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(-) Description

Title :  CRYSTAL STRUCTURE OF THE NON-NEUTRALIZING HIV ANTIBODY 13H11 FAB FRAGMENT WITH A GP41 MPER-DERIVED PEPTIDE BEARING ALA SUBSTITUTIONS IN A HELICAL CONFORMATION
 
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) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A,B,P
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 - GP41 MPER-DERIVED PEPTIDE
    Chains: P
    Engineered: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Other Details: CHEMICALLY SYNTHESIZED PEPTIDE OF SEQUENCE DERIVED FROM THE MEMBRANE PROXIMAL EXTERNAL REGION OF GP41
    Synthetic: YES
 
Molecule 2 - ANTI-HIV-1 ANTIBODY 13H11 LIGHT CHAIN
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293T CELL
    Expression System Common: HUMAN
    Expression System Organ: KIDNEY
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: MOUSE FV,HUMAN FC
    Organism Common: MOUSE, HUMAN
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606
 
Molecule 3 - ANTI-HIV-1 ANTIBODY 13H11 HEAVY CHAIN
    Chains: B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293T CELL
    Expression System Common: HUMAN
    Expression System Organ: KIDNEY
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Fragment: MOUSE FV,HUMAN FC
    Organism Common: MOUSE, HUMAN
    Organism Scientific: MUS MUSCULUS, HOMO SAPIENS
    Organism Taxid: 10090, 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABP

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1NA1Ligand/IonSODIUM ION
2NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:10 , THR B:108 , THR B:110 , HOH B:363BINDING SITE FOR RESIDUE NA B 231

(-) 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 3MNZ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3MNZ)

(-) 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:220
 aligned with Q8TCD0_HUMAN | Q8TCD0 from UniProtKB/TrEMBL  Length:239

    Alignment length:220
                                                             53                                                                                                                                                                                         
                                                           52 |                                                                                                                                                                                         
                                    29        39        49  | |   58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238
         Q8TCD0_HUMAN    20 GDVVMTQSPLSLPVTLGQPASISCRSTQSLVYS-DGNTYLNWFQQRPGQSPRRLIYKVSNRDSGVPDRFSGSGSGTDFTLKITRVEAEDVGVYFCMQGTHWPSTFGQGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 238
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------V-set-3mnzA02 A:32-106                                                     ------------C1-set-3mnzA01 A:119-206                                                                ------- Pfam domains
         Sec.struct. author ....eeee..eeee.....eeeeeee.............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh..eeeeeee.......eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mnz A   0 LDIQLTQSPSSLAMSGGQKVTMRCKSSQSLLNSRNERNYLAWYQQKPGQSPKLLVYFASIRESGVPDRFIGSGSGTDFTLTISSVQAEDLADYFCLQHYNTPWTFGGGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGE 213
                                     9        19        29 |||||| 33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213
                                                         30A|||||                                                                                                                                                                                       
                                                          30B||||                                                                                                                                                                                       
                                                           30C|||                                                                                                                                                                                       
                                                            30D||                                                                                                                                                                                       
                                                             30E|                                                                                                                                                                                       
                                                              30F                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:205
 aligned with S6B291_HUMAN | S6B291 from UniProtKB/TrEMBL  Length:466

    Alignment length:217
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       
         S6B291_HUMAN    20 EVQLLESGGDLVQPGGSLRLSCAASGFTFSTYAMSWVRQAPGKGLEWVSGIGDSGHSIYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCATGSQWPGDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP 236
               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..------..eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mnz B   1 QIQLVQSGPELKKPGETVKISCKASGYTFTDYSVHWVKQVP--GLKWMGWINTETGEPTYADDFKGRFAFSLESSASTAYLEIHNLKNEDTATYFCALGW----LHWGLGTTLTVSSASTKGPSVFPLAP------GGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEP 225
                                    10        20        30        40|  |    50  |     59        69        79   |||  86        96    |  106       116       126      |138       148     ||163     ||174     ||185       195    |||208       218       
                                                                   41 44      52A                            82A||            96  101                      126    135                154|||    169|      180|               200||                    
                                                                                                              82B|                                                                    156||     171       182                203|                    
                                                                                                               82C                                                                     157|                                   205                    
                                                                                                                                                                                        162                                                          


Chain P from PDB  Type:PROTEIN  Length:17
                                                 
               SCOP domains ----------------- SCOP domains
               CATH domains ----------------- CATH domains
               Pfam domains ----------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------- SAPs(SNPs)
                    PROSITE ----------------- PROSITE
                 Transcript ----------------- Transcript
                 3mnz P 656 NAQELLELDKWASLWNx 672
                                   665      |
                                          672-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  (0, 0)

(no "SCOP Domain" information available for 3MNZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Ig (577)

(-) Gene Ontology  (0, 0)

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

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  S6B291_HUMAN | S6B291
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q8TCD0_HUMAN | Q8TCD0: 1hzh 1n0x 3mnv 3mnw 3pgf 4d9q 4nug 4nuj 4nwt 5viy 5vj6 5vod
        S6B291_HUMAN | S6B291: 3mnw 4eow 5c7k 5cus 5d9q 5veb 5vic 5vig 5viy 5vj6 5vob 5voc 5vod
UniProtKB/TrEMBL
        Q8TCD0_HUMAN | Q8TCD0: 3cfj 3cfk 4nwu
        S6B291_HUMAN | S6B291: 4llw 4lly 4oqt 4ydv

(-) Related Entries Specified in the PDB File

3mnv CRYSTAL STRUCTURE OF THE NON-NEUTRALIZING HIV ANTIBODY 13H11 FAB FRAGMENT
3mnw CRYSTAL STRUCTURE OF THE NON-NEUTRALIZING HIV ANTIBODY 13H11 FAB FRAGMENT WITH A GP41 MPER-DERIVED PEPTIDE IN A HELICAL CONFORMATION
3mo1 CRYSTAL STRUCTURE OF THE NON-NEUTRALIZING HIV ANTIBODY 13H11 FAB FRAGMENT
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