3F12 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   GERMLINE V-GENES SCULPT THE BINDING SITE OF A FAMILY OF ANTIBODIES NEUTRALIZING HUMAN CYTOMEGALOVIRUS

Authors :   C. A. Thomson, S. Bryson, G. R. Mclean, A. L. Creagh, E. F. Pai, J. W. Schrader

Date :   27 Oct 08 (Deposition) - 15 Sep 09 (Release) - 15 Sep 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.95

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Human Cytomegalovirus, Antibody, Germline, Immunoglobulin Domain, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. A. Thomson, S. Bryson, G. R. Mclean, A. L. Creagh, E. F. Pai, J. W. Schrader
Germline V-Genes Sculpt The Binding Site Of A Family Of Antibodies Neutralizing Human Cytomegalovirus.
Embo J. V. 27 2592 2008
PubMed-ID: 18772881 | Reference-DOI: 10.1038/EMBOJ.2008.179
(for further references see the PDB file header)

Molecule 1 - M2J1 FAB
	Chains	:	A, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET32B
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - 8F9 FAB
	Chains	:	B, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET40
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3F12)

(no "Site" information available for 3F12)

Asymmetric Unit

No.	Residues
1	A:23	-	A:88
2	A:135	-	A:195
3	B:22	-	B:96
4	B:152	-	B:208
5	C:23	-	C:88
6	C:135	-	C:195
7	D:22	-	D:96
8	D:152	-	D:208

Asymmetric Unit

No.	Residues
1	Ser A:7	-	Pro A:8
2	Trp A:94	-	Pro A:95
3	Pro A:95	-	Pro A:96
4	Tyr A:141	-	Pro A:142
5	Phe B:158	-	Pro B:159
6	Glu B:160	-	Pro B:161
7	Ser C:7	-	Pro C:8
8	Trp C:94	-	Pro C:95
9	Pro C:95	-	Pro C:96
10	Tyr C:141	-	Pro C:142
11	Phe D:158	-	Pro D:159
12	Glu D:160	-	Pro D:161

(no "SAP(SNP)/Variant" information available for 3F12)

(no "PROSITE Motif" information available for 3F12)

(no "Exon" information available for 3F12)

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:211
                                                                                                                                                                                                                                                   
               SCOP domains d3f12a1 A:1-108 automated matches                                                                           d3f12a2 A:110-212 automated matches                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------3f12A02 A:111-212 Immunoglobulins                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......ee.ee...ee.......eeeee....eeeee.........eeeeee............eeeee......eeeee..........eeeeeeeeeee.....eeeeee........ee............eeeeeeeeeehhhhhh...eeeeee.......eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f12 A   1 EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPPWTFGQGTKVEIKTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 212
                                    10        20        30        40        50        60        70        80        90       100       111       121       131       141       151       161       171       181       191       201       211 
                                                                                                                                     108|                                                                                                      
                                                                                                                                      110

Chain B from PDB  Type:PROTEIN  Length:199
                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3f12B01 B:2-124 Immunoglobulins                                                                                    3f12B02 B:128-224 Immunoglobulins                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...eee.....ee..ee..........eeeeee......eeeeee.................eeee.....eeeeee........eeee...............eeeee.....eeeee....eeeeeeee......eee........eee..........eeeeeee.......eeeeeee....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f12 B   2 VQLVESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVISYDGSNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDGSGLLDYWGQGTLVTVSFKGPSVFPLATAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSQTYICNVNHKPSNTKVDKKVE 224
                                    11        21        31        41        51        61        71        81        91       109       119    || 132    || 151       161       171       181       191       205       215         
                                                                                                                            100|            124|      137|                                                 199|                    
                                                                                                                             109             128       147                                                  204

