2FX9 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HIV-1 NEUTRALIZING HUMAN FAB 4E10 IN COMPLEX WITH A THIOETHER-LINKED PEPTIDE ENCOMPASSING THE 4E10 EPITOPE ON GP41

Authors :   R. M. F. Cardoso, F. M. Brunel, S. Ferguson, D. R. Burton, P. E. Dawson, I. A. Wilson

Date :   03 Feb 06 (Deposition) - 19 Dec 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Immunoglobulin Fold, Beta-Sandwich, Antibody-Epitope Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. M. Cardoso, F. M. Brunel, S. Ferguson, M. Zwick, D. R. Burton, P. E. Dawson, I. A. Wilson
Structural Basis Of Enhanced Binding Of Extended And Helically Constrained Peptide Epitopes Of The Broadly Neutralizing Hiv-1 Antibody 4E10.
J. Mol. Biol. V. 365 1533 2007
PubMed-ID: 17125793 | Reference-DOI: 10.1016/J.JMB.2006.10.088
(for further references see the PDB file header)

Molecule 1 - FAB 4E10
	Chains	:	L, M
	Engineered	:	YES
	Expression System	:	CRICETULUS GRISEUS
	Expression System Common	:	CHINESE HAMSTER
	Expression System Taxid	:	10029
	Fragment	:	LIGHT CHAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 2 - FAB 4E10
	Chains	:	H, I
	Engineered	:	YES
	Expression System	:	CRICETULUS GRISEUS
	Expression System Common	:	CHINESE HAMSTER
	Expression System Taxid	:	10029
	Fragment	:	HEAVY CHAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

Molecule 3 - FRAGMENT OF HIV GLYCOPROTEIN GP41
	Chains	:	P, Q
	Engineered	:	YES
	Fragment	:	PEPTIDE EPITOPE OF 4E10
	Other Details	:	THIS SEQUENCE INCLUDES A FRAGMENT OF THE HIV ENVELOPE PROTEIN GP41
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	ORQ	2	Mod. Amino Acid	N~5~-ACETYL-L-ORNITHINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	ORQ	1	Mod. Amino Acid	N~5~-ACETYL-L-ORNITHINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	ORQ	1	Mod. Amino Acid	N~5~-ACETYL-L-ORNITHINE

(no "Site" information available for 2FX9)

Asymmetric Unit

No.	Residues
1	H:22	-	H:92
2	H:142	-	H:208
3	I:22	-	I:92
4	I:142	-	I:208
5	L:23	-	L:88
6	L:134	-	L:194
7	M:23	-	M:88
8	M:134	-	M:194

Asymmetric Unit

No.	Residues
1	Ser L:7	-	Pro L:8
2	Tyr L:140	-	Pro L:141
3	Phe H:148	-	Pro H:149
4	Glu H:150	-	Pro H:151
5	Ser M:7	-	Pro M:8
6	Tyr M:140	-	Pro M:141
7	Phe I:148	-	Pro I:149
8	Glu I:150	-	Pro I:151

(no "SAP(SNP)/Variant" information available for 2FX9)

(no "PROSITE Motif" information available for 2FX9)

(no "Exon" information available for 2FX9)

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 H from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                    
               SCOP domains d2fx9h1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                                 d2fx9h2 H:114-227 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 2fx9H01 H:1-109 Immunoglobulins                                                                                            2fx9H02 H:110-227 Immunoglobulins                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee.....eeeeeeeehhhheeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeee........eeeeeeee...eeeee........eeeee..hhhhh...eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2fx9 H    1 QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGWGWLGKPIGAFAHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  227
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||||   106       116       126   ||  138       148     ||163     ||174     ||185       195    |||208       218   ||  
                                                                              52A                            82A||               100A|||||100J                           130|                  154|||    169|      180|               200||              222|  
                                                                                                              82B|                100B|||||||                             133                   156||     171       182                203|               225  
                                                                                                               82C                 100C||||||                                                    157|                                   205                    
                                                                                                                                    100D|||||                                                     162                                                          
                                                                                                                                     100E||||                                                                                                                  
                                                                                                                                      100F|||                                                                                                                  
                                                                                                                                       100G||                                                                                                                  
                                                                                                                                        100H|                                                                                                                  
                                                                                                                                         100I

Chain I from PDB  Type:PROTEIN  Length:227
                                                                                                                                                                                                                                                                    
               SCOP domains d2fx9i1 I:1-113 Immunoglobulin heavy chain variable domain, VH                                                                 d2fx9i2 I:114-227 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 2fx9I01 I:1-109 Immunoglobulins                                                                                            2fx9I02 I:110-227 Immunoglobulins                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee........eeeeee.....eeeeeeee....eeee.hhhh..eeeeee....eeeeee...hhhhheeeeeeeeee........eeeeeeee...eeeee........eeeee..hhhhh...eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2fx9 I    1 QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGWGWLGKPIGAFAHWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  227
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||||   106       116       126   ||  138       148     ||163     ||174     ||185       195    |||208       218   ||  
                                                                              52A                            82A||               100A|||||100J                           130|                  154|||    169|      180|               200||              222|  
                                                                                                              82B|                100B|||||||                             133                   156||     171       182                203|               225  
                                                                                                               82C                 100C||||||                                                    157|                                   205                    
                                                                                                                                    100D|||||                                                     162                                                          
                                                                                                                                     100E||||                                                                                                                  
                                                                                                                                      100F|||                                                                                                                  
                                                                                                                                       100G||                                                                                                                  
                                                                                                                                        100H|                                                                                                                  
                                                                                                                                         100I

Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d2fx9l1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                  d2fx9l2 L:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 2fx9L01 L:1-108 Immunoglobulins                                                                              2fx9L02 L:109-211 Immunoglobulins                                                                      -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee...hhhh.eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2fx9 L    1 EIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20       |29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209    
                                                     27A

Chain M from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                       
               SCOP domains d2fx9m1 M:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                  d2fx9m2 M:108-213 Immunoglobulin light chain kappa constant domain, CL-kappa                               SCOP domains
               CATH domains 2fx9M01 M:1-108 Immunoglobulins                                                                              2fx9M02 M:109-211 Immunoglobulins                                                                      -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeeee...hhhh.eeeeee......eeee.............eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee....eeeeee.........eeeee.........eeeeeeeeeehhhhh...eeeeeeee......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2fx9 M    1 EIVLTQSPGTQSLSPGERATLSCRASQSVGNNKLAWYQQRPGQAPRLLIYGASSRPSGVADRFSGSGSGTDFTLTISRLEPEDFAVYYCQQYGQSLSTFGQGTKVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE  213
                                    10        20       |29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209    
                                                     27A

Chain P from PDB  Type:PROTEIN  Length:14
 aligned with ENV_HV1W2 | P05880 from UniProtKB/Swiss-Prot  Length:847

    Alignment length:14
                                   671    
           ENV_HV1W2    662 NWFDITNWLWYIKI  675
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                2fx9 P  671 NWFCITrWLWKKKK  684
                                  |680    
                                  |       
                                677-ORQ

Chain Q from PDB  Type:PROTEIN  Length:14
 aligned with ENV_HV1W2 | P05880 from UniProtKB/Swiss-Prot  Length:847

    Alignment length:14
                                   671    
           ENV_HV1W2    662 NWFDITNWLWYIKI  675
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                2fx9 Q  671 NWFCITrWLWKKKK  684
                                  |680    
                                677-ORQ

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: Immunoglobulins (2282)

Human (Homo sapiens) (912)

1a	2fx9L02	L:109-211
1b	2fx9L01	L:1-108
1c	2fx9M01	M:1-108
1d	2fx9H02	H:110-227
1e	2fx9I02	I:110-227
1f	2fx9H01	H:1-109
1g	2fx9I01	I:1-109
1h	2fx9M02	M:109-211

(no "Pfam Domain" information available for 2FX9)

Asymmetric Unit(hide GO term definitions)

Chain P,Q (ENV_HV1W2 | P05880)

molecular function
	GO:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
	GO:0075512	clathrin-dependent endocytosis of virus by host cell	Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
	GO:0075509	endocytosis involved in viral entry into host cell	Any endocytosis that is involved in the uptake of a virus into a host cell.
	GO:0030683	evasion or tolerance by virus of host immune response	Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0039654	fusion of virus membrane with host endosome membrane	Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
	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: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:0002223	stimulatory C-type lectin receptor signaling pathway	Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
	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.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0019082	viral protein processing	Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a viral protein.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0044174	host cell endosome	A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
	GO:0044175	host cell endosome membrane	The lipid bilayer surrounding a host cell endosome.
	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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	Sites
(no "Sites" information available for 2fx9)

	Cis Peptide Bonds
		Glu H:150 - Pro H:151	[ RasMol ]
		Glu I:150 - Pro I:151	[ RasMol ]
		Phe H:148 - Pro H:149	[ RasMol ]
		Phe I:148 - Pro I:149	[ RasMol ]
		Ser L:7 - Pro L:8	[ RasMol ]
		Ser M:7 - Pro M:8	[ RasMol ]
		Tyr L:140 - Pro L:141	[ RasMol ]
		Tyr M:140 - Pro M:141	[ RasMol ]

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	2fx9
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	ENV_HV1W2 \| P05880
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UniProtKB/Swiss-Prot
	ENV_HV1W2 \| P05880	:	2fx7 2fx8 4wy7

1tzg	FAB 4E10 BOUND TO A 13-RESIDUE PEPTIDE EPITOPE
2fx7	FAB 4E10 BOUND TO A 16-RESIDUE PEPTIDE EPITOPE
2fx8	FAB 4E10 BOUND TO AN AIB-INDUCED PEPTIDE EPITOPE

Description

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (0, 0)

SS Bonds (8, 8)

Cis Peptide Bonds (8, 8)

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