3LEV - JenaLib

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Title :   HIV-1 ANTIBODY 2F5 IN COMPLEX WITH EPITOPE SCAFFOLD ES2

Authors :   G. Ofek, F. J. Guenaga, W. R. Schief, J. Skinner, D. Baker, R. Wyatt, P. D.

Date :   15 Jan 10 (Deposition) - 29 Sep 10 (Release) - 24 Nov 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,H,L
Biol. Unit 1: A,H,L  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: H,L  (1x)

Keywords :   Hiv-1, Gp41, Monoclonal Antibody, 2F5, Scaffold, Epitope, Transplant, Graft, Sigma Factor, Re-Elicitation, Immune System, Vaccine Design (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Ofek, F. J. Guenaga, W. R. Schief, J. Skinner, D. Baker, R. Wyatt, P. D. Kwong
Elicitation Of Structure-Specific Antibodies By Epitope Scaffolds.
Proc. Natl. Acad. Sci. Usa V. 107 17880 2010
PubMed-ID: 20876137 | Reference-DOI: 10.1073/PNAS.1004728107

Molecule 1 - RNA POLYMERASE SIGMA FACTOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Plasmid	:	CMV-R
	Expression System Strain	:	EMBRYONIC KIDNEY CELL LINE 293 FREESTYLE
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 93-271
	Gene	:	SIGMA FACTOR SIGA
	Organism Scientific	:	THERMUS AQUATICUS
	Organism Taxid	:	271

Molecule 2 - 2F5 ANTIBODY LIGHT CHAIN
	Chains	:	L
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Common	:	HUMAN
	Expression System Strain	:	CELL LINE CB-F7
	Expression System Taxid	:	9606
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	HETEROMYELOMA CELL LINE FUSED WITH PERIPHERAL BLOOD MONONUCLEAR CELLS

Molecule 3 - 2F5 ANTIBODY HEAVY CHAIN
	Chains	:	H
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Common	:	HUMAN
	Expression System Strain	:	CELL LINE CB-F7
	Expression System Taxid	:	9606
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	HETEROMYELOMA CELL LINE FUSED WITH PERIPHERAL BLOOD MONONUCLEAR CELLS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 1 (3, 3)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	GOL	1	Ligand/Ion	GLYCEROL

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	1PE	-1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	ATP	-1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	GOL	-1	Ligand/Ion	GLYCEROL

Biological Unit 3 (3, 3)

No.	Name	Count	Type	Full Name
1	1PE	1	Ligand/Ion	PENTAETHYLENE GLYCOL
2	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
3	GOL	1	Ligand/Ion	GLYCEROL

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER L:9 , PRO L:40 , GLY L:41 , TYR L:87 , GLY L:101 , ARG L:103	BINDING SITE FOR RESIDUE 1PE L 215
2	AC2	SOFTWARE	ARG A:97 , LYS A:149 , ASP A:175 , LYS A:179 , LYS A:186 , LEU A:189 , ARG A:193 , SER A:212 , PRO H:61 , ASN H:64 , THR H:65 , HOH H:257	BINDING SITE FOR RESIDUE ATP H 219
3	AC3	SOFTWARE	ARG H:100H , HOH H:283 , HOH H:284 , HOH H:285 , HOH H:286 , HOH H:287	BINDING SITE FOR RESIDUE GOL H 220

Asymmetric Unit

No.	Residues
1	H:22	-	H:92
2	H:140	-	H:196
3	L:23	-	L:88
4	L:134	-	L:194

Asymmetric Unit

No.	Residues
1	Ser L:7	-	Pro L:8
2	Tyr L:94	-	Pro L:95
3	Tyr L:140	-	Pro L:141
4	Phe H:146	-	Pro H:147
5	Glu H:148	-	Pro H:149

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

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

(no "Exon" information available for 3LEV)

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:177
 aligned with SIGA_THEAQ | Q9EZJ8 from UniProtKB/Swiss-Prot  Length:438