Chain C from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d3f12c1 C:1-108 automated matches                                                                           d3f12c2 C:110-214 automated matches                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------3f12C02 C:111-214 Immunoglobulins                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eee......ee.eeee.......eeeeee......ee.ee...ee.......eeeee...eeeeee...hhhhh.eeeeee.............eee.......eeeee....hhhhhh...eeeeeeee.....eeeeee..ee....eeeee.........eeeeeee..hhhhhh...eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f12 C   1 EIVLTQSPATLSLSPGERATLSCRASQSVSSYLAWYQQKPGQAPRLLIYDASNRATGIPARFSGSGSGTDFTLTISSLEPEDFAVYYCQQRSNWPPWTFGQGTKVEIKTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 214
                                    10        20        30        40        50        60        70        80        90       100       111       121       131       141       151       161       171       181       191       201       211   
                                                                                                                                     108|                                                                                                        
                                                                                                                                      110

Chain D from PDB  Type:PROTEIN  Length:202
                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3f12D01 D:1-125 Immunoglobulins                                                                                      3f12D02 D:126-224 Immunoglobulins                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee.......ee.hhhh..eeeee.....eeeeee........eeeeeee.......ee...eeeee........eeee...eeeeeeeeee..................ee...ee.....eeeeeeeee......eeeeehhhheeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3f12 D   1 QVQLVESGGGVVQPGRSLRLSCAASGFTFSSYGMHWVRQAPGKGLEWVAVISYDGSNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDGSGLLDYWGQGTLVTVSSASFKGPSVFPLATAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSTYICNVNHKPSNTKVDKKVE 224
                                    10        20        30        40        50        60        70        80        90       100|      118       128       147       157       167       177       187       197 ||    212       222  
                                                                                                                             100|                         137|                                                 199|                   
                                                                                                                              109                          147                                                  205

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: Immunoglobulin (5995)

Family: C1 set domains (antibody constant domain-like) (3013)

Protein domain: automated matches (652)

Human (Homo sapiens) [TaxId: 9606] (334)

1a	d3f12a2	A:110-212
1b	d3f12c2	C:110-214

Family: V set domains (antibody variable domain-like) (1919)

Protein domain: automated matches (311)

Human (Homo sapiens) [TaxId: 9606] (85)

2a	d3f12a1	A:1-108
2b	d3f12c1	C:1-108

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Homo sapiens. Organism_taxid: 9606. (14)

1a	3f12C02	C:111-214
1b	3f12A02	A:111-212
1c	3f12D02	D:126-224
1d	3f12B02	B:128-224
1e	3f12B01	B:2-124
1f	3f12D01	D:1-125

(no "Pfam Domain" information available for 3F12)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 3F12)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3f12)

	Sites
(no "Sites" information available for 3f12)

	Cis Peptide Bonds
		Glu B:160 - Pro B:161	[ RasMol ]
		Glu D:160 - Pro D:161	[ RasMol ]
		Phe B:158 - Pro B:159	[ RasMol ]
		Phe D:158 - Pro D:159	[ RasMol ]
		Pro A:95 - Pro A:96	[ RasMol ]
		Pro C:95 - Pro C:96	[ RasMol ]
		Ser A:7 - Pro A:8	[ RasMol ]
		Ser C:7 - Pro C:8	[ RasMol ]
		Trp A:94 - Pro A:95	[ RasMol ]
		Trp C:94 - Pro C:95	[ RasMol ]
		Tyr A:141 - Pro A:142	[ RasMol ]
		Tyr C:141 - Pro C:142	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	3f12
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3eyf	8F9 FAB PLUS PEPTIDE. MATURE, HIGH-AFFINITY VERSION OF M2J1.
3eyo	8F9 FAB WITHOUT PEPTIDE. MATURE, HIGH-AFFINITY VERSION OF M2J1
3eyq	CRYSTAL STRUCTURE OF 8F9 FAB AND M2J5, A GERMLINE VARIANT OF M2J1 FAB.

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (8, 8)

Cis Peptide Bonds (12, 12)

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SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (2, 4)

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