4ZYK - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF QUATERNARY-SPECIFIC RSV-NEUTRALIZING HUMAN ANTIBODY AM14

Authors :   M. S. A. Gilman, J. S. Mclellan

Date :   21 May 15 (Deposition) - 29 Jul 15 (Release) - 29 Jul 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Ig Domain, Fab, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. S. Gilman, S. M. Moin, V. Mas, M. Chen, N. K. Patel, K. Kramer, Q. Zhu, S. C. Kabeche, A. Kumar, C. Palomo, T. Beaumont, U. Baxa, N. D. Ulbrandt J. A. Melero, B. S. Graham, J. S. Mclellan
Characterization Of A Prefusion-Specific Antibody That Recognizes A Quaternary, Cleavage-Dependent Epitope On The Rsv Fusion Glycoprotein.
Plos Pathog. V. 11 05035 2015
PubMed-ID: 26161532 | Reference-DOI: 10.1371/JOURNAL.PPAT.1005035

Molecule 1 - AM14 FAB HEAVY CHAIN
	Chains	:	H, A
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293F
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PVRC8400
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - AM14 LIGHT CHAIN
	Chains	:	L, B
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293F
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PVRC8400
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric Unit	:	A	B	H	L
Biological Unit 1 (1x)	:			H	L
Biological Unit 2 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	EDO	5	Ligand/Ion	1,2-ETHANEDIOL
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 5)

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

Biological Unit 2 (2, 3)

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

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS H:64 , GLY H:65 , EDO H:302 , HOH H:421	binding site for residue SO4 H 301
2	AC2	SOFTWARE	ASN A:56 , THR A:57 , TYR A:58 , LYS H:64 , SO4 H:301	binding site for residue EDO H 302
3	AC3	SOFTWARE	LEU H:141 , VAL H:169 , SER H:177 , SER H:179 , HOH H:411 , HOH H:423 , THR L:178	binding site for residue EDO H 303
4	AC4	SOFTWARE	SER H:17	binding site for residue EDO H 304
5	AC5	SOFTWARE	LYS B:145 , GLN B:147 , SER L:156 , GLY L:157 , HOH L:405	binding site for residue SO4 L 301
6	AC6	SOFTWARE	LEU A:141 , VAL A:169 , SER A:177 , SER A:179 , HOH A:410 , HOH A:413 , THR B:178	binding site for residue EDO A 301
7	AC7	SOFTWARE	SER A:28 , PHE A:29 , SER A:30 , ASN A:76 , LYS L:188 , HIS L:189	binding site for residue ACT A 302
8	AC8	SOFTWARE	HIS B:37 , LYS B:39 , GLU B:45 , PHE B:62 , GLU B:81 , ASP B:82	binding site for residue EDO B 301

Asymmetric Unit

No.	Residues
1	A:22	-	A:92
2	A:140	-	A:196
3	B:23	-	B:88
4	B:134	-	B:194
5	H:22	-	H:92
6	H:140	-	H:196
7	L:23	-	L:88
8	L:134	-	L:194

Asymmetric Unit

No.	Residues
1	Phe H:146	-	Pro H:147
2	Glu H:148	-	Pro H:149
3	Ser L:7	-	Pro L:8
4	Leu L:94	-	Pro L:95
5	Pro L:95	-	Pro L:95A
6	Tyr L:140	-	Pro L:141
7	Phe A:146	-	Pro A:147
8	Glu A:148	-	Pro A:149
9	Ser B:7	-	Pro B:8
10	Pro B:95	-	Pro B:95A
11	Tyr B:140	-	Pro B:141

(no "SAP(SNP)/Variant" information available for 4ZYK)

(no "PROSITE Motif" information available for 4ZYK)

(no "Exon" information available for 4ZYK)

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..eee.....eeeeeeee..hhh.eeeeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeeee.......eeee...eeeee........eeeee.....eeeeeeeeeee.....eeee........eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4zyk A    2 VQLVESGGGVVQPGRSLRLSCAASGFSFSHYAMHWVRQAPGKGLEWVAVISYDGENTYYADSVKGRFSISRDNSKNTVSLQMNSLRPEDTALYYCARDRIVDDYYYYGMDVWGQGATVTVSSASTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  213
                                    11        21        31        41        51 |      60        70        80  |||   87        97   ||||101       111       121      |136       146       156       166       176       186       196       206       
                                                                             52A                            82A||               100A|||||                         128|                                                                               
                                                                                                             82B|                100B||||                          134                                                                               
                                                                                                              82C                 100C|||                                                                                                            
                                                                                                                                   100D||                                                                                                            
                                                                                                                                    100E|                                                                                                            
                                                                                                                                     100F

Chain B from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4zyk B    1 DIQMTQSPSSLSASVGDRVTITCQASQDIKKYLNWYHQKPGKVPELLMHDASNLETGVPSRFSGRGSGTDFTLTISSLQPEDIGTYYCQQYDNLPPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20        30        40        50        60        70        80        90     |  99       109       119       129       139       149       159       169       179       189       199       209    
                                                                                                                         95A

Chain H from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eee.....eeeeeeee..hhhhheeeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee..............eeeee........eeeee.....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4zyk H    2 VQLVESGGGVVQPGRSLRLSCAASGFSFSHYAMHWVRQAPGKGLEWVAVISYDGENTYYADSVKGRFSISRDNSKNTVSLQMNSLRPEDTALYYCARDRIVYYYGMDVWGQGATVTVSSASTKGPSVFPLAPSSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  213
                                    11        21        31        41        51 |      60        70        80  |||   87        97|||||| 104       114       124   ||  139       149       159       169       179       189       199       209    
                                                                             52A                            82A||              98|||||                         128|                                                                               
                                                                                                             82B|             100B||||                          134                                                                               
                                                                                                              82C              100C|||                                                                                                            
                                                                                                                                100D||                                                                                                            
                                                                                                                                 100E|                                                                                                            
                                                                                                                                  100F

Chain L from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee.......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4zyk L    1 DIQMTQSPSSLSASVGDRVTITCQASQDIKKYLNWYHQKPGKVPELLMHDASNLETGVPSRFSGRGSGTDFTLTISSLQPEDIGTYYCQQYDNLPPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    10        20        30        40        50        60        70        80        90     |  99       109       119       129       139       149       159       169       179       189       199       209   
                                                                                                                         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 4ZYK)

(no "CATH Domain" information available for 4ZYK)

(no "Pfam Domain" information available for 4ZYK)

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(no "Gene Ontology" information available for 4ZYK)

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:148 - Pro A:149	[ RasMol ]
		Glu H:148 - Pro H:149	[ RasMol ]
		Leu L:94 - Pro L:95	[ RasMol ]
		Phe A:146 - Pro A:147	[ RasMol ]
		Phe H:146 - Pro H:147	[ RasMol ]
		Pro B:95 - Pro B:95A	[ RasMol ]
		Pro L:95 - Pro L:95A	[ RasMol ]
		Ser B:7 - Pro B:8	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Tyr B:140 - Pro B:141	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (8, 8)

Cis Peptide Bonds (11, 11)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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