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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NON-NEUTRALIZING HIV ANTIBODY 13H11 FAB FRAGMENT
 
Authors :  N. I. Nicely, S. M. Dennison, G. Kelsoe, H. -X. Liao, S. M. Alam, B. F. Hayn
Date :  22 Apr 10  (Deposition) - 17 Nov 10  (Release) - 28 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hiv-1, Hiv, Gp41 Mper, 13H11, 2F5, Z13, 4E10, Fab Antibody, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. I. Nicely, S. M. Dennison, G. Kelsoe, Y. Ueda, H. -X. Liao, S. M. Alam, B. F. Haynes
Crystal Structure Of A Non-Neutralizing Hiv-1 Gp41 Envelope Antibody Demonstrates Neutralization Mechanism Of Gp41 Antibodies
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN
    ChainsA
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293T CELL
    Expression System CommonHUMAN
    Expression System OrganKIDNEY
    Expression System Taxid9606
    Expression System Vector TypePLASMID
    FragmentFUSION PROTEIN BETWEEN MOUSE FV AND A HUMAN FC
    Organism CommonMOUSE,HUMAN
    Organism ScientificMUS MUSCULUS,HOMO SAPIENS
    Organism Taxid10090,9606
 
Molecule 2 - ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN
    ChainsB
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293T CELL
    Expression System CommonHUMAN
    Expression System OrganKIDNEY
    Expression System Taxid9606
    Expression System Vector TypePLASMID
    FragmentFUSION PROTEIN BETWEEN MOUSE FV AND A HUMAN FC
    Organism CommonMOUSE,HUMAN
    Organism ScientificMUS MUSCULUS,HOMO SAPIENS
    Organism Taxid10090,9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:17 , LYS A:18 , HOH A:329 , HOH A:333BINDING SITE FOR RESIDUE ACT A 217
2AC2SOFTWARELYS A:39 , GLN A:42 , LYS A:45 , HOH A:261BINDING SITE FOR RESIDUE ACT A 218
3AC3SOFTWARETYR A:32 , HIS A:91 , TRP B:96 , HOH B:249 , HOH B:327BINDING SITE FOR RESIDUE ACT B 231
4AC4SOFTWARETHR B:30 , SER B:33 , ASN B:52 , THR B:52ABINDING SITE FOR RESIDUE ACT B 232
5AC5SOFTWAREGLY B:55BINDING SITE FOR RESIDUE ACT B 233
6AC6SOFTWARETHR B:116 , LYS B:117 , GLY B:118 , HOH B:329BINDING SITE FOR RESIDUE SO4 B 234

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:23 -A:88
2A:134 -A:194
3B:22 -B:92
4B:142 -B:208

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser A:7 -Pro A:8
2Thr A:94 -Pro A:95
3Tyr A:140 -Pro A:141
4Phe B:148 -Pro B:149
5Glu B:150 -Pro B:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3MO1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MO1)

(-) Exons   (0, 0)

(no "Exon" information available for 3MO1)

(-) 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 A from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains d3mo1a1 A:0-107 automated matches                                                                                 d3mo1a2 A:108-211 automated matches                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee..eeeee....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeeee......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhh...eeeeeee.......eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mo1 A   0 LDIQLTQSPSSLAMSGGQKVTMRCKSSQSLLNSRNERNYLAWYQQKPGQSPKLLVYFASIRESGVPDRFIGSGSGTDFTLTISSVQAEDLADYFCLQHYNTPWTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR 211
                                     9        19        29 |||||| 33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203        
                                                         30A|||||                                                                                                                                                                                     
                                                          30B||||                                                                                                                                                                                     
                                                           30C|||                                                                                                                                                                                     
                                                            30D||                                                                                                                                                                                     
                                                             30E|                                                                                                                                                                                     
                                                              30F                                                                                                                                                                                     

Chain B from PDB  Type:PROTEIN  Length:215
                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......eee.hhhh..eeeeeehhh.eeeeee...hhhhheeeeeee...ee...eeeee........eeeee......ee..eeeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mo1 B   0 LQIQLVQSGPELKKPGETVKISCKASGYTFTDYSVHWVKQVPGKGLKWMGWINTETGEPTYADDFKGRFAFSLESSASTAYLEIHNLKNEDTATYFCALGWLHWGLGTTLTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK 226
                                     9        19        29        39        49   |    58        68        78    ||| 85        95||     109       119       129||     141       151  |||| 166  ||   177  ||   188       198 |||   211       221     
                                                                               52A                            82A||            96|                          130|                  154|||    169|      180|               200||                     
                                                                                                               82B|            101                           133                   156||     171       182                203|                     
                                                                                                                82C                                                                 157|                                   205                     
                                                                                                                                                                                     162                                                           

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  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  (1, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MO1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3MO1)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3MO1)

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  Cis Peptide Bonds
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 Related Entries

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(-) Related Entries Specified in the PDB File

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3mnw CRYSTAL STRUCTURE OF THE NON-NEUTRALIZING HIV ANTIBODY 13H11 FAB FRAGMENT WITH A GP41 MPER-DERIVED PEPTIDE IN A HELICAL CONFORMATION
3mnz CRYSTAL STRUCTURE OF THE NON-NEUTRALIZING HIV ANTIBODY 13H11 FAB FRAGMENT WITH A GP41 MPER-DERIVED PEPTIDE BEARING ALA SUBSTITUTIONS IN A HELICAL CONFORMATION
3moa CRYSTAL STRUCTURE OF THE NEUTRALIZING HIV ANTIBODY 2F5 FAB FRAGMENT (RECOMBINANTLY PRODUCED FAB) WITH 17 AA GP41 MPER- DERIVED PEPTIDE
3mob CRYSTAL STRUCTURE OF THE NEUTRALIZING HIV ANTIBODY 2F5 FAB FRAGMENT (RECOMBINANTLY PRODUCED FAB) WITH 11 AA GP41 MPER- DERIVED PEPTIDE
3mod CRYSTAL STRUCTURE OF THE NEUTRALIZING HIV ANTIBODY 2F5 FAB FRAGMENT (RECOMBINANTLY PRODUCED IGG) WITH 11 AA GP41 MPER- DERIVED PEPTIDE