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Contents |
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* Residue conservation analysis
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Obsolete entry |
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PDB id:
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Immune system
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Title:
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Fab 2g12 unliganded
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Structure:
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Fab 2g12, light chain. Chain: l, m. Fragment: light chain. Engineered: yes. Fab 2g12, heavy chain. Chain: h, k. Fragment: heavy chain. Engineered: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Expressed in: cricetulus griseus. Expression_system_taxid: 10029. Expression_system_organ: ovary. Expression_system_organ: ovary
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Biol. unit:
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Tetramer (from
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Resolution:
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2.20Å
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R-factor:
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0.227
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R-free:
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0.266
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Authors:
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D.A.Calarese,C.N.Scanlan,M.B.Zwick,S.Deechongkit,Y.Mimura,R.Kunert, R.L.Stanfield,J.W.Kelly,P.M.Rudd,R.A.Dwek,H.Katinger,D.R.Burton, I.A.Wilson
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Key ref:
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D.A.Calarese
et al.
(2003).
Antibody domain exchange is an immunological solution to carbohydrate cluster recognition.
Science,
300,
2065-2071.
PubMed id:
DOI:
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Date:
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24-Feb-03
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Release date:
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15-Jul-03
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PROCHECK
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Headers
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References
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DOI no:
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Science
300:2065-2071
(2003)
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PubMed id:
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Antibody domain exchange is an immunological solution to carbohydrate cluster recognition.
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D.A.Calarese,
C.N.Scanlan,
M.B.Zwick,
S.Deechongkit,
Y.Mimura,
R.Kunert,
P.Zhu,
M.R.Wormald,
R.L.Stanfield,
K.H.Roux,
J.W.Kelly,
P.M.Rudd,
R.A.Dwek,
H.Katinger,
D.R.Burton,
I.A.Wilson.
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ABSTRACT
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Human antibody 2G12 neutralizes a broad range of human immunodeficiency virus
type 1 (HIV-1) isolates by binding an unusually dense cluster of carbohydrate
moieties on the "silent" face of the gp120 envelope glycoprotein.
Crystal structures of Fab 2G12 and its complexes with the disaccharide
Manalpha1-2Man and with the oligosaccharide Man9GlcNAc2 revealed that two Fabs
assemble into an interlocked VH domain-swapped dimer. Further biochemical,
biophysical, and mutagenesis data strongly support a Fab-dimerized antibody as
the prevalent form that recognizes gp120. The extraordinary configuration of
this antibody provides an extended surface, with newly described binding sites,
for multivalent interaction with a conserved cluster of oligomannose type sugars
on the surface of gp120. The unique interdigitation of Fab domains within an
antibody uncovers a previously unappreciated mechanism for high-affinity
recognition of carbohydrate or other repeating epitopes on cell or microbial
surfaces.
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Selected figure(s)
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Figure 4.
Fig. 4. The antibody-combining site interactions with the
disaccharide Man  1-2Man. (A) The
2F[obs] - F[calc] electron density for Man 1-2Man is
contoured at 1.7  and the CDR loops
are labeled. (B) The combining site showing Fab atoms within
hydrogen bonding distance (dotted lines) of Man 1-2Man. The Fab
heavy chain and light chain are shown in purple and cyan,
respectively. We generated the figures using programs Bobscript
(64), Molscript (65), and Raster3D (66).
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Figure 6.
Fig. 6. Model of 2G12 glycan recognition of gp120. On the basis
of our model, three separate Man[9]GlcNAc[2] moieties, shown in
red (two in the primary combining sites and one in the
V[H]/V[H]' interface), potentially mediate the binding of 2G12
to gp120. The glycans at the primary combining sites originate
from Asn332 and Asn392 (labeled) in gp120, whereas the
carbohydrate located at the V[H]/V[H]' interface would arise
from Asn339 (labeled). N-linked glycans occurring at Asn332 and
Asn392 have previously been implicated as critical for 2G12
binding (13). The N-linked glycan at Asn 339 is not as critical
for 2G12 binding, although this glycan could potentially
interact with the V[H]/V[H]' interface. Figure was generated
using programs Molscript (65) and Raster3D (66).
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The above figures are
reprinted
by permission from the AAAs:
Science
(2003,
300,
2065-2071)
copyright 2003.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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D.C.Ekiert,
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R.A.Lerner,
R.R.Bhatt,
and
I.A.Wilson
(2012).
Cross-neutralization of influenza A viruses mediated by a single antibody loop.
|
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Nature,
489,
526-532.
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PDB codes:
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B.F.Haynes,
M.A.Moody,
H.X.Liao,
L.Verkoczy,
and
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B cell responses to HIV-1 infection and vaccination: pathways to preventing infection.
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Trends Mol Med,
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D.K.Wijesundara,
R.J.Jackson,
I.A.Ramshaw,
and
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(2011).
