3O41 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF 101F FAB BOUND TO 15-MER PEPTIDE EPITOPE

Authors :   J. S. Mclellan, M. Chen, J. S. Chang, Y. Yang, A. Kim, B. S. Graham, P. D. Kw

Date :   26 Jul 10 (Deposition) - 13 Oct 10 (Release) - 17 Nov 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

Keywords :   Immunoglobulin, Immune System-Viral Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. S. Mclellan, M. Chen, J. S. Chang, Y. Yang, A. Kim, B. S. Graham, P. D. Kwong
Structure Of A Major Antigenic Site On The Respiratory Syncytial Virus Fusion Glycoprotein In Complex With Neutralizing Antibody 101F.
J. Virol. V. 84 12236 2010
PubMed-ID: 20881049 | Reference-DOI: 10.1128/JVI.01579-10

Molecule 1 - MOUSE MONOCLONAL ANTIBODY 101F FAB LIGHT CHAIN
	Chains	:	L, B
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293
	Expression System Common	:	HUMAN
	Expression System Taxid	:	9606
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 2 - MOUSE MONOCLONAL ANTIBODY 101F FAB HEAVY CHAIN
	Chains	:	H, A
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293
	Expression System Common	:	HUMAN
	Expression System Taxid	:	9606
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

Molecule 3 - FUSION GLYCOPROTEIN F1
	Chains	:	P, C
	Engineered	:	YES
	Fragment	:	RESIDUES 422-436
	Organism Scientific	:	HUMAN RESPIRATORY SYNCYTIAL VIRUS A
	Organism Taxid	:	208893
	Other Details	:	SYNTHETIC PEPTIDE
	Synonym	:	PROTEIN F
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 16)

No.	Name	Count	Type	Full Name
1	NH2	2	Mod. Amino Acid	AMINO GROUP
2	SO4	14	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 9)

No.	Name	Count	Type	Full Name
1	NH2	1	Mod. Amino Acid	AMINO GROUP
2	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 7)

No.	Name	Count	Type	Full Name
1	NH2	1	Mod. Amino Acid	AMINO GROUP
2	SO4	6	Ligand/Ion	SULFATE ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG B:18 , HOH B:223 , SER L:65 , GLY L:66 , HOH L:484 , HOH L:508 , HOH L:602	BINDING SITE FOR RESIDUE SO4 L 215
02	AC2	SOFTWARE	LYS L:39 , GLN L:42 , LYS L:45 , HOH L:339	BINDING SITE FOR RESIDUE SO4 L 216
03	AC3	SOFTWARE	LYS B:169 , PRO L:59 , ALA L:60 , HOH L:522 , HOH L:621	BINDING SITE FOR RESIDUE SO4 L 217
04	AC4	SOFTWARE	GLY H:162 , LYS L:169	BINDING SITE FOR RESIDUE SO4 L 218
05	AC5	SOFTWARE	LYS A:43 , ARG L:155 , GLN L:156 , ASN L:157	BINDING SITE FOR RESIDUE SO4 L 219
06	AC6	SOFTWARE	SER A:32 , TRP A:53 , LYS H:64	BINDING SITE FOR RESIDUE SO4 H 214
07	AC7	SOFTWARE	LYS A:64 , SER H:32 , TRP H:53	BINDING SITE FOR RESIDUE SO4 H 215
08	AC8	SOFTWARE	LYS H:71 , ASP H:72 , THR H:73 , HOH H:289 , HOH H:421	BINDING SITE FOR RESIDUE SO4 H 216
09	AC9	SOFTWARE	SER A:161 , GLY A:162 , LYS B:169	BINDING SITE FOR RESIDUE SO4 A 214
10	BC1	SOFTWARE	ASP A:207 , LYS A:208 , LYS A:209 , HOH A:645	BINDING SITE FOR RESIDUE SO4 A 215
11	BC2	SOFTWARE	LYS A:71 , ASP A:72 , THR A:73 , HOH A:273 , HOH A:435 , HOH A:707	BINDING SITE FOR RESIDUE SO4 A 216
12	BC3	SOFTWARE	GLN B:37 , LYS B:39 , GLN B:42 , LYS B:45 , HOH B:268 , HOH B:630 , HOH B:725	BINDING SITE FOR RESIDUE SO4 B 215
13	BC4	SOFTWARE	VAL B:13 , SER B:14 , GLN B:17 , LYS B:107 , HOH B:497 , ARG L:24	BINDING SITE FOR RESIDUE SO4 B 216
14	BC5	SOFTWARE	THR B:182 , ASP B:184 , ARG B:188	BINDING SITE FOR RESIDUE SO4 B 217

Asymmetric Unit

No.	Residues
1	A:22	-	A:92
2	A:140	-	A:195
3	B:23	-	B:88
4	B:134	-	B:194
5	H:22	-	H:92
6	H:140	-	H:195
7	L:23	-	L:88
8	L:134	-	L:194

Asymmetric Unit

No.	Residues
1	Ser L:7	-	Pro L:8
2	His L:76	-	Pro L:77
3	Asp L:94	-	Pro L:95
4	Tyr L:140	-	Pro L:141
5	Phe H:146	-	Pro H:147
6	Glu H:148	-	Pro H:149
7	Trp H:188	-	Pro H:189
8	Phe A:146	-	Pro A:147
9	Glu A:148	-	Pro A:149
10	Trp A:188	-	Pro A:189
11	Ser B:7	-	Pro B:8
12	His B:76	-	Pro B:77
13	Asp B:94	-	Pro B:95
14	Ser B:127	-	Gly B:128
15	Tyr B:140	-	Pro B:141

