQYVCKRTLVDRGWGNGCGLFGKGSLVTCAKFACSKKMTGKSIQPENLEYRIMLSVHGSQENRAKVEITPNSPRAEATLGGFGSLGLDCEPRTGLDFSDLYYLTMNNKHWLVHKEWFHDIPLPWHPHWNNKEALVEFKDAHAKRQTVVVLGSQEGAVHTALAGALEAEMDGAKGRLSSGHLKCRLKMDKLRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGGSWSHP  443
                                    10   ||   23        33        43        53        63        73        83        93       103       113       123       133       143   ||  167       177       187       197       207       217       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       437      
                                        14|                                                                                                                              147|                                                             226|                                                                                                                                                                      403|      
                                         18                                                                                                                               162                                                              234                                                                                                                                                                       437

Chain H from PDB  Type:PROTEIN  Length:121
                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhh.eeeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeee..........ee...eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                5lbs H    1 EVQLVESGGGLVQPGGSLRLSCSASGFTFSTYSMHWVRQAPGKGLEYVSAITGEGDSAFYADSVKGRFTISRDNSKNTLYFEMNSLRPEDTAVYYCVGGYSNFYYYYTMDVWGQGTTVTVS  112
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||101       111 
                                                                              52A                            82A||               100A||||            
                                                                                                              82B|                100B|||            
                                                                                                               82C                 100C||            
                                                                                                                                    100D|            
                                                                                                                                     100E

Chain I from PDB  Type:PROTEIN  Length:122
                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhh.eeeeeeee.....eeeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeeee..........ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                5lbs I    1 EVQLVESGGGLVQPGGSLRLSCSASGFTFSTYSMHWVRQAPGKGLEYVSAITGEGDSAFYADSVKGRFTISRDNSKNTLYFEMNSLRPEDTAVYYCVGGYSNFYYYYTMDVWGQGTTVTVSS  113
                                    10        20        30        40        50  |     59        69        79   |||  86        96    |||101       111  
                                                                              52A                            82A||               100A||||             
                                                                                                              82B|                100B|||             
                                                                                                               82C                 100C||             
                                                                                                                                    100D|             
                                                                                                                                     100E

Chain L from PDB  Type:PROTEIN  Length:111
                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee............eeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                5lbs L    1 EIVLTQSPATLSLSPGERATLSCRASQSISTFLAWYQHKPGQAPRLLIYDASTRATGVPARFSGSRSGTDFTLTISTLEPEDFAVYYCQQRYNWPPYTFGQGTKVEIKAAA  110
                                    10        20        30        40        50        60        70        80        90     |  99       109 
                                                                                                                         95A

Chain M from PDB  Type:PROTEIN  Length:112
                                                                                                                                                 
               SCOP domains ---------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee............eeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------- Transcript
                5lbs M    0 SEIVLTQSPATLSLSPGERATLSCRASQSISTFLAWYQHKPGQAPRLLIYDASTRATGVPARFSGSRSGTDFTLTISTLEPEDFAVYYCQQRYNWPPYTFGQGTKVEIKAAA  110
                                     9        19        29        39        49        59        69        79        89      | 98       108  
                                                                                                                          95A

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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 5LBS)

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

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

Asymmetric Unit(hide GO term definitions)

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

Asymmetric Unit
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	Cis Peptide Bonds
		Gly B:337 - Pro B:338	[ RasMol ]
		Pro L:95 - Pro L:95A	[ RasMol ]
		Pro M:95 - Pro M:95A	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Ser M:7 - Pro M:8	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 14)

Sites (14, 14)

SS Bonds (16, 16)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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