Human immunodeficiency virus-1 vaccine design: where do we go now?
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Immunol Cell Biol,
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(2011).
Effects of backbone substitutions on the conformational behavior of Shigella flexneri O-antigens: implications for vaccine strategy.
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M.C.Galan,
D.Benito-Alifonso,
and
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P.M.Enríquez-Navas,
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and
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(2011).
A solution NMR study of the interactions of oligomannosides and the anti-HIV-1 2G12 antibody reveals distinct binding modes for branched ligands.
|
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Chemistry,
17,
1547-1560.
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A.J.McMichael,
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N.Goonetilleke,
and
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The immune response during acute HIV-1 infection: clues for vaccine development.
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Nat Rev Immunol,
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A.Kabanova,
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and
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Preparation, characterization and immunogenicity of HIV-1 related high-mannose oligosaccharides-CRM197 glycoconjugates.
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Glycoconj J,
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Computational design of epitope-scaffolds allows induction of antibodies specific for a poorly immunogenic HIV vaccine epitope.
|
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Structure,
18,
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PDB codes:
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D.C.Dunlop,
C.Bonomelli,
F.Mansab,
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Polysaccharide mimicry of the epitope of the broadly neutralizing anti-HIV antibody, 2G12, induces enhanced antibody responses to self oligomannose glycans.
|
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Glycobiology,
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812-823.
|
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F.Sallusto,
Q.J.Sattentau,
R.A.Weiss,
and
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(2010).
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J.A.Hoxie
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J Virol,
84,
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J.P.Julien,
N.Huarte,
R.Maeso,
S.G.Taneva,
A.Cunningham,
J.L.Nieva,
and
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(2010).
Ablation of the complementarity-determining region H3 apex of the anti-HIV-1 broadly neutralizing antibody 2F5 abrogates neutralizing capacity without affecting core epitope binding.
|
| |
J Virol,
84,
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J.R.Mascola,
and
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28,
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H.Quendler,
P.Messner,
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and
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(2010).
Proline is not uniquely capable of providing the pivot point for domain swapping in 2G12, a broadly neutralizing antibody against HIV-1.
|
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J Biol Chem,
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Z.Fulton,
V.Hong,
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M.G.Finn,
D.R.Burton,
I.A.Wilson,
and
B.G.Davis
(2010).
A nonself sugar mimic of the HIV glycan shield shows enhanced antigenicity.
|
| |
Proc Natl Acad Sci U S A,
107,
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PDB codes:
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L.A.Lagenaur,
V.A.Villarroel,
V.Bundoc,
B.Dey,
and
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sCD4-17b bifunctional protein: extremely broad and potent neutralization of HIV-1 Env pseudotyped viruses from genetically diverse primary isolates.
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Retrovirology,
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and
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A limited number of antibody specificities mediate broad and potent serum neutralization in selected HIV-1 infected individuals.
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ChemMedChem,
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Arch Immunol Ther Exp (Warsz),
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and
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HIV-1 neutralization profile and plant-based recombinant expression of actinohivin, an Env glycan-specific lectin devoid of T-cell mitogenic activity.
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PLoS One,
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R.D.Astronomo,
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Carbohydrate vaccines: developing sweet solutions to sticky situations?
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Nat Rev Drug Discov,
9,
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A.K.Udit,
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C.H.Wong,
M.G.Finn,
and
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(2010).
Defining criteria for oligomannose immunogens for HIV using icosahedral virus capsid scaffolds.
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Antibodies against Manalpha1,2-Manalpha1,2-Man oligosaccharide structures recognize envelope glycoproteins from HIV-1 and SIV strains.
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Glycobiology,
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(2010).
Structure and function of broadly reactive antibody PG16 reveal an H3 subdomain that mediates potent neutralization of HIV-1.
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Proc Natl Acad Sci U S A,
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R.Ringe,
M.Thakar,
and
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PDB code:
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Proximal glycans outside of the epitopes regulate the presentation of HIV-1 envelope gp120 helper epitopes.
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K.L.Davis,
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A.Pinter,
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Chem Biol Drug Des,
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M.A.Luftig,
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Structural basis for HIV-1 neutralization by a gp41 fusion intermediate-directed antibody.
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Nat Struct Mol Biol,
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PDB code:
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M.Li,
J.F.Salazar-Gonzalez,
C.A.Derdeyn,
L.Morris,
C.Williamson,
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J Virol,
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Microbicides and other topical strategies to prevent vaginal transmission of HIV.
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Nat Rev Immunol,
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J Virol,
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J Virol,
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PDB codes:
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R.Pantophlet,
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Proc Natl Acad Sci U S A,
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PDB codes:
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D.R.Burton,
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Proc Natl Acad Sci U S A,
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J Virol,
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Hum Antibodies,
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AIDS,
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J Virol,
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Human immunodeficiency virus type 1 env clones from acute and early subtype B infections for standardized assessments of vaccine-elicited neutralizing antibodies.
