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(-) Description

Title :  IGG1 FAB FRAGMENT (83.1) COMPLEX WITH 16-RESIDUE PEPTIDE (RESIDUES 304-321 OF HIV-1 GP120 (MN ISOLATE))
 
Authors :  R. L. Stanfield, J. B. Ghiara, E. O. Saphire, A. T. Profy, I. A. Wilson
Date :  27 Nov 02  (Deposition) - 18 Nov 03  (Release) - 03 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.57
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, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. L. Stanfield, J. B. Ghiara, E. Ollmann Saphire, A. T. Profy, I. A. Wilson
Recurring Conformation Of The Human Immunodeficiency Virus Type 1 Gp120 V3 Loop.
Virology V. 315 159 2003
PubMed-ID: 14592768  |  Reference-DOI: 10.1016/S0042-6822(03)00525-7

(-) Compounds

Molecule 1 - FAB 83.1 - LIGHT CHAIN
    Chains: L, M
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: ASW
 
Molecule 2 - FAB 83.1 - HEAVY CHAIN
    Chains: H, I
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: ASW
 
Molecule 3 - PEPTIDE MP1
    Chains: P, Q
    Engineered: YES
    Other Details: THE PEPTIDE WAS SYNTHESIZED CHEMICALLY;
ITS SEQUENCE OCCURS IN THE MN HIV-1 VIRAL ISOLATE.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : HILMPQ
Biological Unit 1 (1x): H L P 
Biological Unit 2 (1x):  I M Q

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1NAK)

(-) Sites  (0, 0)

(no "Site" information available for 1NAK)

(-) SS Bonds  (8, 8)

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

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Asp L:94 -Pro L:95
3Tyr L:140 -Pro L:141
4Phe H:148 -Pro H:149
5Glu H:150 -Pro H:151
6Arg H:200 -Pro H:202
7Ser M:7 -Pro M:8
8Asp M:94 -Pro M:95
9Tyr M:140 -Pro M:141
10Phe I:148 -Pro I:149
11Glu I:150 -Pro I:151
12Arg I:200 -Pro I:202

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NAK)

(-) Sequences/Alignments

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:214
                                                                                                                                                                                                                                                      
               SCOP domains d1nakh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                   d1nakh2 H:114-229 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 1nakH01 H:1-113 Immunoglobulins                                                                                  1nakH02 H:114-226 Immunoglobulins                                                                 --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeee.........eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eeeeeeeee..eeeeeeeeeee.........eeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nak H   1 EVQLQESGPSLVKPSQTLSLTCSVTGVSITSGYWNWIRKFPGNKFEYMGYISKSGSAYYNPSLKSRISFTRDTSKNQFYLKLNSVTTEDTATYYCAIDDFDIWGAGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRD 229
                                    10        20        30        40        50        60        70        80  |||   87        97|      110       120       130|      142       152 ||||  167 ||    178 ||    190     ||203       213       223|   
                                                                                                            82A||             97|                          130|                  154|||    169|      180|          196|||                  223|   
                                                                                                             82B|             101                           133                   156||     171       183           199||                   226   
                                                                                                              82C                                                                  157|                              200|                         
                                                                                                                                                                                    162                               202                         


Chain I from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains d1naki1 I:1-113 Immunoglobulin heavy chain variable domain, VH                                                   d1naki2 I:114-229 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                       SCOP domains
               CATH domains 1nakI01 I:1-113 Immunoglobulins                                                                                  1nakI02 I:114-226 Immunoglobulins                                                                 --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeeee...eeeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeee.........eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.........eeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nak I   1 EVQLQESGPSLVKPSQTLSLTCSVTGVSITSGYWNWIRKFPGNKFEYMGYISKSGSAYYNPSLKSRISFTRDTSKNQFYLKLNSVTTEDTATYYCAIDDFDIWGAGTTVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSPRPSETVTCNVAHPASSTKVDKKIVPRD 229
                                    10        20        30        40        50        60        70        80  |||   87        97|      110       120       130|      142       152 ||||  167 ||    178 ||    190     ||203       213       223|   
                                                                                                            82A||             97|                          130|                  154|||    169|      180|          196|||                  223|   
                                                                                                             82B|             101                           133                   156||     171       183           199||                   226   
                                                                                                              82C                                                                  157|                              200|                         
                                                                                                                                                                                    162                               202                         


Chain L from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d1nakl1 L:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1nakl2 L:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains 1nakL01 L:1-108 Immunoglobulins                                                                                  -1nakL02 L:110-209 Immunoglobulins                                                                   --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee...........eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nak L   1 DVVMTQSPVSLPVSLGDQASISCRSSQSLGHSSGNTYLHWFLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTFKISRVEAEDLGVYFCFQTTHDPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 212
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       
                                                     27A||||                                                                                                                                                                                         
                                                      27B|||                                                                                                                                                                                         
                                                       27C||                                                                                                                                                                                         
                                                        27D|                                                                                                                                                                                         
                                                         27E                                                                                                                                                                                         


Chain M from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains d1nakm1 M:1-107 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1nakm2 M:108-212 Immunoglobulin light chain kappa constant domain, CL-kappa                              SCOP domains
               CATH domains 1nakM01 M:1-108 Immunoglobulins                                                                                  -1nakM02 M:110-209 Immunoglobulins                                                                   --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee.....eeeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nak M   1 DVVMTQSPVSLPVSLGDQASISCRSSQSLGHSSGNTYLHWFLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTFKISRVEAEDLGVYFCFQTTHDPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN 212
                                    10        20       27C||      35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       
                                                     27A||||                                                                                                                                                                                         
                                                      27B|||                                                                                                                                                                                         
                                                       27C||                                                                                                                                                                                         
                                                        27D|                                                                                                                                                                                         
                                                         27E                                                                                                                                                                                         


Chain P from PDB  Type:PROTEIN  Length:10
 aligned with ENV_HV1MN | P05877 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:10
                                   319
            ENV_HV1MN   310 KRIHIGPGRA 319
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 1nak P 312 KRIHIGPGRA 323
                                || 323
                              316|    
                               319    


Chain Q from PDB  Type:PROTEIN  Length:10
 aligned with ENV_HV1MN | P05877 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:10
                                   319
            ENV_HV1MN   310 KRIHIGPGRA 319
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 1nak Q 312 KRIHIGPGRA 323
                                || 323
                              316|    
                               319
   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, 8)

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

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
House mouse (Mus musculus) (616)
1a1nakL02L:110-209
1b1nakH02H:114-226
1c1nakI02I:114-226
1d1nakL01L:1-108
1e1nakM01M:1-108
1f1nakH01H:1-113
1g1nakI01I:1-113
1h1nakM02M:110-209

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1NAK)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)
Chain P,Q   (ENV_HV1MN | P05877)
molecular function
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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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  Cis Peptide Bonds
    Arg H:200 - Pro H:202   [ RasMol ]  
    Arg I:200 - Pro I:202   [ RasMol ]  
    Asp L:94 - Pro L:95   [ RasMol ]  
    Asp M:94 - Pro M:95   [ RasMol ]  
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  1nak
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  ENV_HV1MN | P05877
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 Related Entries

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

UniProtKB/Swiss-Prot
        ENV_HV1MN | P05877: 1acy 1ai1 1f58 1ggi 1k5m 1niz 1nj0 1q1j 2b0s 2qsc 3e6h 3go1 3mlw 3mlx 3uji 4m1d 4xaw 4xbe 4xc1 4xc3 4xcf 4xmk

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1NAK)