    Alignment length:177
                                   102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       
          SIGA_THEAQ     93 SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTARIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIADQ  269
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh...eehhhhhhhhhhhhhhh.hhhhhh.......hhhhhhhhhhhhhh................hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3lev A   93 SDPVRQYLHEIGEVLELDKWAELGAAAKVEEGMEAIKKLSEATGLDQELIREVVRAKILGTAAIQKIPGLKEKPDPKTVEEVDGKLKSLPKELKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRGFAFSTYATWWIRQAINRAIADQ  269
                                   102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262

Chain H from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                              
               SCOP domains d3levh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                                      d3levh2 H:114-218 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.........eeeeeee......eeeeeee....eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee...eee..eeeehhhhh...ee...eeeee........eeeee.............eeeeeeee.....eeee.hhh....eee...ee.....eeeeeee............eeeeeehhhheeeeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3lev H    1 RITLKESGPPLVKPTQTLTLTCSFSGFSLSDFGVGVGWIRQPPGKALEWLAIIYSDDDKRYSPSLNTRLTITKDTSKNQVVLVMTRVSPVDTATYFCAHRRGPTTLFGVPIARGPVNAMDVWGQGITVTISSTSTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK  218
                                    10        20        30     || 38        48        58        68        78    ||| 85        95     |100E|||||||101       111       121       131       141       151       161       171       181       191       201       211       
                                                             35A|                                             82A||               100A|||||100J||||                                                                                                                      
                                                              35B                                              82B|                100B|||||100K|||                                                                                                                      
                                                                                                                82C                 100C|||||100L||                                                                                                                      
                                                                                                                                     100D|||||100M|                                                                                                                      
                                                                                                                                      100E|||| 100N                                                                                                                      
                                                                                                                                       100F|||                                                                                                                           
                                                                                                                                        100G||                                                                                                                           
                                                                                                                                         100H|                                                                                                                           
                                                                                                                                          100I

Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d3levl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d3levl2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee..ee.......eeeee.......ee.....hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhh...eeeeeee.......ee..ee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3lev L    1 ALQLTQSPSSLSASVGDRITITCRASQGVTSALAWYRQKPGSPPQLLIYDASSLESGVPSRFSGSGSGTEFTLTISTLRPEDFATYYCQQLHFYPHTFGGGTRVDVRRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC  214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210

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 "CATH Domain" information available for 3LEV)

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

Asymmetric Unit(hide GO term definitions)

Chain A (SIGA_THEAQ | Q9EZJ8)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0016987	sigma factor activity	A sigma factor is the promoter specificity subunit of eubacterial-type multisubunit RNA polymerases, those whose core subunit composition is often described as alpha(2)-beta-beta-prime. (This type of multisubunit RNA polymerase complex is known to be found in eubacteria and plant plastids). Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, this binds specifically to promoter sequences, with the sigma factor making sequence specific contacts with the promoter elements. The sigma subunit is released from the elongating form of the polymerase and is thus free to act catalytically for multiple RNA polymerase core enzymes.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
	GO:0006352	DNA-templated transcription, initiation	Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
	GO:0010468	regulation of gene expression	Any process that modulates the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0001123	transcription initiation from bacterial-type RNA polymerase promoter	Any process involved in the assembly of bacterial-type RNA polymerase preinitiation complex (PIC) at the core promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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

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	3lev
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1tji	CRYSTAL STRUCTURE OF THE BROADLY NEUTRALIZING ANTI-HIV-1 ANTIBODY 2F5 IN COMPLEX WITH A GP41 17MER
3les	2F5 EPITOPE SCAFFOLD ES2
3lex	2F5 EPITOPE SCAFFOLD ELICITED ANTI-HIV-1 MONOCLONAL ANTIBODY 11F10 IN COMPLEX WITH HIV-1 GP41
3ley	2F5 EPITOPE SCAFFOLD ELICITED ANTI-HIV-1 MONOCLONAL ANTIBODY 6A7 IN COMPLEX WITH HIV-1 GP41

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (4, 4)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (4, 4)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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