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J Virol,
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M.Witvrouw,
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J Virol,
79,
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N.Ojima,
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Analysis of neutral oligosaccharides for structural characterization by matrix-assisted laser desorption/ionization quadrupole ion trap time-of-flight mass spectrometry.
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J Mass Spectrom,
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R.M.Cardoso,
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Broadly neutralizing anti-HIV antibody 4E10 recognizes a helical conformation of a highly conserved fusion-associated motif in gp41.
|
| |
Immunity,
22,
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PDB code:
|
|
|
|
|
|
|
|
R.T.Lee,
G.Lauc,
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Y.C.Lee
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Glycoproteomics: protein modifications for versatile functions. Meeting on glycoproteomics.
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EMBO Rep,
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S.Selvarajah,
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Comparing antigenicity and immunogenicity of engineered gp120.
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J Virol,
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T.Zhou,
D.H.Hamer,
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Q.J.Sattentau,
and
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(2005).
Interfacial metal and antibody recognition.
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| |
Proc Natl Acad Sci U S A,
102,
14575-14580.
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|
PDB codes:
|
|
|
|
|
|
|
|
A.Pinter,
W.J.Honnen,
Y.He,
M.K.Gorny,
S.Zolla-Pazner,
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The V1/V2 domain of gp120 is a global regulator of the sensitivity of primary human immunodeficiency virus type 1 isolates to neutralization by antibodies commonly induced upon infection.
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J Virol,
78,
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C.A.Bewley,
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New carbohydrate specificity and HIV-1 fusion blocking activity of the cyanobacterial protein MVL: NMR, ITC and sedimentation equilibrium studies.
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J Mol Biol,
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C.C.Huang,
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M.Y.Zhang,
D.S.Dimitrov,
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Structural basis of tyrosine sulfation and VH-gene usage in antibodies that recognize the HIV type 1 coreceptor-binding site on gp120.
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| |
Proc Natl Acad Sci U S A,
101,
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PDB codes:
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|
|
|
|
|
|
|
D.A.Garber,
G.Silvestri,
and
M.B.Feinberg
(2004).
Prospects for an AIDS vaccine: three big questions, no easy answers.
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Lancet Infect Dis,
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D.Steinmann,
H.Barth,
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M.I.Adah,
J.T.Gerlach,
G.R.Pape,
E.Depla,
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A.H.Patel,
G.Inchauspé,
T.J.Liang,
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Inhibition of hepatitis C virus-like particle binding to target cells by antiviral antibodies in acute and chronic hepatitis C.
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J Virol,
78,
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D.Y.Chirgadze,
M.Demydchuk,
M.Becker,
S.Moran,
and
M.Paoli
(2004).
Snapshot of protein structure evolution reveals conservation of functional dimerization through intertwined folding.
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| |
Structure,
12,
1489-1494.
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|
PDB codes:
|
|
|
|
|
|
|
|
G.Ofek,
M.Tang,
A.Sambor,
H.Katinger,
J.R.Mascola,
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P.D.Kwong
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Structure and mechanistic analysis of the anti-human immunodeficiency virus type 1 antibody 2F5 in complex with its gp41 epitope.
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J Virol,
78,
10724-10737.
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PDB codes:
|
|
|
|
|
|
|
|
I.K.Srivastava,
J.B.Ulmer,
and
S.W.Barnett
(2004).
Neutralizing antibody responses to HIV: role in protective immunity and challenges for vaccine design.
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Expert Rev Vaccines,
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J.L.Heeney
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Requirement of diverse T-helper responses elicited by HIV vaccines: induction of highly targeted humoral and CTL responses.
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Expert Rev Vaccines,
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J.M.Binley,
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Comprehensive cross-clade neutralization analysis of a panel of anti-human immunodeficiency virus type 1 monoclonal antibodies.
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J Virol,
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L.Cavacini,
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AIDS Res Hum Retroviruses,
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L.Dacheux,
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Evolutionary dynamics of the glycan shield of the human immunodeficiency virus envelope during natural infection and implications for exposure of the 2G12 epitope.
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J Virol,
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L.X.Wang,
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O.Blixt,
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M.C.Bryan,
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J.Stevens,
N.Razi,
D.J.Stevens,
J.J.Skehel,
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Printed covalent glycan array for ligand profiling of diverse glycan binding proteins.
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Proc Natl Acad Sci U S A,
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J Virol,
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Structural rationale for the broad neutralization of HIV-1 by human monoclonal antibody 447-52D.
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| |
Structure,
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PDB code:
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|
|
|
|
|
|
|
S.Mehandru,
T.Wrin,
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G.Stiegler,
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T.Uda,
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G.Lin,
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R.Pantophlet,
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Immunofocusing: antigen engineering to promote the induction of HIV-neutralizing antibodies.
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Trends Mol Med,
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
|
 |
Links