(no "SAP(SNP)/Variant" information available for 3O41)

(no "PROSITE Motif" information available for 3O41)

(no "Exon" information available for 3O41)

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:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeeee......eeeeeee....eee.hhhhh.eeeeeehhh.eeeeee...hhhhheeeeeeeee.....eeee...eeeee........eeeee.......eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3o41 A    1 QVTLKESGPGILQPSQTLSLTCSFSGFSLSTSGMGVSWIRQPSGKGLEWLAHIYWDDDKRYNPSLKSRLTISKDTSRNQVFLKITSVDTADTATYYCARLYGFTYGFAYWGQGTLVTVSAAKTTPPSVYPLAPGSANSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR  213
                                    10        20        30     || 38        48        58        68        78    ||| 85        95     ||103       113       123     ||136       146       156       166       176       186       196       206       
                                                             35A|                                             82A||               100A|                          129|                                                                                
                                                              35B                                              82B|                100B                           133                                                                                
                                                                                                                82C

Chain B from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee..ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3o41 B    1 DIVLTQSPASLAVSLGQRATIFCRASQSVDYNGISYMHWFQQKPGQPPKLLIYAASNPESGIPARFTGSGSGTDFTLNIHPVEEEDAATYYCQQIIEDPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE  213
                                    10        20       27C|       36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       
                                                     27A|||                                                                                                                                                                                          
                                                      27B||                                                                                                                                                                                          
                                                       27C|                                                                                                                                                                                          
                                                        27D

Chain C from PDB  Type:PROTEIN  Length:10
 aligned with FUS_HRSVA | P03420 from UniProtKB/Swiss-Prot  Length:574

    Alignment length:10
                                   437
           FUS_HRSVA    428 NRGIIKTFSN  437
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                3o41 C  428 NRGIIKTFSx  437
                                   437
                                   437-NH2

Chain H from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeeee......eeeeeee....eee...hhh.eeeeeehhh.eeeeee...hhhhheeeeeeeee.......ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3o41 H    1 QVTLKESGPGILQPSQTLSLTCSFSGFSLSTSGMGVSWIRQPSGKGLEWLAHIYWDDDKRYNPSLKSRLTISKDTSRNQVFLKITSVDTADTATYYCARLYGFTYGFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR  213
                                    10        20        30     || 38        48        58        68        78    ||| 85        95     ||103       113       123       133       143       153       163       173       183       193       203       213
                                                             35A|                                             82A||               100A|                                                                                                                 
                                                              35B                                              82B|                100B                                                                                                                 
                                                                                                                82C

Chain L from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee....ee..ee.eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.hhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3o41 L    1 DIVLTQSPASLAVSLGQRATIFCRASQSVDYNGISYMHWFQQKPGQPPKLLIYAASNPESGIPARFTGSGSGTDFTLNIHPVEEEDAATYYCQQIIEDPWTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC  214
                                    10        20       27C|       36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206        
                                                     27A|||                                                                                                                                                                                           
                                                      27B||                                                                                                                                                                                           
                                                       27C|                                                                                                                                                                                           
                                                        27D

Chain P from PDB  Type:PROTEIN  Length:11
 aligned with FUS_HRSVA | P03420 from UniProtKB/Swiss-Prot  Length:574

    Alignment length:11
                                   436 
           FUS_HRSVA    427 KNRGIIKTFSN  437
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
           Pfam domains (1) Fusion_gly- Pfam domains (1)
           Pfam domains (2) Fusion_gly- Pfam domains (2)
         Sec.struct. author ........... Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                3o41 P  427 KNRGIIKTFSx  437
                                   436|
                                    437-NH2

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 "SCOP Domain" information available for 3O41)

(no "CATH Domain" information available for 3O41)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Fusion_gly] (9)

Family: Fusion_gly (9)

Human respiratory syncytial virus A (strain A2) (5)

1a	Fusion_gly-3o41P01	P:427-436
1b	Fusion_gly-3o41P02	P:427-436

Asymmetric Unit(hide GO term definitions)

Chain C,P (FUS_HRSVA | P03420)

biological process
	GO:0019064	fusion of virus membrane with host plasma membrane	Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
	GO:0006948	induction by virus of host cell-cell fusion	The process of syncytia-forming cell-cell fusion, caused by a virus.
	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:0060141	positive regulation of syncytium formation by virus	The process in which a virus increases the frequency, rate or extent of the formation of a syncytium, a mass of cytoplasm containing several nuclei enclosed within a single plasma membrane, by the fusion of the plasma membranes of two or more individual cells.
	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.
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:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	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:0019031	viral envelope	The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Asp B:94 - Pro B:95	[ RasMol ]
		Asp L:94 - Pro L:95	[ RasMol ]
		Glu A:148 - Pro A:149	[ RasMol ]
		Glu H:148 - Pro H:149	[ RasMol ]
		His B:76 - Pro B:77	[ RasMol ]
		His L:76 - Pro L:77	[ RasMol ]
		Phe A:146 - Pro A:147	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Ser B:127 - Gly B:128	[ RasMol ]
		Ser B:7 - Pro B:8	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Trp A:188 - Pro A:189	[ RasMol ]
		Trp H:188 - Pro H:189	[ RasMol ]
		Tyr B:140 - Pro B:141	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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		Biological Unit 2	[ Jena3D ]

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	3o41
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 16)

Sites (14, 14)

SS Bonds (8, 8)

Cis Peptide Bonds (15, 15)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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