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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BROADLY NEUTRALIZING ANTI-HIV-1 ANTIBODY 2F5 IN COMPLEX WITH A GP41 17MER EPITOPE
 
Authors :  G. Ofek, M. Tang, A. Sambor, H. Katinger, J. R. Mascola, R. Wyatt, P. D. Kwong
Date :  04 Jun 04  (Deposition) - 05 Oct 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  H,L,P
Keywords :  2F5, Antibody, Gp41, Hiv-1, Neutralizing, Membrane-Proximal, Viral Protein/Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Ofek, M. Tang, A. Sambor, H. Katinger, J. R. Mascola, R. Wyatt, P. D. Kwong
Structure And Mechanistic Analysis Of The Anti-Human Immunodeficiency Virus Type 1 Antibody 2F5 In Complex With Its Gp41 Epitope
J. Virol. V. 78 10724 2004
PubMed-ID: 15367639  |  Reference-DOI: 10.1128/JVI.78.19.10724-10737.2004
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CB-F7
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: HETEROMYELOMA CELL LINE FUSED WITH PERIPHERAL BLOOD MONONUCLEAR CELLS
 
Molecule 2 - ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell Line: CB-F7
    Expression System Common: CHINESE HAMSTER
    Expression System Taxid: 10029
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: HETEROMYELOMA CELL LINE FUSED WITH PERIPHERAL BLOOD MONONUCLEAR CELLS
 
Molecule 3 - ENVELOPE GLYCOPROTEIN GP41
    Chains: P
    Engineered: YES
    Fragment: TRANSMEMBRANE GLYCOPROTEIN (RESIDUES 653-659)
    Other Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE IS NATURALLY FOUND IN THE HUMAN IMMUNODEFICIENCY VIRUS (HIV-1;
STRAIN JRFL).
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : HLP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2IPA6Ligand/IonISOPROPYL ALCOHOL
3NH21Mod. Amino AcidAMINO GROUP
4YCM2Mod. Amino AcidS-(2-AMINO-2-OXOETHYL)-L-CYSTEINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN H:204 , THR H:205 , LYS H:206 , ASN L:152BINDING SITE FOR RESIDUE EDO L 771
2AC2SOFTWARESER L:10 , SER L:12 , PRO L:141 , GLU L:143 , HOH L:796BINDING SITE FOR RESIDUE EDO L 772
3AC3SOFTWAREPHE H:32 , GLY H:33 , SER H:53 , ASP H:54 , HOH H:1009 , HOH L:775 , LYS P:665BINDING SITE FOR RESIDUE EDO H 773
4AC4SOFTWAREILE H:51 , ASP H:55 , LYS H:57 , THR H:70 , LYS H:71 , THR H:99 , GLY H:100IBINDING SITE FOR RESIDUE IPA H 661
5AC5SOFTWARESER L:65 , GLY L:66 , GLU L:70 , THR L:72BINDING SITE FOR RESIDUE IPA L 662
6AC6SOFTWAREGLN L:38 , GLY L:41 , SER L:42BINDING SITE FOR RESIDUE IPA L 663
7AC7SOFTWARESER H:120 , VAL H:121 , HOH H:901 , SER L:156BINDING SITE FOR RESIDUE IPA H 664
8AC8SOFTWARETHR H:73 , SER H:74 , ASN H:76 , SER L:67BINDING SITE FOR RESIDUE IPA H 665

(-) SS Bonds  (4, 4)

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

(-) Cis Peptide Bonds  (5, 5)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TJI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1TJI)

(-) Exons   (0, 0)

(no "Exon" information available for 1TJI)

(-) Sequences/Alignments

Asymmetric/Biological 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:237
                                                                                                                                                                                                                                                                              
               SCOP domains d1tjih1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                                      d1tjih2 H:114-216 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                        -- SCOP domains
               CATH domains 1tjiH01 H:1-113 Immunoglobulins                                                                                                     1tjiH02 H:114-213 Immunoglobulins                                                                   ----- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.........eeeeeee......eeeeeee....eee.......eeeeee....eeeeee...hhhhheeeeeeee...eee..eeeehhhhh...ee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee...hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1tji 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||||                                                                                                                 216-YCM
                                                              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 d1tjil1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                 d1tjil2 L:108-214 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1tjiL01 L:1-107 Immunoglobulins                                                                            1tjiL02 L:108-211 Immunoglobulins                                                                       --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhh.eeeeee..ee..ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1tji 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   |
                                                                                                                                                                                                                                               214-YCM


Chain P from PDB  Type:PROTEIN  Length:15
 aligned with ENV_HV1Z6 | P04580 from UniProtKB/Swiss-Prot  Length:855

    Alignment length:15
                                   665     
           ENV_HV1Z6    656 EQELLELDKWASLWN  670
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains GP41-1tjiP01  - Pfam domains
         Sec.struct. author .....ee........ Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                1tji P  657 EQELLELDKWASLWx  671
                                   666    |
                                        671-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 '|'

 Classification and Annotation

(-) SCOP Domains  (4, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: GP41] (22)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)
Chain P   (ENV_HV1Z6 | P04580)
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.

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  1tji
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  ENV_HV1Z6 | P04580
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ENV_HV1Z6 | P04580: 1tjh 2zzo 3f4y 3f50 3g7a 3moa 3mob 3mod 4i2l

(-) Related Entries Specified in the PDB File

1tjg 2F5 FAB COMPLEXED WITH A GP41 7MER
1tjh 2F5 FAB COMPLEXED WITH A GP41 11MER
2f5b 2F5 IN COMPLEX WITH ITS GP41 EPITOPE